diff --git a/mathmech/CMakeLists.txt b/mathmech/CMakeLists.txt index 0a557d0..2e2da06 100644 --- a/mathmech/CMakeLists.txt +++ b/mathmech/CMakeLists.txt @@ -24,8 +24,13 @@ if (CMAKE_SYSTEM_NAME MATCHES Linux) elseif (CMAKE_SYSTEM_NAME MATCHES Windows) set (QWT_INCLUDE_PATH "C:/Qwt-6.1.0/include" CACHE STRING "Path to qwt include") set (QWT_LIBRARY_PATH "C:/Qwt-6.1.0/lib" CACHE STRING "Path to qwt library") -endif() +endif () foreach (COMP ${COMPS}) add_subdirectory (${COMP}) -endforeach() \ No newline at end of file +endforeach () + +# set docs file +if (ADD_DOCS) + include (docs.cmake) +endif () \ No newline at end of file diff --git a/mathmech/PKGBUILD b/mathmech/PKGBUILD index 93efb79..2b5106b 100644 --- a/mathmech/PKGBUILD +++ b/mathmech/PKGBUILD @@ -9,28 +9,30 @@ arch=(any) url="https://github.com/arcan1s/moldyn" license=('GPL') depends=('qt4' 'qwt') -makedepends=('unzip' 'cmake' 'automoc4') +makedepends=('cmake' 'automoc4') source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip) -md5sums=('4eccb72efd4a8a531d7fda1aabc04f62') +md5sums=('80420d6aa723d0944891113a510f06fe') _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr -DQWT_INCLUDE_PATH=/usr/include/qwt + -DQWT_LIBRARY_PATH=/usr/lib -DMM_PREFIX=mm_ + -DADD_INCLUDE=0 + -DADD_DOCS=0 -DCMAKE_BUILD_TYPE=Release" build () { - unzip -o -q ${srcdir}/${pkgname}-${pkgver}-src.zip -d ${srcdir}/${pkgname} - if [ -d ${srcdir}/${pkgname}/build ]; then - rm -rf ${srcdir}/${pkgname}/build + if [ -d ${srcdir}/build ]; then + rm -rf ${srcdir}/build fi - mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build + mkdir ${srcdir}/build && cd ${srcdir}/build cmake ${_cmakekeys} ../ make } package() { - cd ${srcdir}/${pkgname}/build + cd ${srcdir}/build make DESTDIR=${pkgdir} install } diff --git a/mathmech/README.doc b/mathmech/README.doc deleted file mode 100644 index f62e22c..0000000 Binary files a/mathmech/README.doc and /dev/null differ diff --git a/mathmech/docs.cmake b/mathmech/docs.cmake new file mode 100644 index 0000000..000f43e --- /dev/null +++ b/mathmech/docs.cmake @@ -0,0 +1,5 @@ +set (PROJECT mathmech) +# set directory +set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs) +install (DIRECTORY ${PROJECT_DOCS_DIR} + DESTINATION share/doc/${PROJECT}) diff --git a/mathmech/docs/eng/help_agl.html b/mathmech/docs/eng/help_agl.html new file mode 100644 index 0000000..8a22b2e --- /dev/null +++ b/mathmech/docs/eng/help_agl.html @@ -0,0 +1,31 @@ + + +

agl

+


Program that creates PDB file with chosen agglomerate.

+


Usage
mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]
Parametrs
-a FILE – input file with agglomerate
-i FILE – input trajectory file
-c X,Y,Z – cell size, A
-o FILE – output PDB file
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Agglomerate file (*.agl)

+ +

Trajectory file (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Reading of source file.
    3. +
  3. Search for the best configuration.
    4. +
  4. Print the result to the file.
+


Working with GUI

+
  1. Select Menu -> File creator -> Agglomerate file.
    2. +
  2. Set the file generated by statgen. Push "Select".
    3. +
  3. Select the trajectory file from the drop down list. Select the agglomerate.
    4. +
  4. Set the output file. Create file.
    5. +
  5. Go to the tab "Generate PDB". Select "From agglomerate" from the drop down list.
    6. +
  6. Set the work directory.
    7. +
  7. Set the input trajectory file.
    8. +
  8. Set the agglomerate file.
    9. +
  9. Set the cell size, A.
    10. +
  10. Set the output PDB file.
    11. +
  11. Set the log file if this needed.
    12. +
  12. Run application.
\ No newline at end of file diff --git a/mathmech/docs/eng/help_envir.html b/mathmech/docs/eng/help_envir.html new file mode 100644 index 0000000..af1cfcc --- /dev/null +++ b/mathmech/docs/eng/help_envir.html @@ -0,0 +1,23 @@ + + +

envir

+


Program that searchs environment for chosen molecule by geometric criterion.

+


Usage
mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]
Parametrs
-i FILE – input trajectory file
-c X,Y,Z – cell size, A
-o FILE – output PDB file
-n NUMBER – number of molecule for search. Default is 1
-r NUMBER – radius of environment. Default is 6.0
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Trajectory file (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Reading of source file.
    3. +
  3. Search for the environment.
    4. +
  4. Print the environment to the file.
+


Working with GUI

+
  1. Go to the tab "Environment". Set the work directory.
    2. +
  2. Set the input trajectory file.
    3. +
  3. Set the cell size, A.
    4. +
  4. Set the output PDB file.
    5. +
  5. Set the number of molecule for search and the radius of environment.
    6. +
  6. Set the log file if this needed.
    7. +
  7. Run application.
\ No newline at end of file diff --git a/mathmech/docs/eng/help_radf.html b/mathmech/docs/eng/help_radf.html new file mode 100644 index 0000000..d06ddf6 --- /dev/null +++ b/mathmech/docs/eng/help_radf.html @@ -0,0 +1,27 @@ + + +

radf

+


Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).

+


Usage
mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]
Parametrs
-i MASK – mask of trajectory files
-s NUMBER,NUMBER – first and last trajectory steps
-c X,Y,Z – cell size, A
-at FORMAT – numerical atom types between which the function is calculated. Format is "1-2" or "1,2,3-4,5,6" (automatically enable calculation of radial distribution function between centers of mass)
-o FILE – output file
-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0
-rs NUMBER – radius change step, A. Default is 0.2
-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0
-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function
-as – enable matrix output
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Output file (*.dat)

+ +


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Step by step reading of source files, settings values of variables.
    Calculating of the number of pairs of molecules in various relative configurations.
    3. +
  3. Print the result to the file.
    Radial distribution function calculated by:
    RDF(r) = (1 / norm) * sum(d(r_n-r), n),
    norm(r) = (4*PI*r^2*dr) * ro * N * N_step,
    where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.
    Radial-angles distribution function calculated by:
    RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),
    norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,
    where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.
+


Working with GUI

+
  1. Go to the tab "RADF". Set the work directory.
    2. +
  2. Set the mask of trajectory files.
    3. +
  3. Set the first and the last trajectory steps.
    4. +
  4. Set the cell size, A.
    5. +
  5. Set the output file.
    6. +
  6. Set needed atoms.
    7. +
  7. Set radial criteria. Set angular criteria if this needed.
    8. +
  8. Set the matrix output, the log file and the graph generate if this needed.
    9. +
  9. Run application.
\ No newline at end of file diff --git a/mathmech/docs/eng/help_statgen.html b/mathmech/docs/eng/help_statgen.html new file mode 100644 index 0000000..8f8535e --- /dev/null +++ b/mathmech/docs/eng/help_statgen.html @@ -0,0 +1,29 @@ + + +

statgen

+


Program that analyzes molecular dynamics trajectories using topological analysis.

+


Usage
mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]
Parametrs
-i MASK – mask of trajectory files
-s NUMBER,NUMBER – first and last trajectory steps
-c X,Y,Z – cell size, A
-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated
-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example "0-0:2.4,0-1:3.0" means set 0-0 interaction as <2.4 А and 0-1 interaction as <3.0 A
-o FILE – output file
-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (>= 3)
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Output file (*.dat)

+ +


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Step by step reading of source files, settings values of variables.
    Search for interactions that satisfy the specified criteria.
    The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.
    Adding molecules to agglomerates according to the obtained connectivity matrix.
    Print agglomerates to the file, adding the summary statistics.
    3. +
  3. Print the summary statistic to the file.
+


Working with GUI

+
  1. Go to the tab "Agglomeration". Set the work directory.
    2. +
  2. Set the mask of trajectory files.
    3. +
  3. Set the first and the last trajectory steps.
    4. +
  4. Set the cell size, A.
    5. +
  5. Set needed atoms.
    6. +
  6. Set interactions. Select type of interaction from the drop down list, change its criterion and press "Save". Press "Add" after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press "Remove".
    7. +
  7. Set the output file.
    8. +
  8. Set the maximum depth for search cycles, the log file and the graph generate if this needed.
    9. +
  9. For the variation of geometric criteria you need specify the criteria step changes and the number of steps.
    10. +
  10. Run application.
\ No newline at end of file diff --git a/mathmech/docs/eng/help_trj.html b/mathmech/docs/eng/help_trj.html new file mode 100644 index 0000000..ed0b761 --- /dev/null +++ b/mathmech/docs/eng/help_trj.html @@ -0,0 +1,29 @@ + + +

trj

+


Program that generates trajectory files in special format from input trajectory.

+


Usage
mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]
Parametrs
-i FILE – input trajectory file
-t TYPE – trajectory type. Supported formats: gmx, puma
-s NUMBER – number of trajectory steps
-a FILE – file with atom types
-o MASK – mask of output trajectory files
-tt NUMBER – maximum number of different atom types. Default is 1024
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Trajectory files (*.[0-9])

+ +

Atom types file (*.types)

+ +


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Step by step reading of source files, print results to the specified output file.
+


Working with GUI

+
  1. Select Menu -> File creator -> Atom types file.
    2. +
  2. Set the output file.
    3. +
  3. Set atom types. To add a new molecule you need select "Add new molecule" from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press "Add". After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press "Remove".
    4. +
  4. Create the atom types file.
    5. +
  5. Go to the tab "Generate trajectory". Set the work directory.
    6. +
  6. Set the input trajectory file.
    7. +
  7. Select the trajectory type from the drop down list, set the number of trajectory steps.
    8. +
  8. Set the atom types file.
    9. +
  9. Set the mask of output files.
    10. +
  10. Set the maximum number of different atom types and the log file if this needed.
    11. +
  11. Run application.
\ No newline at end of file diff --git a/mathmech/docs/eng/help_trj2pdb.html b/mathmech/docs/eng/help_trj2pdb.html new file mode 100644 index 0000000..c4a257d --- /dev/null +++ b/mathmech/docs/eng/help_trj2pdb.html @@ -0,0 +1,21 @@ + + +

trj2pdb

+


Program that creates PDB file from trajetory snapshot.

+


Usage
mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]
Parametrs
-i FILE – input trajectory file
-o FILE – output PDB file
-l FILE – print log to specified file
-q – do not print messages to STDOUT
-h – show this help and exit

+


File formats

+

Trajectory file (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Operation of the application

+
  1. Reading titles of source files, setting values of initial variables.
    2. +
  2. Reading of source file.
    3. +
  3. Print the result to the file.
+


Working with GUI

+
  1. Go to the tab "Generate PDB". Select "From trajectory snapshot" from the drop down list.
    2. +
  2. Set the work directory.
    3. +
  3. Set the input trajectory file.
    4. +
  4. Set the output PDB file.
    5. +
  5. Set the log file if this needed.
    6. +
  6. Run application.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_agl.html b/mathmech/docs/rus/help_agl.html new file mode 100644 index 0000000..9454c8e --- /dev/null +++ b/mathmech/docs/rus/help_agl.html @@ -0,0 +1,31 @@ + + +

agl

+


Программа для генерации PDB файлов с агломератами.

+


Использование
mm_agl -a ФАЙЛ -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-a ФАЙЛ – исходный файл с агломератом
-i ФАЙЛ – исходный файл с координатами
-c X,Y,Z – размер элементарной ячейки, А
-o ФАЙЛ – генерируемый PDB файл с координатами
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Файл с агломератом (*.agl)

+ +

Файл траектории (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Работа приложения

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Чтение исходных файлов.
    3. +
  3. Поиск оптимальной конфигурации.
    4. +
  4. Печать результата в файл.
+


Работа с графическим интерфейсом

+
  1. Меню -> Создание файлов -> Файл с агломератом.
    2. +
  2. Указать файл, сгенерированный приложением statgen. Нажать "Выбор".
    3. +
  3. Выбрать траекторный снимок в выпадающем списке. Выбрать агломерат.
    4. +
  4. Указать выходной файл. Создать файл с агломератом.
    5. +
  5. 5. Перейти во вкладку "Создать PDB". Из выпадающего списка выбрать "Из агломерата".
    6. +
  6. Указать рабочую директорию.
    7. +
  7. Указать файл траектории.
    8. +
  8. Указать сгенерированный файл с агломератом.
    9. +
  9. Указать размер ячейки в А.
    10. +
  10. Указать генерируемый PDB файл.
    11. +
  11. При необходимости указать файл лога.
    12. +
  12. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_envir.html b/mathmech/docs/rus/help_envir.html new file mode 100644 index 0000000..c954cd4 --- /dev/null +++ b/mathmech/docs/rus/help_envir.html @@ -0,0 +1,23 @@ + + +

envir

+


Программа для генерации PDB файла указанной молекулы с окружением указанного радиуса.

+


Использование
mm_envir -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -n ЧИСЛО ] [ -r ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-i ФАЙЛ – исходный файл с координатами
-c X,Y,Z – размер элементарной ячейки, А
-o ФАЙЛ – генерируемый PDB файл с координатами
-n ЧИСЛО – номер молекулы для поиска окружения. По умолчанию 1
-r ЧИСЛО – радиус окружения, А. По умолчанию 6.0
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Файл траектории (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Работа приложения

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Чтение исходного файла.
    3. +
  3. Поиск окружения.
    4. +
  4. Печать окружения в файл.
+


Работа с графическим интерфейсом

+
  1. Перейти во вкладку "Окружение". Указать рабочую директорию.
    2. +
  2. Указать исходный файл.
    3. +
  3. Указать размер ячейки в А.
    4. +
  4. Указать генерируемый PDB файл.
    5. +
  5. Указать молекулу для поиска окружения и радиус окружения в А.
    6. +
  6. При необходимости указать файл лога.
    7. +
  7. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_radf.html b/mathmech/docs/rus/help_radf.html new file mode 100644 index 0000000..d306c2f --- /dev/null +++ b/mathmech/docs/rus/help_radf.html @@ -0,0 +1,27 @@ + + +

radf

+


Программа для расчета функций радиального (ФРР) и радиально-углового распределения (ФРУР).

+


Использование
mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-i МАСКА – маска снимков траектории
-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории
-c X,Y,Z – размер элементарной ячейки, А
-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат "1-2" или "1,2,3,-4,5,6" (автоматически включит расчет функции радиального распределения между центрами масс).
-o ФАЙЛ – генерируемый файл
-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0
-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2
-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0
-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения
-m – печать в виде матрицы
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Генерируемый файл (*.dat)

+ +


Работа приложенияn

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Пошаговое чтение исходных файлов. Установка переменных.
    Расчет количества пар молекул, находящихся в различных взаимных конфигурациях.
    3. +
  3. Печать результата в файл.
    Функция радиального распределения рассчитывается по формуле:
    RDF(r) = (1 / norm) * sum(d(r_n-r), n),
    norm(r) = (4*PI*r^2*dr) * ro * N * N_step,
    где d(r_n-r) – дельта-функция, r – радиус сферы, n – номер молекулы, dr – шаг изменения радиуса, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.
    Функция радиально-углового распределения рассчитывается по формуле:
    RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),
    norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,
    где d(r_n-r) и d(fi_n-fi) – дельта-функции, r – радиус сферы, fi – угол, n – номер молекулы, dr – шаг изменения радиуса, dfi – шаг изменения угла, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.
+


Работа с графическим интерфейсом

+
  1. Перейти во вкладку "ФРУР". Указать рабочую директорию.
    2. +
  2. Указать маску траекторных файлов.
    3. +
  3. Указать первый и последний шаги траектории.
    4. +
  4. Указать размер ячейки в А.
    5. +
  5. Указать генерируемый файл.
    6. +
  6. Указать искомые атомы.
    7. +
  7. Указать радиальные параметры функции в А. При необходимости указать угловые параметры функции в градусах.
    8. +
  8. При необходимости указать печать в виде матрицы, файл лога и генерацию графика.
    9. +
  9. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_statgen.html b/mathmech/docs/rus/help_statgen.html new file mode 100644 index 0000000..61c3bca --- /dev/null +++ b/mathmech/docs/rus/help_statgen.html @@ -0,0 +1,29 @@ + + +

statgen

+


Программа для анализа снимков молекулярно-динамических траекторий – выделяет молекулы в агломераты согласно указанному геометрическому критерию.

+


Использование
mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-i МАСКА – маска снимков траектории
-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории
-c X,Y,Z – размер элементарной ячейки, А
-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую
-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, "0-0:2.4,0-1:3.0" означает указание 0-0 взаимодействия <2.4 А и 0-1 <3.0 А.
-o ФАЙЛ – генерируемый файл
-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (>= 3)
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Генерируемый файл (*.dat)

+ +


Работа приложения

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Пошаговое чтение исходных файлов, установка переменных.
    Поиск взаимодействий, удовлетворяющих указанным критериям.
    Анализ всех связей и указание связи двух молекул, если удовлетворяется условия хотя бы одного из указанных критериев.
    Добавление молекул в агломераты согласно полученной матрице связанности.
    Печать агломератов в файл, дополнение общей статистики.
    3. +
  3. Печать общей статистики в файл.
+


Работа с графическим интерфейсом

+
  1. Перейти во вкладку "Агломерация". Указать рабочую директорию.
    2. +
  2. Указать маску траекторных файлов.
    3. +
  3. Указать первый и последний шаги траектории.
    4. +
  4. Указать размер ячейки в А.
    5. +
  5. Указать искомые атомы.
    6. +
  6. Указать взаимодействия. Из выпадающего списка выбрать тип взаимодействия, изменить при его критерий (А) и нажать "Сохранить". После завершения редактирования нажать "Добавить" – после этого взаимодействие появится в специальном окошке.. Для удаления взаимодействия необходимо выделить нужное взаимодействие в окошке и нажать "Удалить".
    7. +
  7. Указать генерируемый файл.
    8. +
  8. При необходимости указать максимальную глубину для проверки числа циклов в агломератах, файл лога и генерацию графика.
    9. +
  9. Для вариации геометрических критериев необходимо указать шаг изменения критериев и число шагов.
    10. +
  10. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_trj.html b/mathmech/docs/rus/help_trj.html new file mode 100644 index 0000000..d691bbe --- /dev/null +++ b/mathmech/docs/rus/help_trj.html @@ -0,0 +1,29 @@ + + +

trj

+


Программа для генерации специальных траекторных файлов из указанных исходных.

+


Использование
mm_trj -i ФАЙЛ -t ТИП -s ЧИСЛО -a ФАЙЛ -o МАСКА [ -tt ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-i ФАЙЛ – исходный траекторный файл
-t ТИП – тип траектории. Поддерживаемые форматы: gmx, puma
-s ЧИСЛО – число шагов траектории
-a ФАЙЛ – файл с указанием типов атомов
-o МАСКА – маска получаемых траекторных файлов
-tt ЧИСЛО – максимальное число различных типов атомов. По умолчанию 1024
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Файлы траектории (*.[0-9])

+ +

Файл с указанием типов атомов (*.types)

+ +


Работа приложения

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Пошаговое чтение исходных файлов и вывод шагов в указанные файлы.
+


Работа с графическим интерфейсом

+
  1. Выбрать Меню -> Создание файлов -> Файл типов атомов.
    2. +
  2. Указать генерируемый файл.
    3. +
  3. Заполнить типы атомов. Для добавления новой молекулы выбрать из выпадающего списка "Добавить новую молекулу". Для изменения числа молекул изменить соответствующее числовое значение. Для добавления нового атома необходимо ввести 2 символа в специальное поле, указать численный тип атома и нажать "Добавить" – после этого атом появится в специальном окошке. Для удаления атома необходимо выделить нужный атом в окошке и нажать "Удалить".
    4. +
  4. Создать файл типов атомов.
    5. +
  5. Перейти во вкладку "Создать траекторию". Указать рабочую директорию.
    6. +
  6. Указать исходный траекторный файл.
    7. +
  7. Выбрать тип траектории из выпадающего списка, указать число шагов траектории.
    8. +
  8. Указать созданный ранее файл типов атомов.
    9. +
  9. Указать маску генерируемых файлов.
    10. +
  10. При необходимости указать максимальное число различных типов атомов и файл лога.
    11. +
  11. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/docs/rus/help_trj2pdb.html b/mathmech/docs/rus/help_trj2pdb.html new file mode 100644 index 0000000..b9d3bd0 --- /dev/null +++ b/mathmech/docs/rus/help_trj2pdb.html @@ -0,0 +1,21 @@ + + +

trj2pdb

+


Программа для генерации PDB файла из исходных траекторных файлов.

+


Использование
mm_trj2pdb -i ФАЙЛ -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]
Параметры
-i ФАЙЛ – исходный файл с координатами
-o ФАЙЛ – генерируемый PDB файл с координатами
-l ФАЙЛ – запись лога в указанный файл
-q – не выводить сообщения в STDOUT
-h – показать эту справку и выйти

+


Форматы файлов

+

Файл траектории (*.pdb)

+

http://www.wwpdb.org/documentation/format33/sect9.html

+


Работа приложения

+
  1. Чтение заголовков исходных файлов, установка начальных переменных.
    2. +
  2. Чтение исходного файла.
    3. +
  3. Печать в файл.
+


Работа с графическим интерфейсом

+
  1. Перейти во вкладку "Создать PDB". Из выпадающего списка выбрать "Из снимка траектории".
    2. +
  2. Указать рабочую директорию.
    3. +
  3. Указать файл траектории.
    4. +
  4. Указать генерируемый PDB файл.
    5. +
  5. При необходимости указать файл лога.
    6. +
  6. Запустить приложение.
\ No newline at end of file diff --git a/mathmech/mathmech-1.0.3-src.zip b/mathmech/mathmech-1.0.3-src.zip deleted file mode 100644 index 02ae2fb..0000000 Binary files a/mathmech/mathmech-1.0.3-src.zip and /dev/null differ diff --git a/mathmech/mathmech-1.0.3-win32.zip b/mathmech/mathmech-1.0.3-win32.zip deleted file mode 100755 index 2655135..0000000 Binary files a/mathmech/mathmech-1.0.3-win32.zip and /dev/null differ diff --git a/mathmech/mathmech-1.1.0-src.zip b/mathmech/mathmech-1.1.0-src.zip new file mode 100644 index 0000000..d1dd973 Binary files /dev/null and b/mathmech/mathmech-1.1.0-src.zip differ diff --git a/mathmech/mathmech/CMakeLists.txt b/mathmech/mathmech/CMakeLists.txt index 6e94e6e..9282715 100644 --- a/mathmech/mathmech/CMakeLists.txt +++ b/mathmech/mathmech/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT mathmech) diff --git a/mathmech/mathmech/resources/translations/eng.qm b/mathmech/mathmech/resources/translations/eng.qm deleted file mode 100644 index 0439d63..0000000 Binary files a/mathmech/mathmech/resources/translations/eng.qm and /dev/null differ diff --git a/mathmech/mathmech/resources/translations/eng.ts b/mathmech/mathmech/resources/translations/eng.ts index fc871c2..02f1cbc 100644 --- a/mathmech/mathmech/resources/translations/eng.ts +++ b/mathmech/mathmech/resources/translations/eng.ts @@ -512,162 +512,890 @@ p, li { white-space: pre-wrap; } Ok + + HelpWindow + + + Help + Help + + + + Help about trj + Help about trj + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The enumeration of atoms block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The enumeration of atoms block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + trj + trj + + + + Help about statgen + Help about statgen + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamic trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying of the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamic trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying of the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + statgen + statgen + + + + Help about envir + Help about envir + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + envir + envir + + + + Help about radf + Help about radf + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF)</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF)</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + radf + radf + + + + Help about agl + Help about agl + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + agl + agl + + + + Help about trj2pdb + Help about trj2pdb + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + trj2pdb + trj2pdb + + + + Save help to html + Save help to html + + + + Save html + Save html + + + + Close window + Close window + + + + Close + Close + + + + Save file as + Save file as + + + + html files (*.html);;All files (*.*) + html files (*.html);;All files (*.*) + + + 'statgen' output files (*.dat);;All files (*.*) + 'statgen' output files (*.dat);;All files (*.*) + + MainWindow - + Ready Ready - - - - - + + + + + Select work directory Select work directory - - - + + + Select trajectory file Select trajectory file - + All files (*.*) All files (*.*) - + Select atom types file Select atom types file - + Atom types files (*.types);;All files (*.*) Atom types files (*.types);;All files (*.*) - + Save files as Save files as - + Mask of trajectory files Mask of trajectory files - - - - - + + + + + Save log file as... Save log file as... - - - - - + + + + + Log files (*.log) Log files (*.log) - - + + Select trajectory files Select trajectory files - - - - + + + + Trajectory files (*.*[0-9]) Trajectory files (*.*[0-9]) - - + + Save output file as... Save output file as... - - + + Output files (*.dat) Output files (*.dat) - - + + Save PDB file as... Save PDB file as... - - + + PDB files (*.pdb) PDB files (*.pdb) - + Select agglomerate file Select agglomerate file - + Agglomerate files (*.agl);;All files (*.*) Agglomerate files (*.agl);;All files (*.*) - + Processing 'trj'... Processing 'trj'... - - - - - + + + + + Done Done - + Processing 'statgen'... Processing 'statgen'... - + Processing 'envir'... Processing 'envir'... - + Processing 'radf'... Processing 'radf'... - + Processing 'agl'... Processing 'agl'... - + Processing 'trj2pdb'... Processing 'trj2pdb'... @@ -692,12 +1420,14 @@ p, li { white-space: pre-wrap; } Ctrl+Q + &Help - &Help + &Help + F1 - F1 + F1 @@ -733,146 +1463,137 @@ p, li { white-space: pre-wrap; } statgen_all statgen_all - - - - - - - Work directory - Work directory - + Work directory + Work directory + + + + + + + Path to work directory Path to work directory - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + Browse Browse - - - - - Input file - Input file - + Input file + Input file + + + + + Path to input file Path to input file - + Type of trajectory Type of trajectory - + GROMACS text GROMACS text - + PUMA PUMA - + Input trajectory type Input trajectory type - + Number of steps Number of steps - + Number of steps in trajectory Number of steps in trajectory - + Atom type file Atom type file - + Path to file with atom types Path to file with atom types - + Mask of output files Mask of output files - + Total atom types Total atom types - + Maximum number of atom types Maximum number of atom types - - - - - - - Log - Log - - Path to log file - Path to log file + Log + Log - - - - - - Clear window - Clear window + + + + + + Path to log file + Path to log file @@ -880,17 +1601,17 @@ p, li { white-space: pre-wrap; } - Clear - Clear + Clear window + Clear window - + - Start application - Start application + Clear + Clear @@ -898,220 +1619,229 @@ p, li { white-space: pre-wrap; } + Start application + Start application + + + + + + + Start Start - + Generate trajectory Generate trajectory - - + + Mask of input files Mask of input files - - + + Steps Steps - - + + first first - - + + First trajectory step First trajectory step - - + + last last - - + + Last trajectory step Last trajectory step - - - - + + + + Cell, A Cell, A - - - - - - X - X - - Cell size, X - Cell size, X + X + X - Y - Y + Cell size, X + Cell size, X - Cell size, Y - Cell size, Y + Y + Y - Z - Z + Cell size, Y + Cell size, Y + Z + Z + + + + + + Cell size, Z Cell size, Z - + atom 0 atom 0 - + atom0 type atom0 type - - - + + + atom 1 atom 1 - - - + + + atom1 type atom1 type - - - + + + atom 2 atom 2 - - - + + + atom2 type atom2 type - - - + + + atom 3 atom 3 - - - + + + atom3 type atom3 type - + Interaction Interaction - + 0-0 0-0 - + Type of interaction Type of interaction - + Criterion Criterion - + Save this criterion Save this criterion - + Save Save - + Add this interaction Add this interaction - + Add Add - + Added interactions Added interactions - + Remove selected interaction Remove selected interaction - + Remove Remove - - - - + + + + Output file Output file @@ -1120,215 +1850,215 @@ p, li { white-space: pre-wrap; } Path to ouput file - + Depth of search Depth of search - + Search depth of related graphs Search depth of related graphs - + Analysis Analysis - + Step of analysis Step of analysis - + Number of steps of analysis Number of steps of analysis - - + + Show graph Show graph - - + + Graph Graph - + Agglomeration Agglomeration - - - - + + + + Path to output file Path to output file - + Molecule Molecule - + Number of selected molecule Number of selected molecule - + Radius Radius - + Radius of environment Radius of environment - + Environment Environment - + One atom function One atom function - + Three atom function Three atom function - + Type of function Type of function - + R, A R, A - - + + min min - + Minimal radius Minimal radius - - + + max max - + Maximal radius Maximal radius - - + + step step - + Radius step Radius step - + Angle, deg Angle, deg - + Minimal angle Minimal angle - + Maximal angle Maximal angle - + Angle step Angle step - + Matrix output Matrix output - + Matrix Matrix - + RADF RADF - + From agglomerate - + From trajectory snapshot From trajectory snapshot - + Input file type Input file type - + File with agglomerate File with agglomerate - + Path to file with agglomerate Path to file with agglomerate - + Generate PDB Generate PDB - + Menu Menu - + File &creator File &creator - + &Tools &Tools - + Help Help diff --git a/mathmech/mathmech/resources/translations/rus.qm b/mathmech/mathmech/resources/translations/rus.qm deleted file mode 100644 index 86e7e35..0000000 Binary files a/mathmech/mathmech/resources/translations/rus.qm and /dev/null differ diff --git a/mathmech/mathmech/resources/translations/rus.ts b/mathmech/mathmech/resources/translations/rus.ts index 5fc7f32..deb6e4f 100644 --- a/mathmech/mathmech/resources/translations/rus.ts +++ b/mathmech/mathmech/resources/translations/rus.ts @@ -512,162 +512,890 @@ p, li { white-space: pre-wrap; } Ok + + HelpWindow + + + Help + Справка + + + + Help about trj + Справка по trj + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The enumeration of atoms block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации специальных траекторных файлов из указанных исходных.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_trj -i ФАЙЛ -t ТИП -s ЧИСЛО -a ФАЙЛ -o МАСКА [ -tt ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ – исходный траекторный файл<br />-t ТИП – тип траектории. Поддерживаемые форматы: gmx, puma<br />-s ЧИСЛО – число шагов траектории<br />-a ФАЙЛ – файл с указанием типов атомов<br />-o МАСКА – маска получаемых траекторных файлов<br />-tt ЧИСЛО – максимальное число различных типов атомов. По умолчанию 1024.<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файлы траектории (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число атомов (7 символов).</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Снимок траектории (перечисление всех атомов). Формат<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />Порядковый номер атома (5 символов), пробел, символьный тип атома (2 символа), 2 пробела, координата X (11 символов, 6 десятичной части), координата Y (11 символов, 6 десятичной части), координата Z (11 символов, 6 десятичной части), 4 пробела, численный тип атома (2 символа), пробел, номер молекулы (4 символа).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл с указанием типов атомов (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число молекул (NUMTYPES=1).</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок перечисления молекул. Переменные число молекул (NUMMOL=1), число атомов (NUMAT=1).<br />Блок перечисления атомов в молекуле. Формат<br />CA=1<br />Символьный тип атома (2 символа), символ равенства, численный тип атома.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов и вывод шагов в указанные файлы.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать Меню -&gt; Создание файлов -&gt; Файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заполнить типы атомов. Для добавления новой молекулы выбрать из выпадающего списка &quot;Добавить новую молекулу&quot;. Для изменения числа молекул изменить соответствующее числовое значение. Для добавления нового атома необходимо ввести 2 символа в специальное поле, указать численный тип атома и нажать &quot;Добавить&quot; – после этого атом появится в специальном окошке. Для удаления атома необходимо выделить нужный атом в окошке и нажать &quot;Удалить&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Создать файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Создать траекторию&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный траекторный файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать тип траектории из выпадающего списка, указать число шагов траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать созданный ранее файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску генерируемых файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальное число различных типов атомов и файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + trj + trj + + + + Help about statgen + Справка по statgen + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamic trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying of the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для анализа снимков молекулярно-динамических траекторий – выделяет молекулы в агломераты согласно указанному геометрическому критерию.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую<br />-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &quot;0-0:2.4,0-1:3.0&quot; означает указание 0-0 взаимодействия &lt;2.4 А и 0-1 &lt;3.0 А.<br />-o ФАЙЛ – генерируемый файл<br />-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&gt;= 3)<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.0&quot;. Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), маска файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), типы атомов (ATOMS=1,2,3,4), взаимодействия (INTERACTION=формат), максимальная глубина для проверки числа циклов (DEPTH=0, 0 – не проверять изоморфизм). Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление статистики по файлам.<br />Имя файла (FILE=mask.001), блок статистики по файлу &quot;STATISTIC … -----------------&quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000001 <br />Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).<br />Перечисление агломератов, найденных в данном файле. Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма). Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика &quot;.SUMMARY STATISTIC … ------------------------------------------------&quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Пробел, размер агломерата (7 символов), пробел, общее число агломератов данной стехиометрии (7 символов), пробел, средняя концентрация агломератов данной стехиометрии (9 символов, 2 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии (9 символов, 5 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии, умноженная на число молекул в агломерате (10 символов, 5 десятичной части).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика агломератов по классам (если указана проверка изоморфизма). Доля линейных (LINEAR=0.10000) и циклических (CYCLE=0.10000) агломератов, пропуск строки, доля неразветвленных (NOT BRANCHED=0.10000) и разветвленных (BRANCHED=0.10000) агломератов, пропуск строки, доля найденных циклов указанного размера (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов, установка переменных.<br />Поиск взаимодействий, удовлетворяющих указанным критериям.<br />Анализ всех связей и указание связи двух молекул, если удовлетворяется условия хотя бы одного из указанных критериев.<br />Добавление молекул в агломераты согласно полученной матрице связанности.<br />Печать агломератов в файл, дополнение общей статистики.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать общей статистики в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Агломерация&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать взаимодействия. Из выпадающего списка выбрать тип взаимодействия, изменить при его критерий (А) и нажать &quot;Сохранить&quot;. После завершения редактирования нажать &quot;Добавить&quot; – после этого взаимодействие появится в специальном окошке.. Для удаления взаимодействия необходимо выделить нужное взаимодействие в окошке и нажать &quot;Удалить&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальную глубину для проверки числа циклов в агломератах, файл лога и генерацию графика.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Для вариации геометрических критериев необходимо указать шаг изменения критериев и число шагов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + statgen + statgen + + + + Help about envir + Справка по envir + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файла указанной молекулы с окружением указанного радиуса.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_envir -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -n ЧИСЛО ] [ -r ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ – исходный файл с координатами<br />-c X,Y,Z – размер элементарной ячейки, А<br />-o ФАЙЛ – генерируемый PDB файл с координатами<br />-n ЧИСЛО – номер молекулы для поиска окружения. По умолчанию 1<br />-r ЧИСЛО – радиус окружения, А. По умолчанию 6.0<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл траектории (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходного файла.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск окружения.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать окружения в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Окружение&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать молекулу для поиска окружения и радиус окружения в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + envir + envir + + + + Help about radf + Справка по radf + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF)</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, log file and graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для расчета функций радиального (ФРР) и радиально-углового распределения (ФРУР).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &quot;1-2&quot; или &quot;1,2,3,-4,5,6&quot; (автоматически включит расчет функции радиального распределения между центрами масс).<br />-o ФАЙЛ – генерируемый файл<br />-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0<br />-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2<br />-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0<br />-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения<br />-m – печать в виде матрицы<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.0&quot;. Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), матричный вывод (MATRIX=1), файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), тип расчета (MODE=0) (0 – для функции радиального распределения, 1 – для функции радиального распределения для центров масс, 2 – для функции радиально-углового распределения), радиальные критерии (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), угловые критерии для функции радиально-углового распределения (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), типы атомов (ATOM=1-2) или (ATOM=1,2,3-4,5,6). Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок результатов &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).<br />Формат таблицы для функций радиального распределения (матричный вывод отключен)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, объем сферы (10 символов, 4 десятичной части), пробел, число молекул в данной сфере (9 символов), функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиального распределения (матричный вывод включен)<br /> 0001.0000 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, угол (9 символов, 2 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиально-углового распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)<br /> 0001.0000 04.000000 …<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Конец таблицы.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложенияn</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов. Установка переменных.<br />Расчет количества пар молекул, находящихся в различных взаимных конфигурациях.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.<br />Функция радиального распределения рассчитывается по формуле:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />где d(r_n-r) – дельта-функция, r – радиус сферы, n – номер молекулы, dr – шаг изменения радиуса, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.<br />Функция радиально-углового распределения рассчитывается по формуле:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />где d(r_n-r) и d(fi_n-fi) – дельта-функции, r – радиус сферы, fi – угол, n – номер молекулы, dr – шаг изменения радиуса, dfi – шаг изменения угла, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;ФРУР&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать радиальные параметры функции в А. При необходимости указать угловые параметры функции в градусах.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать печать в виде матрицы, файл лога и генерацию графика.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + radf + radf + + + + Help about agl + Справка по agl + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файлов с агломератами.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_agl -a ФАЙЛ -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-a ФАЙЛ – исходный файл с агломератом<br />-i ФАЙЛ – исходный файл с координатами<br />-c X,Y,Z – размер элементарной ячейки, А<br />-o ФАЙЛ – генерируемый PDB файл с координатами<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл с агломератом (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл траектории (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск оптимальной конфигурации.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Меню -&gt; Создание файлов -&gt; Файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл, сгенерированный приложением statgen. Нажать &quot;Выбор&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать траекторный снимок в выпадающем списке. Выбрать агломерат.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать выходной файл. Создать файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">5. Перейти во вкладку &quot;Создать PDB&quot;. Из выпадающего списка выбрать &quot;Из агломерата&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать сгенерированный файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации специальных траекторных файлов из указанных исходных.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_trj -i ФАЙЛ -t ТИП -s ЧИСЛО -a ФАЙЛ -o МАСКА [ -tt ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ – исходный траекторный файл<br />-t ТИП – тип траектории. Поддерживаемые форматы: gmx, puma<br />-s ЧИСЛО – число шагов траектории<br />-a ФАЙЛ – файл с указанием типов атомов<br />-o МАСКА – маска получаемых траекторных файлов<br />-tt ЧИСЛО – максимальное число различных типов атомов. По умолчанию 1024<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файлы траектории (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число атомов (7 символов).</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Снимок траектории (перечисление всех атомов). Формат<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />Порядковый номер атома (5 символов), пробел, символьный тип атома (2 символа), 2 пробела, координата X (11 символов, 6 десятичной части), координата Y (11 символов, 6 десятичной части), координата Z (11 символов, 6 десятичной части), 4 пробела, численный тип атома (2 символа), пробел, номер молекулы (4 символа).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл с указанием типов атомов (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается число молекул (NUMTYPES=1).</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок перечисления молекул. Переменные число молекул (NUMMOL=1), число атомов (NUMAT=1).<br />Блок перечисления атомов в молекуле. Формат<br />CA=1<br />Символьный тип атома (2 символа), символ равенства, численный тип атома.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов и вывод шагов в указанные файлы.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать Меню -&gt; Создание файлов -&gt; Файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заполнить типы атомов. Для добавления новой молекулы выбрать из выпадающего списка &quot;Добавить новую молекулу&quot;. Для изменения числа молекул изменить соответствующее числовое значение. Для добавления нового атома необходимо ввести 2 символа в специальное поле, указать численный тип атома и нажать &quot;Добавить&quot; – после этого атом появится в специальном окошке. Для удаления атома необходимо выделить нужный атом в окошке и нажать &quot;Удалить&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Создать файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Создать траекторию&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный траекторный файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать тип траектории из выпадающего списка, указать число шагов траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать созданный ранее файл типов атомов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску генерируемых файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальное число различных типов атомов и файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для анализа снимков молекулярно-динамических траекторий – выделяет молекулы в агломераты согласно указанному геометрическому критерию.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую<br />-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &quot;0-0:2.4,0-1:3.0&quot; означает указание 0-0 взаимодействия &lt;2.4 А и 0-1 &lt;3.0 А.<br />-o ФАЙЛ – генерируемый файл<br />-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&gt;= 3)<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.0&quot;. Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), маска файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), типы атомов (ATOMS=1,2,3,4), взаимодействия (INTERACTION=формат), максимальная глубина для проверки числа циклов (DEPTH=0, 0 – не проверять изоморфизм). Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление статистики по файлам.<br />Имя файла (FILE=mask.001), блок статистики по файлу &quot;STATISTIC … -----------------&quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000001 <br />Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).<br />Перечисление агломератов, найденных в данном файле. Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма). Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика &quot;.SUMMARY STATISTIC … ------------------------------------------------&quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Пробел, размер агломерата (7 символов), пробел, общее число агломератов данной стехиометрии (7 символов), пробел, средняя концентрация агломератов данной стехиометрии (9 символов, 2 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии (9 символов, 5 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии, умноженная на число молекул в агломерате (10 символов, 5 десятичной части).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика агломератов по классам (если указана проверка изоморфизма). Доля линейных (LINEAR=0.10000) и циклических (CYCLE=0.10000) агломератов, пропуск строки, доля неразветвленных (NOT BRANCHED=0.10000) и разветвленных (BRANCHED=0.10000) агломератов, пропуск строки, доля найденных циклов указанного размера (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов, установка переменных.<br />Поиск взаимодействий, удовлетворяющих указанным критериям.<br />Анализ всех связей и указание связи двух молекул, если удовлетворяется условия хотя бы одного из указанных критериев.<br />Добавление молекул в агломераты согласно полученной матрице связанности.<br />Печать агломератов в файл, дополнение общей статистики.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать общей статистики в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Агломерация&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать взаимодействия. Из выпадающего списка выбрать тип взаимодействия, изменить при его критерий (А) и нажать &quot;Сохранить&quot;. После завершения редактирования нажать &quot;Добавить&quot; – после этого взаимодействие появится в специальном окошке.. Для удаления взаимодействия необходимо выделить нужное взаимодействие в окошке и нажать &quot;Удалить&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать максимальную глубину для проверки числа циклов в агломератах, файл лога и генерацию графика.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Для вариации геометрических критериев необходимо указать шаг изменения критериев и число шагов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файла указанной молекулы с окружением указанного радиуса.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_envir -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -n ЧИСЛО ] [ -r ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ – исходный файл с координатами<br />-c X,Y,Z – размер элементарной ячейки, А<br />-o ФАЙЛ – генерируемый PDB файл с координатами<br />-n ЧИСЛО – номер молекулы для поиска окружения. По умолчанию 1<br />-r ЧИСЛО – радиус окружения, А. По умолчанию 6.0<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл траектории (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходного файла.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск окружения.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать окружения в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Окружение&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать исходный файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать молекулу для поиска окружения и радиус окружения в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для расчета функций радиального (ФРР) и радиально-углового распределения (ФРУР).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &quot;1-2&quot; или &quot;1,2,3,-4,5,6&quot; (автоматически включит расчет функции радиального распределения между центрами масс).<br />-o ФАЙЛ – генерируемый файл<br />-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0<br />-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2<br />-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0<br />-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения<br />-m – печать в виде матрицы<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.0&quot;. Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), матричный вывод (MATRIX=1), файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), тип расчета (MODE=0) (0 – для функции радиального распределения, 1 – для функции радиального распределения для центров масс, 2 – для функции радиально-углового распределения), радиальные критерии (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), угловые критерии для функции радиально-углового распределения (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), типы атомов (ATOM=1-2) или (ATOM=1,2,3-4,5,6). Пустая строка.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок результатов &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).<br />Формат таблицы для функций радиального распределения (матричный вывод отключен)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиального распределения (матричный вывод включен)<br /> 0001.0000 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, угол (9 символов, 2 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиально-углового распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)<br /> 0001.0000 04.000000 …<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Конец таблицы.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложенияn</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Пошаговое чтение исходных файлов. Установка переменных.<br />Расчет количества пар молекул, находящихся в различных взаимных конфигурациях.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.<br />Функция радиального распределения рассчитывается по формуле:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />где d(r_n-r) – дельта-функция, r – радиус сферы, n – номер молекулы, dr – шаг изменения радиуса, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.<br />Функция радиально-углового распределения рассчитывается по формуле:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />где d(r_n-r) и d(fi_n-fi) – дельта-функции, r – радиус сферы, fi – угол, n – номер молекулы, dr – шаг изменения радиуса, dfi – шаг изменения угла, ro – число молекул в единице объема, N – число молекул, N_step – число шагов траектории.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;ФРУР&quot;. Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать маску траекторных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать первый и последний шаги траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать искомые атомы.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать радиальные параметры функции в А. При необходимости указать угловые параметры функции в градусах.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать печать в виде матрицы, файл лога и генерацию графика.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файлов с агломератами.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_agl -a ФАЙЛ -i ФАЙЛ -c X,Y,Z -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-a ФАЙЛ – исходный файл с агломератом<br />-i ФАЙЛ – исходный файл с координатами<br />-c X,Y,Z – размер элементарной ячейки, А<br />-o ФАЙЛ – генерируемый PDB файл с координатами<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл с агломератом (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл траектории (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходных файлов.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Поиск оптимальной конфигурации.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать результата в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Меню -&gt; Создание файлов -&gt; Файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл, сгенерированный приложением statgen. Нажать &quot;Выбор&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Выбрать траекторный снимок в выпадающем списке. Выбрать агломерат.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать выходной файл. Создать файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">5. Перейти во вкладку &quot;Создать PDB&quot;. Из выпадающего списка выбрать &quot;Из агломерата&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать сгенерированный файл с агломератом.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать размер ячейки в А.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + agl + agl + + + + Help about trj2pdb + Справка по trj2pdb + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Программа для генерации PDB файла из исходных траекторных файлов.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_trj2pdb -i ФАЙЛ -o ФАЙЛ [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i ФАЙЛ – исходный файл с координатами<br />-o ФАЙЛ – генерируемый PDB файл с координатами<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Файл траектории (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа приложения</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение заголовков исходных файлов, установка начальных переменных.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Чтение исходного файла.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Печать в файл.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Работа с графическим интерфейсом</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перейти во вкладку &quot;Создать PDB&quot;. Из выпадающего списка выбрать &quot;Из снимка траектории&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать рабочую директорию.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать файл траектории.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Указать генерируемый PDB файл.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">При необходимости указать файл лога.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Запустить приложение.</li></ol></body></html> + + + + trj2pdb + trj2pdb + + + + Save help to html + Сохранить справку в html + + + + Save html + Сохранить html + + + + Close window + Закрыть окно + + + + Close + Закрыть + + + + Save file as + Сохранить файл как + + + + html files (*.html);;All files (*.*) + html файлы (*.html);;Все файлы (*.*) + + + 'statgen' output files (*.dat);;All files (*.*) + Файлы 'statgen' (*.dat);;Все файлы (*.*) + + MainWindow - + Ready Готов - - - - - + + + + + Select work directory Выбор рабочей директории - - - + + + Select trajectory file Выбор файла траектории - + All files (*.*) Все файлы (*.*) - + Select atom types file Выбор файла типов атомов - + Atom types files (*.types);;All files (*.*) Файл типов атомов (*.types);;Все файлы (*.*) - + Save files as Сохранить файл как... - + Mask of trajectory files Маска файлов траектории - - - - - + + + + + Save log file as... Сохранить лог как... - - - - - + + + + + Log files (*.log) Лог (*.log) - - + + Select trajectory files Выбор файла траектории - - - - + + + + Trajectory files (*.*[0-9]) Файлы траектории (*.*[0-9]) - - + + Save output file as... Сохранить файл как... - - + + Output files (*.dat) Выходной файл (*.dat) - - + + Save PDB file as... Сохранить PDB как... - - + + PDB files (*.pdb) PDB файл (*.pdb) - + Select agglomerate file Выбор файла с агломератом - + Agglomerate files (*.agl);;All files (*.*) Файл с агломератом (*.agl);Все файлы (*.*) - + Processing 'trj'... Выполняется 'trj'... - - - - - + + + + + Done Готово - + Processing 'statgen'... Выполняется 'statgen'... - + Processing 'envir'... Выполняется 'envir'... - + Processing 'radf'... Выполняется 'radf'... - + Processing 'agl'... Выполняется 'agl'... - + Processing 'trj2pdb'... Выполняется 'trj2pdb'... @@ -677,125 +1405,125 @@ p, li { white-space: pre-wrap; } Mathematical Molecular Mechanics - + Generate trajectory Создать траекторию - - - - - + + + + + Work directory Рабочая директория - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + Browse Обзор - - - + + + Input file Входной файл - + Type of trajectory Тип траектории - + GROMACS text GROMACS - + PUMA PUMA - + Number of steps Число шагов - + Atom type file Файл типов атомов - + Mask of output files Маска файлов - + Total atom types Всего типов атомов - - - - - + + + + + Log Лог - - - - - + + + + + Clear Очистить - - - - - + + + + + Start Старт - + Agglomeration Агломерация - - + + Mask of input files Маска файлов @@ -805,266 +1533,266 @@ p, li { white-space: pre-wrap; } Ctrl+P - - - - - + + + + + Path to work directory Путь к рабочей директории - - - + + + Path to input file Путь ко входному файлу - + Input trajectory type Тип входной траектории - + Number of steps in trajectory Число шагов в траектории - + Path to file with atom types Путь к файлу с типами атомов - + Maximum number of atom types Максимальное число типов атомов - - - - - + + + + + Path to log file Путь к логу - - - - - + + + + + Clear window Очистить окно - - - - - + + + + + Start application Запустить приложение - - + + Steps Шаги - - + + first первый - - + + First trajectory step Первый шаг траектории - - + + last последний - - + + Last trajectory step Последний шаг траектории - - - - + + + + Cell, A Ячейка, А - - - - - - X - X - - Cell size, X - Размер ячейки, X + X + X - Y - Y + Cell size, X + Размер ячейки, X - Cell size, Y - Размер ячейки, Y + Y + Y - Z - Z + Cell size, Y + Размер ячейки, Y + Z + Z + + + + + + Cell size, Z Размер ячейки, Z - + atom 0 атом 0 - + atom0 type тип 1го атома - - - + + + atom 1 атом 1 - - - + + + atom1 type тип 2го атома - - - + + + atom 2 атом 2 - - - + + + atom2 type тип 3го атома - - - + + + atom 3 атом 3 - - - + + + atom3 type тип 4го атома - + Interaction Взаимодействие - + 0-0 0-0 - + Type of interaction Тип взаимодействия - + Criterion Критерий - + Save this criterion Сохранить данный критерий - + Save Сохранить - + Add this interaction Добавить данное взаимодействие - + Add Добавить - + Added interactions Добавленные взаимодействия - + Remove selected interaction Удалить выбранное взаимодействие - + Remove Удалить - - - - + + + + Output file Выходной файл @@ -1073,210 +1801,210 @@ p, li { white-space: pre-wrap; } Путь к выходному файлу - + Depth of search Глубина поиска - + Search depth of related graphs Глубина поиска родственных графов - + Analysis Анализ - + Step of analysis Шаг анализа - + Number of steps of analysis Число шагов в анализе - - + + Show graph Показать график - - + + Graph График - - - - + + + + Path to output file Путь к выходному файлу - + Number of selected molecule Номер выбранной молекулы - + Radius of environment Радиус окружения - + Environment Окружение - + Molecule Молекула - + Radius Радиус - + RADF ФРУР - + One atom function Одноатомная функция - + Three atom function Трехатомная функция - + Type of function Тип функции - + R, A R, A - - + + min min - + Minimal radius Минимальный радиус - - + + max max - + Maximal radius Максимальный радиус - - + + step шаг - + Radius step Шаг - + Angle, deg Угол, град - + Minimal angle Минимальный угол - + Maximal angle Максимальный угол - + Angle step Шаг - + Matrix output Результат в виде матрицы - + Matrix Матрица - + Input file type Тип входного файла - + Path to file with agglomerate Путь к файлу с агломератом - + Generate PDB Создать PDB - + From agglomerate Из агломерата - + From trajectory snapshot Из снимка траектории - + File with agglomerate Файл с агломератом - + Menu Меню - + File &creator &Создание файлов - + &Tools &Утилиты - + Help Помощь @@ -1296,12 +2024,14 @@ p, li { white-space: pre-wrap; } Ctrl+Q + &Help - &Помощь + &Помощь + F1 - F1 + F1 diff --git a/mathmech/mathmech/src/Makefile b/mathmech/mathmech/src/Makefile index 0d83f1e..5c453ec 100644 --- a/mathmech/mathmech/src/Makefile +++ b/mathmech/mathmech/src/Makefile @@ -1,6 +1,6 @@ ############################################################################# # Makefile for building: mathmech -# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 26 15:52:26 2013 +# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 3 02:36:06 2013 # Project: mathmech.pro # Template: app # Command: /usr/bin/qmake-qt4 -o Makefile mathmech.pro @@ -54,7 +54,8 @@ SOURCES = main.cpp \ aboutwindow.cpp \ statgengraphwindow.cpp \ settingswindow.cpp \ - aglallwindow.cpp moc_mainwindow.cpp \ + aglallwindow.cpp \ + helpwindow.cpp moc_mainwindow.cpp \ moc_errorwindow.cpp \ moc_clear_items.cpp \ moc_start_events.cpp \ @@ -64,7 +65,8 @@ SOURCES = main.cpp \ moc_aboutwindow.cpp \ moc_statgengraphwindow.cpp \ moc_settingswindow.cpp \ - moc_aglallwindow.cpp + moc_aglallwindow.cpp \ + moc_helpwindow.cpp OBJECTS = main.o \ mainwindow.o \ errorwindow.o \ @@ -77,6 +79,7 @@ OBJECTS = main.o \ statgengraphwindow.o \ settingswindow.o \ aglallwindow.o \ + helpwindow.o \ moc_mainwindow.o \ moc_errorwindow.o \ moc_clear_items.o \ @@ -87,7 +90,8 @@ OBJECTS = main.o \ moc_aboutwindow.o \ moc_statgengraphwindow.o \ moc_settingswindow.o \ - moc_aglallwindow.o + moc_aglallwindow.o \ + moc_helpwindow.o DIST = /usr/share/qt4/mkspecs/common/unix.conf \ /usr/share/qt4/mkspecs/common/linux.conf \ /usr/share/qt4/mkspecs/common/gcc-base.conf \ @@ -146,7 +150,7 @@ first: all all: Makefile $(TARGET) -$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h $(OBJECTS) +$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h $(OBJECTS) $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) Makefile: mathmech.pro /usr/share/qt4/mkspecs/linux-g++/qmake.conf /usr/share/qt4/mkspecs/common/unix.conf \ @@ -219,7 +223,7 @@ qmake: FORCE dist: @$(CHK_DIR_EXISTS) .tmp/mathmech1.0.0 || $(MKDIR) .tmp/mathmech1.0.0 - $(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0 + $(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h helpwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp helpwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui helpwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0 clean:compiler_clean @@ -240,9 +244,9 @@ mocclean: compiler_moc_header_clean compiler_moc_source_clean mocables: compiler_moc_header_make_all compiler_moc_source_make_all -compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp +compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp compiler_moc_header_clean: - -$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp + -$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp moc_mainwindow.cpp: mainwindow.h /usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) mainwindow.h -o moc_mainwindow.cpp @@ -276,6 +280,9 @@ moc_settingswindow.cpp: settingswindow.h moc_aglallwindow.cpp: aglallwindow.h /usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) aglallwindow.h -o moc_aglallwindow.cpp +moc_helpwindow.cpp: helpwindow.h + /usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) helpwindow.h -o moc_helpwindow.cpp + compiler_rcc_make_all: compiler_rcc_clean: compiler_image_collection_make_all: qmake_image_collection.cpp @@ -283,9 +290,9 @@ compiler_image_collection_clean: -$(DEL_FILE) qmake_image_collection.cpp compiler_moc_source_make_all: compiler_moc_source_clean: -compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h +compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h compiler_uic_clean: - -$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h + -$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h ui_mainwindow.h: mainwindow.ui /usr/lib/qt4/bin/uic mainwindow.ui -o ui_mainwindow.h @@ -310,6 +317,9 @@ ui_settingswindow.h: settingswindow.ui ui_aglallwindow.h: aglallwindow.ui /usr/lib/qt4/bin/uic aglallwindow.ui -o ui_aglallwindow.h +ui_helpwindow.h: helpwindow.ui + /usr/lib/qt4/bin/uic helpwindow.ui -o ui_helpwindow.h + compiler_yacc_decl_make_all: compiler_yacc_decl_clean: compiler_yacc_impl_make_all: @@ -327,10 +337,11 @@ mainwindow.o: mainwindow.cpp aboutwindow.h \ agglwindow.h \ aglallwindow.h \ atomtypeswindow.h \ + helpwindow.h \ settingswindow.h \ + statgengraphwindow.h \ clear_items.h \ start_events.h \ - statgengraphwindow.h \ update_fields.h \ mainwindow.h \ ui_mainwindow.h @@ -386,6 +397,10 @@ aglallwindow.o: aglallwindow.cpp errorwindow.h \ ui_aglallwindow.h $(CXX) -c $(CXXFLAGS) $(INCPATH) -o aglallwindow.o aglallwindow.cpp +helpwindow.o: helpwindow.cpp helpwindow.h \ + ui_helpwindow.h + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o helpwindow.o helpwindow.cpp + moc_mainwindow.o: moc_mainwindow.cpp $(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_mainwindow.o moc_mainwindow.cpp @@ -419,6 +434,9 @@ moc_settingswindow.o: moc_settingswindow.cpp moc_aglallwindow.o: moc_aglallwindow.cpp $(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_aglallwindow.o moc_aglallwindow.cpp +moc_helpwindow.o: moc_helpwindow.cpp + $(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_helpwindow.o moc_helpwindow.cpp + ####### Install install: FORCE diff --git a/mathmech/mathmech/src/helpwindow.cpp b/mathmech/mathmech/src/helpwindow.cpp index 668cc50..5b6251c 100644 --- a/mathmech/mathmech/src/helpwindow.cpp +++ b/mathmech/mathmech/src/helpwindow.cpp @@ -1,3 +1,10 @@ +#include +#include +#include +#include + +#include "errorwindow.h" + #include "helpwindow.h" #include "ui_helpwindow.h" @@ -19,3 +26,43 @@ void HelpWindow::keyPressEvent(QKeyEvent *pressedKey) if (pressedKey->key() == Qt::Key_Escape) close(); } + +void HelpWindow::on_pushButton_save_clicked() +{ + errorwin = new ErrorWindow(this); + + QString filename = QFileDialog::getSaveFileName( + this, + tr("Save file as"), + QDir::currentPath(), + tr("html files (*.html);;All files (*.*)")); + if (filename.isEmpty()) + return; + filename = QFileInfo(filename).absoluteFilePath(); + QFile f_out(filename); + if (!f_out.open(QIODevice::WriteOnly | QIODevice::Text)) + { + errorwin->set_message(9); + errorwin->show(); + return; + } + QTextStream out(&f_out); + QString text = QString(""); + int page = ui->toolBox->currentIndex(); + if (page == 0) + text = ui->textBrowser_trj->toHtml(); + else if (page == 1) + text = ui->textBrowser_statgen->toHtml(); + else if (page == 2) + text = ui->textBrowser_envir->toHtml(); + else if (page == 3) + text = ui->textBrowser_radf->toHtml(); + else if (page == 4) + text = ui->textBrowser_agl->toHtml(); + else if (page == 5) + text = ui->textBrowser_trj2pdb->toHtml(); + out << text; + f_out.close(); + + delete errorwin; +} diff --git a/mathmech/mathmech/src/helpwindow.h b/mathmech/mathmech/src/helpwindow.h index b85f55f..86f4b92 100644 --- a/mathmech/mathmech/src/helpwindow.h +++ b/mathmech/mathmech/src/helpwindow.h @@ -3,6 +3,8 @@ #include +class ErrorWindow; + namespace Ui { class HelpWindow; } @@ -15,8 +17,12 @@ public: explicit HelpWindow(QWidget *parent = 0); ~HelpWindow(); +private slots: + void on_pushButton_save_clicked(); + private: Ui::HelpWindow *ui; + ErrorWindow *errorwin; // ESC pressed event void keyPressEvent(QKeyEvent *pressedKey); diff --git a/mathmech/mathmech/src/helpwindow.ui b/mathmech/mathmech/src/helpwindow.ui index ba7efb6..6420112 100644 --- a/mathmech/mathmech/src/helpwindow.ui +++ b/mathmech/mathmech/src/helpwindow.ui @@ -20,27 +20,6 @@ 0 - - - - 0 - 0 - 580 - 233 - - - - General help - - - General - - - - - - - @@ -58,7 +37,39 @@ - + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + @@ -67,8 +78,8 @@ 0 0 - 580 - 233 + 98 + 88 @@ -79,7 +90,39 @@ - + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + @@ -88,8 +131,8 @@ 0 0 - 580 - 233 + 98 + 88 @@ -100,7 +143,33 @@ - + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + @@ -109,8 +178,8 @@ 0 0 - 580 - 233 + 98 + 88 @@ -121,7 +190,92 @@ - + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> +<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + + + + + + + + 0 + 0 + 98 + 88 + + + + Help about agl + + + agl + + + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li> +<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + @@ -130,8 +284,8 @@ 0 0 - 580 - 233 + 98 + 88 @@ -142,7 +296,31 @@ - + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> +<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p> +<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol> +<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p> +<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li> +<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html> + + @@ -164,7 +342,26 @@ - + + + + 80 + 23 + + + + Save help to html + + + Save html + + + true + + + + + 80 @@ -188,18 +385,19 @@ - textBrowser_general - pushButton textBrowser_trj textBrowser_statgen textBrowser_envir textBrowser_radf + textBrowser_agl textBrowser_trj2pdb + pushButton_save + pushButton_close - pushButton + pushButton_close clicked() HelpWindow close() diff --git a/mathmech/mathmech/src/mathmech.pro.user b/mathmech/mathmech/src/mathmech.pro.user index 8f5c685..f48318b 100644 --- a/mathmech/mathmech/src/mathmech.pro.user +++ b/mathmech/mathmech/src/mathmech.pro.user @@ -1,6 +1,6 @@ - + ProjectExplorer.Project.ActiveTarget diff --git a/mathmech/mm_agl/CMakeLists.txt b/mathmech/mm_agl/CMakeLists.txt index a0656e7..fc12b62 100644 --- a/mathmech/mm_agl/CMakeLists.txt +++ b/mathmech/mm_agl/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}agl) diff --git a/mathmech/mm_agl/mm_agl.pdf b/mathmech/mm_agl/mm_agl.pdf index 2be6f5a..ed2a85f 100644 Binary files a/mathmech/mm_agl/mm_agl.pdf and b/mathmech/mm_agl/mm_agl.pdf differ diff --git a/mathmech/mm_agl/src/CMakeLists.txt b/mathmech/mm_agl/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_agl/src/CMakeLists.txt +++ b/mathmech/mm_agl/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}") diff --git a/mathmech/mm_envir/CMakeLists.txt b/mathmech/mm_envir/CMakeLists.txt index a7ca1aa..142624d 100644 --- a/mathmech/mm_envir/CMakeLists.txt +++ b/mathmech/mm_envir/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}envir) diff --git a/mathmech/mm_envir/mm_envir.pdf b/mathmech/mm_envir/mm_envir.pdf index 8362440..b979143 100644 Binary files a/mathmech/mm_envir/mm_envir.pdf and b/mathmech/mm_envir/mm_envir.pdf differ diff --git a/mathmech/mm_envir/src/CMakeLists.txt b/mathmech/mm_envir/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_envir/src/CMakeLists.txt +++ b/mathmech/mm_envir/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}") diff --git a/mathmech/mm_radf/CMakeLists.txt b/mathmech/mm_radf/CMakeLists.txt index 7b2a242..7f3c1af 100644 --- a/mathmech/mm_radf/CMakeLists.txt +++ b/mathmech/mm_radf/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}radf) diff --git a/mathmech/mm_radf/README b/mathmech/mm_radf/README index 31a3525..ee12a00 100644 --- a/mathmech/mm_radf/README +++ b/mathmech/mm_radf/README @@ -1,5 +1,5 @@ mm_radf - program that calculates radial distribution function (RDF) or radial-angles -distribution function +distribution function (RADF) Version : 1.0.3 License : GPL diff --git a/mathmech/mm_radf/mm_radf.pdf b/mathmech/mm_radf/mm_radf.pdf index 533dfcb..1d0a837 100644 Binary files a/mathmech/mm_radf/mm_radf.pdf and b/mathmech/mm_radf/mm_radf.pdf differ diff --git a/mathmech/mm_radf/src/CMakeLists.txt b/mathmech/mm_radf/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_radf/src/CMakeLists.txt +++ b/mathmech/mm_radf/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}") diff --git a/mathmech/mm_statgen/CMakeLists.txt b/mathmech/mm_statgen/CMakeLists.txt index 7a65536..b54fcff 100644 --- a/mathmech/mm_statgen/CMakeLists.txt +++ b/mathmech/mm_statgen/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}statgen) diff --git a/mathmech/mm_statgen/mm_statgen.pdf b/mathmech/mm_statgen/mm_statgen.pdf index 044c596..d610230 100644 Binary files a/mathmech/mm_statgen/mm_statgen.pdf and b/mathmech/mm_statgen/mm_statgen.pdf differ diff --git a/mathmech/mm_statgen/src/CMakeLists.txt b/mathmech/mm_statgen/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_statgen/src/CMakeLists.txt +++ b/mathmech/mm_statgen/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}") diff --git a/mathmech/mm_trj/CMakeLists.txt b/mathmech/mm_trj/CMakeLists.txt index 37d03c3..bdf648e 100644 --- a/mathmech/mm_trj/CMakeLists.txt +++ b/mathmech/mm_trj/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}trj) diff --git a/mathmech/mm_trj/mm_trj.pdf b/mathmech/mm_trj/mm_trj.pdf index 7148f52..8f306cc 100644 Binary files a/mathmech/mm_trj/mm_trj.pdf and b/mathmech/mm_trj/mm_trj.pdf differ diff --git a/mathmech/mm_trj/src/CMakeLists.txt b/mathmech/mm_trj/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_trj/src/CMakeLists.txt +++ b/mathmech/mm_trj/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}") diff --git a/mathmech/mm_trj2pdb/CMakeLists.txt b/mathmech/mm_trj2pdb/CMakeLists.txt index 62429b6..1373d77 100644 --- a/mathmech/mm_trj2pdb/CMakeLists.txt +++ b/mathmech/mm_trj2pdb/CMakeLists.txt @@ -1,8 +1,8 @@ cmake_minimum_required (VERSION 2.8) -cmake_policy(SET CMP0003 OLD) -cmake_policy(SET CMP0011 NEW) -cmake_policy(SET CMP0015 NEW) +cmake_policy (SET CMP0003 OLD) +cmake_policy (SET CMP0011 NEW) +cmake_policy (SET CMP0015 NEW) # set project name set (PROJECT ${MM_PREFIX}trj2pdb) diff --git a/mathmech/mm_trj2pdb/mm_trj2pdb.pdf b/mathmech/mm_trj2pdb/mm_trj2pdb.pdf index d4e68cf..4ec958c 100644 Binary files a/mathmech/mm_trj2pdb/mm_trj2pdb.pdf and b/mathmech/mm_trj2pdb/mm_trj2pdb.pdf differ diff --git a/mathmech/mm_trj2pdb/src/CMakeLists.txt b/mathmech/mm_trj2pdb/src/CMakeLists.txt index f5fc68a..ba5b6dc 100644 --- a/mathmech/mm_trj2pdb/src/CMakeLists.txt +++ b/mathmech/mm_trj2pdb/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) set (ADDITIONAL_LIB m) else () set (ADDITIONAL_LIB) -endif() +endif () # message message (STATUS "SOURCES: ${SOURCES}")