arcanis/moldyn
1
0
Fork 0
mirror of https://github.com/arcan1s/moldyn.git synced 2025-06-28 14:51:41 +00:00
Code Issues Projects Releases Wiki Activity

Release 1.1.0

Browse Source 
+ added help window
+ added help docs
+ small bug fixes
This commit is contained in:
arcan1s
2013-09-03 06:01:23 +04:00
parent d7f7a9c2b5
commit 6b0a2a47db
48 changed files with 2639 additions and 578 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
mathmech/CMakeLists.txt
View File

@ -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()
endforeach ()
# set docs file
if (ADD_DOCS)
include (docs.cmake)
endif ()

16
mathmech/PKGBUILD
View File

@ -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
}

BIN
mathmech/README.doc
View File

Binary file not shown.

5
mathmech/docs.cmake Normal file
View File

@ -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})

31
mathmech/docs/eng/help_agl.html Normal file
View File

@ -0,0 +1,31 @@
<!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;">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>

23
mathmech/docs/eng/help_envir.html Normal file
View File

@ -0,0 +1,23 @@
<!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>

27
mathmech/docs/eng/help_radf.html Normal file
View File

@ -0,0 +1,27 @@
<!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>

29
mathmech/docs/eng/help_statgen.html Normal file
View File

@ -0,0 +1,29 @@
<!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>

29
mathmech/docs/eng/help_trj.html Normal file
View File

@ -0,0 +1,29 @@
<!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>

21
mathmech/docs/eng/help_trj2pdb.html Normal file
View File

@ -0,0 +1,21 @@
<!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>

31
mathmech/docs/rus/help_agl.html Normal file
View File

@ -0,0 +1,31 @@
<!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;">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>

23
mathmech/docs/rus/help_envir.html Normal file
View File

@ -0,0 +1,23 @@
<!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>

27
mathmech/docs/rus/help_radf.html Normal file
View File

@ -0,0 +1,27 @@
<!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>

29
mathmech/docs/rus/help_statgen.html Normal file
View File

@ -0,0 +1,29 @@
<!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>

29
mathmech/docs/rus/help_trj.html Normal file
View File

@ -0,0 +1,29 @@
<!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>

21
mathmech/docs/rus/help_trj2pdb.html Normal file
View File

@ -0,0 +1,21 @@
<!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>

BIN
mathmech/mathmech-1.0.3-src.zip
View File

Binary file not shown.

BIN
mathmech/mathmech-1.0.3-win32.zip
View File

Binary file not shown.

BIN
mathmech/mathmech-1.1.0-src.zip Normal file
View File

Binary file not shown.

6
mathmech/mathmech/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mathmech/resources/translations/eng.qm
View File

Binary file not shown.

1214
mathmech/mathmech/resources/translations/eng.ts
View File

File diff suppressed because it is too large Load Diff

BIN
mathmech/mathmech/resources/translations/rus.qm
View File

Binary file not shown.

1228
mathmech/mathmech/resources/translations/rus.ts
View File

File diff suppressed because it is too large Load Diff

40
mathmech/mathmech/src/Makefile
View File

@ -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

47
mathmech/mathmech/src/helpwindow.cpp
View File

@ -1,3 +1,10 @@
#include <QDir>
#include <QFileDialog>
#include <QKeyEvent>
#include <QTextStream>
#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;
}

6
mathmech/mathmech/src/helpwindow.h
View File

@ -3,6 +3,8 @@
#include <QMainWindow>
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);

274
mathmech/mathmech/src/helpwindow.ui
View File

@ -20,27 +20,6 @@
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="page_general">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>580</width>
<height>233</height>
</rect>
</property>
<property name="toolTip">
<string>General help</string>
</property>
<attribute name="label">
<string>General</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_general"/>
</item>
</layout>
</widget>
<widget class="QWidget" name="page_trj">
<property name="geometry">
<rect>
@ -58,7 +37,39 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_3">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_trj"/>
<widget class="QTextBrowser" name="textBrowser_trj">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;trj&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that generates trajectory files in special format from input trajectory.&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE – input trajectory file&lt;br /&gt;-t TYPE – trajectory type. Supported formats: gmx, puma&lt;br /&gt;-s NUMBER – number of trajectory steps&lt;br /&gt;-a FILE – file with atom types&lt;br /&gt;-o MASK – mask of output trajectory files&lt;br /&gt;-tt NUMBER – maximum number of different atom types. Default is 1024&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory files (*.[0-9])&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Number of atoms is shown in the title.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Trajectory snapshot (enumeration of all atoms in system). Format&lt;br /&gt;00001 СА 1234.000000 1234.000000 1234.000000 01 0001&lt;br /&gt;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).&lt;/li&gt;&lt;/ul&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Atom types file (*.types)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The number of different molecules (NUMTYPES=1) is shown in the title.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).&lt;br /&gt;The atoms enumeration block. Format&lt;br /&gt;CA=1&lt;br /&gt;Character atom type (2 characters), equal sign, numerical atom type.&lt;/li&gt;&lt;/ul&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, print results to the specified output file.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select Menu -&amp;gt; File creator -&amp;gt; Atom types file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set atom types. To add a new molecule you need select &amp;quot;Add new molecule&amp;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 &amp;quot;Add&amp;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 &amp;quot;Remove&amp;quot;.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Create the atom types file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate trajectory&amp;quot;. Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select the trajectory type from the drop down list, set the number of trajectory steps.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the atom types file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of output files.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the maximum number of different atom types and the log file if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
@ -67,8 +78,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>580</width>
<height>233</height>
<width>98</width>
<height>88</height>
</rect>
</property>
<property name="toolTip">
@ -79,7 +90,39 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_4">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_statgen"/>
<widget class="QTextBrowser" name="textBrowser_statgen">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;statgen&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that analyzes molecular dynamics trajectories using topological analysis.&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;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.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;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).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;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).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;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).&lt;/li&gt;&lt;/ul&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, settings values of variables.&lt;br /&gt;Search for interactions that satisfy the specified criteria.&lt;br /&gt;The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.&lt;br /&gt;Adding molecules to agglomerates according to the obtained connectivity matrix.&lt;br /&gt;Print agglomerates to the file, adding the summary statistics.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the summary statistic to the file.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Agglomeration&amp;quot;. Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of trajectory files.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the first and the last trajectory steps.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set needed atoms.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set interactions. Select type of interaction from the drop down list, change its criterion and press &amp;quot;Save&amp;quot;. Press &amp;quot;Add&amp;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 &amp;quot;Remove&amp;quot;.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the maximum depth for search cycles, the log file and the graph generate if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;For the variation of geometric criteria you need specify the criteria step changes and the number of steps.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
@ -88,8 +131,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>580</width>
<height>233</height>
<width>98</width>
<height>88</height>
</rect>
</property>
<property name="toolTip">
@ -100,7 +143,33 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_5">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_envir"/>
<widget class="QTextBrowser" name="textBrowser_envir">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;envir&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that searchs environment for chosen molecule by geometric criterion.&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE – input trajectory file&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-o FILE – output PDB file&lt;br /&gt;-n NUMBER – number of molecule for search. Default is 1&lt;br /&gt;-r NUMBER – radius of environment. Default is 6.0&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Search for the environment.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the environment to the file.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Environment&amp;quot;. Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the number of molecule for search and the radius of environment.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
@ -109,8 +178,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>580</width>
<height>233</height>
<width>98</width>
<height>88</height>
</rect>
</property>
<property name="toolTip">
@ -121,7 +190,92 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_6">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_radf"/>
<widget class="QTextBrowser" name="textBrowser_radf">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;radf&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;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 ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is calculated. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step, A. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;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.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;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).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;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).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Step by step reading of source files, settings values of variables.&lt;br /&gt;Calculating of the number of pairs of molecules in various relative configurations.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;br /&gt;Radial distribution function calculated by:&lt;br /&gt;RDF(r) = (1 / norm) * sum(d(r_n-r), n),&lt;br /&gt;norm(r) = (4*PI*r^2*dr) * ro * N * N_step,&lt;br /&gt;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.&lt;br /&gt;Radial-angles distribution function calculated by:&lt;br /&gt;RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),&lt;br /&gt;norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,&lt;br /&gt;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.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;RADF&amp;quot;. Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the mask of trajectory files.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the first and the last trajectory steps.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set needed atoms.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set radial criteria. Set angular criteria if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the matrix output, the log file and the graph generate if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="page_agl">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>98</width>
<height>88</height>
</rect>
</property>
<property name="toolTip">
<string>Help about agl</string>
</property>
<attribute name="label">
<string>agl</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_agl">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;agl&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that creates PDB file with chosen agglomerate.&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-a FILE – input file with agglomerate&lt;br /&gt;-i FILE – input trajectory file&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-o FILE – output PDB file&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Agglomerate file (*.agl)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;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).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;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).&lt;/li&gt;&lt;/ul&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Search for the best configuration.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select Menu -&amp;gt; File creator -&amp;gt; Agglomerate file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the file generated by statgen. Push &amp;quot;Select&amp;quot;.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select the trajectory file from the drop down list. Select the agglomerate.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output file. Create file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate PDB&amp;quot;. Select &amp;quot;From agglomerate&amp;quot; from the drop down list.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the agglomerate file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the cell size, A.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
@ -130,8 +284,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>580</width>
<height>233</height>
<width>98</width>
<height>88</height>
</rect>
</property>
<property name="toolTip">
@ -142,7 +296,31 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_7">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser_trj2pdb"/>
<widget class="QTextBrowser" name="textBrowser_trj2pdb">
<property name="html">
<string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;trj2pdb&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;Program that creates PDB file from trajetory snapshot.&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i FILE – input trajectory file&lt;br /&gt;-o FILE – output PDB file&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Trajectory file (*.pdb)&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect9.html&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://www.wwpdb.org/documentation/format33/sect9.html&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Operation of the application&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading titles of source files, setting values of initial variables.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Reading of source file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Print the result to the file.&lt;/li&gt;&lt;/ol&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Working with GUI&lt;/span&gt;&lt;/p&gt;
&lt;ol style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Go to the tab &amp;quot;Generate PDB&amp;quot;. Select &amp;quot;From trajectory snapshot&amp;quot; from the drop down list.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the work directory.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the input trajectory file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the output PDB file.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
&lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
</layout>
</widget>
@ -164,7 +342,26 @@
</spacer>
</item>
<item>
<widget class="QPushButton" name="pushButton">
<widget class="QPushButton" name="pushButton_save">
<property name="minimumSize">
<size>
<width>80</width>
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Save help to html</string>
</property>
<property name="text">
<string>Save html</string>
</property>
<property name="autoDefault">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_close">
<property name="minimumSize">
<size>
<width>80</width>
@ -188,18 +385,19 @@
</widget>
</widget>
<tabstops>
<tabstop>textBrowser_general</tabstop>
<tabstop>pushButton</tabstop>
<tabstop>textBrowser_trj</tabstop>
<tabstop>textBrowser_statgen</tabstop>
<tabstop>textBrowser_envir</tabstop>
<tabstop>textBrowser_radf</tabstop>
<tabstop>textBrowser_agl</tabstop>
<tabstop>textBrowser_trj2pdb</tabstop>
<tabstop>pushButton_save</tabstop>
<tabstop>pushButton_close</tabstop>
</tabstops>
<resources/>
<connections>
<connection>
<sender>pushButton</sender>
<sender>pushButton_close</sender>
<signal>clicked()</signal>
<receiver>HelpWindow</receiver>
<slot>close()</slot>

2
mathmech/mathmech/src/mathmech.pro.user
View File

@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE QtCreatorProject>
<!-- Written by QtCreator 2.8.1, 2013-09-02T16:20:54. -->
<!-- Written by QtCreator 2.8.1, 2013-09-03T05:28:10. -->
<qtcreator>
<data>
<variable>ProjectExplorer.Project.ActiveTarget</variable>

6
mathmech/mm_agl/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mm_agl/mm_agl.pdf
View File

Binary file not shown.

2
mathmech/mm_agl/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")

6
mathmech/mm_envir/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mm_envir/mm_envir.pdf
View File

Binary file not shown.

2
mathmech/mm_envir/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")

6
mathmech/mm_radf/CMakeLists.txt
View File

@ -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)

2
mathmech/mm_radf/README
View File

@ -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

BIN
mathmech/mm_radf/mm_radf.pdf
View File

Binary file not shown.

2
mathmech/mm_radf/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")

6
mathmech/mm_statgen/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mm_statgen/mm_statgen.pdf
View File

Binary file not shown.

2
mathmech/mm_statgen/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")

6
mathmech/mm_trj/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mm_trj/mm_trj.pdf
View File

Binary file not shown.

2
mathmech/mm_trj/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")

6
mathmech/mm_trj2pdb/CMakeLists.txt
View File

@ -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)

BIN
mathmech/mm_trj2pdb/mm_trj2pdb.pdf
View File

Binary file not shown.

2
mathmech/mm_trj2pdb/src/CMakeLists.txt
View File

@ -6,7 +6,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")