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arcanis:mm-1.2.0 arcanis:mm-1.1.1 arcanis:mm-1.0.3 arcanis:mm-1.0.2 arcanis:mm-1.0.1 arcanis:V.1.0.1
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arcanis:master
arcanis:mm-1.2.0 arcanis:mm-1.1.1 arcanis:mm-1.0.3 arcanis:mm-1.0.2 arcanis:mm-1.0.1 arcanis:V.1.0.1

3 Commits
mm-1.0.1 ... mm-1.0.2

Author SHA1 Message Date
arcan1s
d642e083b9 Release 1.0.2 2013-08-30 03:40:53 +04:00
arcan1s
7964d9a360 Editet cmakelists 2013-08-29 17:50:38 +04:00
arcan1s
d049cd091c Release mathmech 1.0.1 2013-08-29 04:46:58 +04:00
85 changed files with 2012 additions and 706 deletions
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17
mathmech/CMakeLists.txt
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@ -1,3 +1,10 @@
set ("PROJECT_VERSION_MAJOR" 1)
set ("PROJECT_VERSION_MINOR" 0)
set ("PROJECT_VERSION_PATCH" 2)
set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
message (STATUS "Version ${PROJECT_VERSION}")
set (COMPS mathmech
mm_agl
mm_envir
@ -6,6 +13,16 @@ set (COMPS mathmech
mm_trj
mm_trj2pdb)
# install options
set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
if (CMAKE_COMPILER_IS_GNUCXX)
set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")
set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
else ()
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()
foreach (COMP ${COMPS})
add_subdirectory (${COMP})
endforeach()

36
mathmech/PKGBUILD Normal file
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@ -0,0 +1,36 @@
# Author: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
pkgname=mathmech
pkgver=1.0.2
pkgrel=1
pkgdesc="Software package for analysis of molecular dynamics trajectories"
arch=(any)
url="https://github.com/arcan1s/moldyn/mathmech"
license=('GPL')
depends=('qt4' 'qwt')
makedepends=('unzip' 'cmake' 'automoc4')
source=(https://github.com/arcan1s/moldyn/releases/download/mm-1.0.2/${pkgname}-${pkgver}-src.zip)
md5sums=('7c80789a74255108581583830258fe1c')
_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
-DQWT_INCLUDE_PATH=/usr/include/qwt
-DMM_PREFIX=mm_
-DCMAKE_BUILD_TYPE=Release"
build ()
{
unzip -o -q ${srcdir}/${pkgname}-${pkgver}.zip -d ${srcdir}/${pkgname}
if [ -d ${srcdir}/${pkgname}/build ]; then
rm -rf ${srcdir}/${pkgname}/build
fi
mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build
cmake ${_cmakekeys} ../
make
}
package()
{
cd ${srcdir}/${pkgname}/build
make DESTDIR=${pkgdir} install
}

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2
mathmech/mathmech/README
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@ -1 +1,3 @@
Mathematical Molecular Mechanics is GUI for "mm" program pack
Version: 1.0.2
License: GPL

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0
mathmech/mathmech/logo.png → mathmech/mathmech/mathmech-logo.png
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9
mathmech/mathmech/mathmech.desktop Normal file
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@ -0,0 +1,9 @@
[Desktop Entry]
Name=Mathematical Molecular Mechanics
Comment=GUI for mathmech program pack
Exec=mathmech
Icon=mathmech-logo
Terminal=false
Encoding=UTF-8
Type=Application
Categories=Qt;Science;Chemistry;Physics;Education;

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19
mathmech/mathmech/src/CMakeLists.txt
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@ -1,10 +1,3 @@
set (PROJECT_VERSION_MAJOR 1)
set (PROJECT_VERSION_MINOR 0)
set (PROJECT_VERSION_PATCH 0)
set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${PROJECT_VERSION}")
# set files
file (GLOB SOURCES *.cpp)
file (GLOB HEADERS *.h)
@ -28,9 +21,11 @@ message (STATUS "FORMS: ${FORMS}")
# compile
project (${PROJECT})
# include_path
link_directories (${QWT_LIBRARY_PATH})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR})
${CMAKE_CURRENT_BINARY_DIR}
${QWT_INCLUDE_PATH})
find_package (Qt4 REQUIRED)
include (${QT_USE_FILE})
@ -46,7 +41,7 @@ foreach (LANGUAGE ${LANGUAGES})
OUTPUT ${QM}
COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS}
MAIN_DEPENDENCY ${TS})
endforeach()
endforeach ()
add_custom_target (
translations
COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS})
@ -65,4 +60,8 @@ add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURC
target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
install (TARGETS ${PROJECT} DESTINATION bin)
install (FILES ../mathmech.desktop
DESTINATION share/applications/)
install (FILES ../mathmech-logo.png
DESTINATION share/pixmaps/)

3
mathmech/mathmech/src/aboutwindow.ui
View File

@ -57,6 +57,9 @@ p, li { white-space: pre-wrap; }
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

33
mathmech/mathmech/src/agglwindow.ui
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@ -44,6 +44,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Path to input file</string>
</property>
</widget>
</item>
<item>
@ -87,6 +90,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Read selected file</string>
</property>
<property name="text">
<string>Select</string>
</property>
@ -98,17 +104,28 @@
</layout>
</item>
<item>
<widget class="QComboBox" name="agl_comboBox"/>
<widget class="QComboBox" name="agl_comboBox">
<property name="toolTip">
<string>File name</string>
</property>
</widget>
</item>
<item>
<widget class="QListWidget" name="agl_listWidget">
<property name="toolTip">
<string>List of agglomerates</string>
</property>
<property name="editTriggers">
<set>QAbstractItemView::NoEditTriggers</set>
</property>
</widget>
</item>
<item>
<widget class="QTextBrowser" name="agl_textBrowser"/>
<widget class="QTextBrowser" name="agl_textBrowser">
<property name="toolTip">
<string>Agglomerate</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="agl_layout_output">
@ -139,6 +156,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -169,6 +189,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -204,6 +227,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Create file</string>
</property>
<property name="text">
<string>Create</string>
</property>
@ -220,6 +246,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

24
mathmech/mathmech/src/aglallwindow.ui
View File

@ -38,6 +38,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -81,6 +84,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to input file</string>
</property>
</widget>
</item>
<item>
@ -124,6 +130,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Mask of output files</string>
</property>
</widget>
</item>
<item>
@ -167,6 +176,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of file. '0' is all files</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -209,6 +221,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of molecules in agglomerates. '0' is all agglomerates</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -252,6 +267,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -287,6 +305,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start analysis</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -303,6 +324,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

33
mathmech/mathmech/src/atomtypeswindow.ui
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@ -44,6 +44,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -93,6 +96,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of molecule</string>
</property>
<item>
<property name="text">
<string>1</string>
@ -126,6 +132,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of selected molecules</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -162,6 +171,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Character atop type</string>
</property>
</widget>
</item>
<item>
@ -185,6 +197,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Numerical atom type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -201,6 +216,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Add atom</string>
</property>
<property name="text">
<string>Add</string>
</property>
@ -213,6 +231,9 @@
</item>
<item>
<widget class="QListWidget" name="atomTypes_listWidget">
<property name="toolTip">
<string>Added atoms</string>
</property>
<property name="editTriggers">
<set>QAbstractItemView::NoEditTriggers</set>
</property>
@ -241,6 +262,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Remove selected atom</string>
</property>
<property name="text">
<string>Remove</string>
</property>
@ -261,6 +285,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -296,6 +323,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Create file</string>
</property>
<property name="text">
<string>Create</string>
</property>
@ -312,6 +342,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

16
mathmech/mathmech/src/mainwindow.cpp
View File

@ -123,9 +123,19 @@ void MainWindow::on_statgen_checkBox_atoms3_stateChanged(int arg1)
void MainWindow::on_statgen_checkBox_anal_stateChanged(int arg1)
{
if (arg1 == 0)
{
ui->statgen_doubleSpinBox_anal->setDisabled(true);
ui->statgen_spinBox_anal->setDisabled(true);
ui->statgen_checkBox_graph->setCheckState(Qt::Checked);
ui->statgen_checkBox_graph->setEnabled(true);
}
else if (arg1 == 2)
{
ui->statgen_doubleSpinBox_anal->setEnabled(true);
ui->statgen_spinBox_anal->setEnabled(true);
ui->statgen_checkBox_graph->setCheckState(Qt::Unchecked);
ui->statgen_checkBox_graph->setDisabled(true);
}
}
void MainWindow::on_envir_checkBox_log_stateChanged(int arg1)
@ -664,8 +674,12 @@ void MainWindow::start_events_statgen()
else
depth = QString("#");
float int_step;
int imax;
if (ui->statgen_checkBox_anal->checkState() == 2)
{
int_step = ui->statgen_doubleSpinBox_anal->value();
imax = ui->statgen_spinBox_anal->value();
}
QString log;
if (ui->statgen_checkBox_log->checkState() == 2)
log = ui->statgen_lineEdit_log->text();
@ -699,7 +713,7 @@ void MainWindow::start_events_statgen()
output,
depth,
log,
int_step);
int_step, imax);
ui->statusBar->showMessage(QApplication::translate("MainWindow", "Done"));
if ((ui->statgen_checkBox_graph->checkState() == 2) && (check == true))

285
mathmech/mathmech/src/mainwindow.ui
View File

@ -48,6 +48,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -91,6 +94,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to input file</string>
</property>
</widget>
</item>
<item>
@ -134,6 +140,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Input trajectory type</string>
</property>
<item>
<property name="text">
<string>GROMACS text</string>
@ -180,6 +189,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of steps in trajectory</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -229,6 +241,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to file with atom types</string>
</property>
</widget>
</item>
<item>
@ -272,6 +287,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Mask of output files</string>
</property>
</widget>
</item>
<item>
@ -315,6 +333,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Maximum number of atom types</string>
</property>
<property name="layoutDirection">
<enum>Qt::LeftToRight</enum>
</property>
@ -353,6 +374,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to log file</string>
</property>
</widget>
</item>
<item>
@ -396,6 +420,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -431,6 +458,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start application</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -471,6 +501,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -514,6 +547,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Mask of input files</string>
</property>
</widget>
</item>
<item>
@ -570,6 +606,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>First trajectory step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -615,6 +654,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Last trajectory step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -683,6 +725,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, X</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -724,6 +769,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Y</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -765,6 +813,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Z</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -816,6 +867,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom0 type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -851,6 +905,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom1 type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -889,6 +946,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom2 type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -927,6 +987,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom3 type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -963,6 +1026,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Type of interaction</string>
</property>
<item>
<property name="text">
<string>0-0</string>
@ -984,6 +1050,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Criterion</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1006,6 +1075,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Save this criterion</string>
</property>
<property name="text">
<string>Save</string>
</property>
@ -1022,6 +1094,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Add this interaction</string>
</property>
<property name="text">
<string>Add</string>
</property>
@ -1040,6 +1115,9 @@
<height>85</height>
</size>
</property>
<property name="toolTip">
<string>Added interactions</string>
</property>
<property name="editTriggers">
<set>QAbstractItemView::NoEditTriggers</set>
</property>
@ -1068,6 +1146,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Remove selected interaction</string>
</property>
<property name="text">
<string>Remove</string>
</property>
@ -1101,6 +1182,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -1147,6 +1231,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Search depth of related graphs</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1185,6 +1272,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to log file</string>
</property>
</widget>
</item>
<item>
@ -1231,6 +1321,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Step of analysis</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1245,6 +1338,28 @@
</property>
</widget>
</item>
<item>
<widget class="QSpinBox" name="statgen_spinBox_anal">
<property name="enabled">
<bool>false</bool>
</property>
<property name="minimumSize">
<size>
<width>80</width>
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of steps of analysis</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="value">
<number>10</number>
</property>
</widget>
</item>
<item>
<spacer name="horizontalSpacer_16">
<property name="orientation">
@ -1266,6 +1381,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Show graph</string>
</property>
<property name="text">
<string>Graph</string>
</property>
@ -1299,6 +1417,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -1334,6 +1455,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start application</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -1374,6 +1498,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -1417,6 +1544,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to input file</string>
</property>
</widget>
</item>
<item>
@ -1479,6 +1609,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, X</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1520,6 +1653,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Y</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1561,6 +1697,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Z</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1600,6 +1739,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -1643,6 +1785,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Number of selected molecule</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1688,6 +1833,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Radius of environment</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1737,6 +1885,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to log file</string>
</property>
</widget>
</item>
<item>
@ -1780,6 +1931,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -1815,6 +1969,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start application</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -1855,6 +2012,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -1898,6 +2058,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Mask of input files</string>
</property>
</widget>
</item>
<item>
@ -1954,6 +2117,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>First trajectory step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -1999,6 +2165,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Last trajectory step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2067,6 +2236,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, X</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2108,6 +2280,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Y</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2149,6 +2324,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Z</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2188,6 +2366,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -2218,6 +2399,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Type of function</string>
</property>
<item>
<property name="text">
<string>One atom function</string>
@ -2263,6 +2447,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom1 type</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2282,6 +2469,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom2 type</string>
</property>
<property name="text">
<string>atom 2</string>
</property>
@ -2323,6 +2513,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom3 type</string>
</property>
<property name="text">
<string>atom 3</string>
</property>
@ -2384,6 +2577,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom1 type</string>
</property>
<property name="text">
<string>atom 1</string>
</property>
@ -2422,6 +2618,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom2 type</string>
</property>
<property name="text">
<string>atom 2</string>
</property>
@ -2463,6 +2662,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>atom3 type</string>
</property>
<property name="text">
<string>atom 3</string>
</property>
@ -2534,6 +2736,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Minimal radius</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2578,6 +2783,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Maximal radius</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2622,6 +2830,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Radius step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2689,6 +2900,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Minimal angle</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2739,6 +2953,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Maximal angle</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2789,6 +3006,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Angle step</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -2821,6 +3041,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Matrix output</string>
</property>
<property name="text">
<string>Matrix</string>
</property>
@ -2850,6 +3073,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to log file</string>
</property>
</widget>
</item>
<item>
@ -2893,6 +3119,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -2922,6 +3151,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Show graph</string>
</property>
<property name="text">
<string>Graph</string>
</property>
@ -2944,6 +3176,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start application</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -2963,6 +3198,9 @@
<layout class="QVBoxLayout" name="verticalLayout_5">
<item>
<widget class="QComboBox" name="pdb_comboBox_mode">
<property name="toolTip">
<string>Input file type</string>
</property>
<item>
<property name="text">
<string>From agglomerate</string>
@ -2998,6 +3236,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to work directory</string>
</property>
</widget>
</item>
<item>
@ -3041,6 +3282,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to input file</string>
</property>
</widget>
</item>
<item>
@ -3084,6 +3328,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to file with agglomerate</string>
</property>
</widget>
</item>
<item>
@ -3146,6 +3393,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, X</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -3187,6 +3437,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Y</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -3228,6 +3481,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Cell size, Z</string>
</property>
<property name="alignment">
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
</property>
@ -3267,6 +3523,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to output file</string>
</property>
</widget>
</item>
<item>
@ -3313,6 +3572,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Path to log file</string>
</property>
</widget>
</item>
<item>
@ -3356,6 +3618,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Clear window</string>
</property>
<property name="text">
<string>Clear</string>
</property>
@ -3391,6 +3656,9 @@
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Start application</string>
</property>
<property name="text">
<string>Start</string>
</property>
@ -3467,14 +3735,6 @@
<string>Ctrl+Q</string>
</property>
</action>
<action name="actionHelp">
<property name="text">
<string>&amp;Help</string>
</property>
<property name="shortcut">
<string>F1</string>
</property>
</action>
<action name="actionAbout">
<property name="text">
<string>About</string>
@ -3494,17 +3754,15 @@
<property name="text">
<string>&amp;Settings</string>
</property>
<property name="shortcut">
<string>Ctrl+P</string>
</property>
</action>
<action name="actionAgl_all">
<property name="text">
<string>agl_all</string>
</property>
</action>
<action name="actionStatgen_all">
<property name="text">
<string>statgen_all</string>
</property>
</action>
</widget>
<layoutdefault spacing="6" margin="11"/>
<tabstops>
@ -3556,6 +3814,7 @@
<tabstop>statgen_pushButton_log</tabstop>
<tabstop>statgen_checkBox_anal</tabstop>
<tabstop>statgen_doubleSpinBox_anal</tabstop>
<tabstop>statgen_spinBox_anal</tabstop>
<tabstop>statgen_checkBox_graph</tabstop>
<tabstop>statgen_pushButton_clear</tabstop>
<tabstop>statgen_pushButton_start</tabstop>

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 2.8.0, 2013-08-28T17:33:30. -->
<!-- Written by QtCreator 2.8.1, 2013-08-30T03:38:54. -->
<qtcreator>
<data>
<variable>ProjectExplorer.Project.ActiveTarget</variable>

14
mathmech/mathmech/src/settingswindow.cpp
View File

@ -30,7 +30,7 @@ SettingsWindow::SettingsWindow(MainWindow *parent) :
else
{
setDefaults();
applySettings();
printSettings();
}
showSettings();
ui->settings_layout_lang_2->setHidden(true);
@ -117,12 +117,12 @@ void SettingsWindow::setDefaults()
suffix = QString(".exe");
#endif
_parent->language = QString("eng");
_parent->mm_trj_path = QDir::currentPath() + QDir::separator() + "mm_trj" + suffix;
_parent->mm_statgen_path = QDir::currentPath() + QDir::separator() + "mm_statgen" + suffix;
_parent->mm_envir_path = QDir::currentPath() + QDir::separator() + "mm_envir" + suffix;
_parent->mm_radf_path = QDir::currentPath() + QDir::separator() + "mm_radf" + suffix;
_parent->mm_trj2pdb_path = QDir::currentPath() + QDir::separator() + "mm_trj2pdb" + suffix;
_parent->mm_agl_path = QDir::currentPath() + QDir::separator() + "mm_agl" + suffix;
_parent->mm_trj_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj" + suffix;
_parent->mm_statgen_path = qApp->applicationDirPath() + QDir::separator() + "mm_statgen" + suffix;
_parent->mm_envir_path = qApp->applicationDirPath() + QDir::separator() + "mm_envir" + suffix;
_parent->mm_radf_path = qApp->applicationDirPath() + QDir::separator() + "mm_radf" + suffix;
_parent->mm_trj2pdb_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj2pdb" + suffix;
_parent->mm_agl_path = qApp->applicationDirPath() + QDir::separator() + "mm_agl" + suffix;
}
void SettingsWindow::readSettings()

45
mathmech/mathmech/src/settingswindow.ui
View File

@ -31,7 +31,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_trj"/>
<widget class="QLineEdit" name="settings_lineEdit_trj">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_trj">
@ -67,7 +71,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_statgen"/>
<widget class="QLineEdit" name="settings_lineEdit_statgen">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_statgen">
@ -103,7 +111,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_envir"/>
<widget class="QLineEdit" name="settings_lineEdit_envir">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_envir">
@ -139,7 +151,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_radf"/>
<widget class="QLineEdit" name="settings_lineEdit_radf">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_radf">
@ -175,7 +191,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_trj2pdb"/>
<widget class="QLineEdit" name="settings_lineEdit_trj2pdb">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_trj2pdb">
@ -211,7 +231,11 @@
</widget>
</item>
<item>
<widget class="QLineEdit" name="settings_lineEdit_agl"/>
<widget class="QLineEdit" name="settings_lineEdit_agl">
<property name="toolTip">
<string>Path to component</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="settings_pushButton_agl">
@ -254,6 +278,9 @@
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Application language</string>
</property>
<item>
<property name="text">
<string>English</string>
@ -336,6 +363,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Save settings</string>
</property>
<property name="text">
<string>Save</string>
</property>
@ -352,6 +382,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

66
mathmech/mathmech/src/start_events.cpp
View File

@ -1,4 +1,5 @@
#include <QDir>
#include <math.h>
#include "mainwindow.h"
#include "ui_mainwindow.h"
@ -189,7 +190,7 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
QString output,
QString depth,
QString log,
float int_step)
float int_step, int imax)
{
// error check
errorwin = new ErrorWindow(parent);
@ -238,12 +239,11 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
delete errorwin;
// parsing criteria
int imax = 10;
QStringList inter_list = inter.split(QString(" -r "), QString::SkipEmptyParts);
float *inter_list_one;
inter_list_one = new float[16*inter_list.count()];
for (int i=0; i<16*inter_list.count(); i++)
inter_list_one[i] = -1.0;
inter_list_one[i] = 0.0;
float item;
int index;
for (int i=0; i<inter_list.count(); i++)
@ -259,15 +259,24 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
split(QString("-"), QString::SkipEmptyParts)[1].toInt() * 4;
inter_list_one[16*i+index] = item;
}
QList<int> inter_list_index;
for (int i=0; i<16*inter_list.count(); i++)
if (inter_list_one[i] > 0.0)
while (imax*int_step > inter_list_one[i])
imax--;
if (inter_list_one[i] != 0.0)
inter_list_index.append(i);
int files = pow((float)2*imax+1, inter_list_index.count());
// exec
for (int i=-imax; i<=imax; i++)
char file[32];
int first, second, step;
float *cur_inter;
cur_inter = new float[16*inter_list.count()];
QString one_inter;
for (int i=0; i<16*inter_list.count(); i++)
cur_inter[i] = 0.0;
for (int i=0; i<files; i++)
{
QString command;
inter = QString("");
command.append(mm_statgen_path);
if (mask.contains(QDir::separator()))
command.append(" -i " + QFileInfo(mask).absoluteFilePath());
@ -282,25 +291,50 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
command.append("," + atom2);
if (atom3 != QString("#"))
command.append("," + atom3);
command.append(inter);
if (output.contains(QDir::separator()))
command.append(" -o " + QFileInfo(output).absoluteFilePath());
else
command.append(" -o " + QFileInfo(QDir(workDir), output).absoluteFilePath());
if (depth != QString("#"))
command.append(" -g " + depth);
command.append(" -q");
step = i;
for (int j=0; j<inter_list_index.count(); j++)
{
index = step % (2 * imax + 1);
cur_inter[inter_list_index[j]] = inter_list_one[inter_list_index[j]] + int_step * (index - imax);
if (cur_inter[inter_list_index[j]] < 0.0)
cur_inter[inter_list_index[j]] = 0.1;
step = step / (2 * imax + 1);
}
for (int j=0; j<inter_list.count(); j++)
{
one_inter = " -r ";
for (int k=0; k<16; k++)
if (cur_inter[16*j+k] != 0.0)
{
first = k % 4;
second = k / 4;
one_inter.append(QString::number(first) + "-" + QString::number(second) +
":" + QString::number(cur_inter[16*j+k], 'f', 3) + ",");
}
one_inter.remove(one_inter.count()-1, 1);
inter.append(one_inter);
}
command.append(inter);
sprintf(file, "_%06i", i);
if (output.contains(QDir::separator()))
command.append(" -o " + QFileInfo(output).absoluteFilePath() + QString(file) + ".dat");
else
command.append(" -o " + QFileInfo(QDir(workDir), output).absoluteFilePath() + QString(file) + ".dat");
if (log != QString("#"))
{
if (log.contains(QDir::separator()))
command.append(" -l " + QFileInfo(log).absoluteFilePath());
command.append(" -l " + QFileInfo(log).absoluteFilePath() + QString(file) + ".log");
else
command.append(" -l " + QFileInfo(QDir(workDir), log).absoluteFilePath());
command.append(" -l " + QFileInfo(QDir(workDir), log).absoluteFilePath() + QString(file) + ".log");
}
command.append(" -q");
system(command.toStdString().c_str());
}
delete inter_list_one;
delete cur_inter;
return true;
}

2
mathmech/mathmech/src/start_events.h
View File

@ -42,7 +42,7 @@ public:
QString output,
QString depth,
QString log,
float int_step);
float int_step, int imax);
bool start_envir(QString mm_envir_path,
QString workDir,
QString input,

6
mathmech/mathmech/src/statgengraphwindow.cpp
View File

@ -3,9 +3,9 @@
#include <QKeyEvent>
#include <QTextStream>
#include <qwt/qwt_plot.h>
#include <qwt/qwt_plot_curve.h>
#include <qwt/qwt_series_data.h>
#include <qwt_plot.h>
#include <qwt_plot_curve.h>
#include <qwt_series_data.h>
#include "statgengraphwindow.h"
#include "ui_statgengraphwindow.h"

2
mathmech/mathmech/src/statgengraphwindow.h
View File

@ -2,7 +2,7 @@
#define STATGENGRAPHWINDOW_H
#include <QMainWindow>
#include <qwt/qwt_plot.h>
#include <qwt_plot.h>
namespace Ui {
class StatgenGraphWindow;

6
mathmech/mathmech/src/statgengraphwindow.ui
View File

@ -38,6 +38,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Save graph</string>
</property>
<property name="text">
<string>Save</string>
</property>
@ -54,6 +57,9 @@
<height>23</height>
</size>
</property>
<property name="toolTip">
<string>Close window</string>
</property>
<property name="text">
<string>Close</string>
</property>

4
mathmech/mm_agl/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_agl)
set (PROJECT ${MM_PREFIX}agl)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

6
mathmech/mm_agl/README
View File

@ -1,12 +1,12 @@
mm_agl - program that creates PDB file with chosen aglomerate
Version: 1.0.1
mm_agl - program that creates PDB file with chosen agglomerate
Version: 1.0.2
License: GPL
Usage:
mm_agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
Parametrs:
-a - input file with aglomerates (in format statgen)
-a - input file with agglomerates (in format statgen)
-i - input file with coordinates
-c - cell size (float), A
-o - output file with coordinates

16
mathmech/mm_agl/mm_agl.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

4
mathmech/mm_agl/mm_agl.doxygen
View File

@ -32,13 +32,13 @@ PROJECT_NAME = mm_agl
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer
# a quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Program that creates PDB file with chosen aglomerate"
PROJECT_BRIEF = "Program that creates PDB file with chosen agglomerate"
# With the PROJECT_LOGO tag one can specify an logo or icon that is
# included in the documentation. The maximum height of the logo should not

BIN
mathmech/mm_agl/mm_agl.pdf
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Binary file not shown.

7
mathmech/mm_agl/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

4
mathmech/mm_agl/src/add_main.c
View File

@ -18,7 +18,7 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
* error_checking (aglinp, cell, input, output);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input input file name
* @param output output file name
@ -83,7 +83,7 @@ int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output
* set_defaults (aglinp, cell, input, &log, output, &quiet);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input mask of trajectory files
* @param log status of log-mode

18
mathmech/mm_agl/src/main.c
View File

@ -9,7 +9,7 @@
*
* <b>About this program</b>:
* <ul>
* <li>Program that creates PDB file with chosen aglomerate
* <li>Program that creates PDB file with chosen agglomerate
* </ul>
*
* <b>Developer</b>:
@ -27,7 +27,7 @@
* mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
*
* Parametrs:
* -a - input file with aglomerates (in format statgen)
* -a - input file with agglomerates (in format statgen)
* -i - input file with coordinates
* -c - cell size (float), A
* -o - output file name
@ -61,7 +61,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -100,7 +100,7 @@ int main(int argc, char *argv[])
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
*true_label_mol;
/* aglinp aglomerate file name
/* aglinp agglomerate file name
* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
@ -127,14 +127,14 @@ int main(int argc, char *argv[])
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_agl\n");
sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);
sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with aglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
@ -238,13 +238,13 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// reading aglomerate
// reading agglomerate
print_message (quiet, stdout, log, f_log, 7, aglinp);
error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
if (error == 0)
{
sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol);
sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
// reading coordinates
print_message (quiet, stdout, log, f_log, 7, input);

2
mathmech/mm_agl/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

10
mathmech/mm_agl/src/read_agl.c
View File

@ -1,7 +1,7 @@
/**
* @file
*/
/* Library for reading aglomerate from statgen-file
/* Library for reading agglomerate from statgen-file
*
* Usage:
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
@ -15,14 +15,14 @@
*/
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
/**
* @brief function that reads aglomerate from statgen-formated file
* @brief function that reads agglomerate from statgen-formated file
* @code
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param num_needed_mol number of needed molecules
* @param agl_class aglomerate class
* @param agl_class agglomerate class
* @param needed_mol massive of numbed of needed molecules
*
* @return 0 - exit without errors
@ -33,7 +33,7 @@ int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *
FILE *f_agl;
/* connect - connectivity matrix for molecule
* f_agl - aglomerate file
* f_agl - agglomerate file
*/
f_agl = fopen (aglinp, "r");

4
mathmech/mm_envir/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_envir)
set (PROJECT ${MM_PREFIX}envir)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

2
mathmech/mm_envir/README
View File

@ -1,5 +1,5 @@
mm_envir - program that searchs environment for chosen molecule by geometric criterion
Version: 1.0.1
Version: 1.0.2
License: GPL
Usage:

16
mathmech/mm_envir/mm_envir.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

2
mathmech/mm_envir/mm_envir.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_envir
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_envir/mm_envir.pdf
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Binary file not shown.

7
mathmech/mm_envir/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

4
mathmech/mm_envir/src/main.c
View File

@ -63,7 +63,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -130,7 +130,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_envir\n");
sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_envir/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

4
mathmech/mm_radf/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_radf)
set (PROJECT ${MM_PREFIX}radf)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

2
mathmech/mm_radf/README
View File

@ -1,6 +1,6 @@
mm_radf - program that calculates radial distribution function (RDF) or radial-angles
distribution function
Version : 1.0.1
Version : 1.0.2
License : GPL
Usage:

16
mathmech/mm_radf/mm_radf.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

2
mathmech/mm_radf/mm_radf.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_radf
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_radf/mm_radf.pdf
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Binary file not shown.

7
mathmech/mm_radf/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

4
mathmech/mm_radf/src/main.c
View File

@ -70,7 +70,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -147,7 +147,7 @@ int main(int argc, char *argv[])
sprintf (tmp_str, " mm_radf\n");
sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
sprintf (tmp_str, "%sdistribution function\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_radf/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

4
mathmech/mm_statgen/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_statgen)
set (PROJECT ${MM_PREFIX}statgen)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

2
mathmech/mm_statgen/README
View File

@ -1,5 +1,5 @@
mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
Version: 1.0.1
Version: 1.0.2
License: GPL
Usage:

16
mathmech/mm_statgen/mm_statgen.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

2
mathmech/mm_statgen/mm_statgen.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_statgen
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_statgen/mm_statgen.pdf
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7
mathmech/mm_statgen/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

10
mathmech/mm_statgen/src/main.c
View File

@ -66,7 +66,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -116,7 +116,7 @@ int main (int argc, char *argv[])
* coords massive of coordinates
* crit massive of criteria
*
* agl massive of aglomerates
* agl massive of agglomerates
* connect connectivity graph for all molecules
* from first trajectory step
* label_atom massive of atom types for interactions
@ -125,14 +125,14 @@ int main (int argc, char *argv[])
* max_depth maximum depth for check cycles in graph analyze
* num_atoms number of atoms
* num_mol number of molecules
* num_mol_agl massive of number of molecules in aglomerates
* num_mol_agl massive of number of molecules in agglomerates
* num_of_inter number of different interactions
* stat massive of statistic
* stat_all massive of summary statistic
* step $(to - from + 1)
* to last trajectory step
* true_label_mol massive of true numbers of molecule for atoms
* type_agl massive of number of aglomerate types
* type_agl massive of number of agglomerate types
* type_atoms massive of atom types
* type_inter number of atoms for interactions
* quiet status of quiet-mode
@ -162,7 +162,7 @@ int main (int argc, char *argv[])
{
sprintf (tmp_str, " mm_statgen\n");
sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_statgen/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

14
mathmech/mm_statgen/src/stat_print.c
View File

@ -15,11 +15,11 @@ int printing_agl (const char *input, const char *output, const int *connect,
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
const int *agl, const int *stat, const int max_depth, int *type_agl)
/**
* @brief function that prints aglomerates to output file
* @brief function that prints agglomerates to output file
* @code
* printing_agl (input_file, output_file, number_of_molecules, true_label_molecules,
* num_of_molecules_in_aglomerates, aglomerates, statistic, max_depth,
* type_of_aglomerate);
* num_of_molecules_in_agglomerates, agglomerates, statistic, max_depth,
* type_of_agglomerate);
* @endcode
*
* @param input input file name
@ -27,11 +27,11 @@ int printing_agl (const char *input, const char *output, const int *connect,
* @param connect connectivity graph for all molecules
* @param num_mol number of molecules
* @param true_label_mol massive of true numbers of molecule for atoms
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param num_mol_agl massive of number of molecules in agglomerates
* @param agl massive of agglomerates
* @param stat massive of statistic
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
* @param type_agl massive of number of agglomerate types
*
* @return 1 - memory error
* @return 0 - exit without errors
@ -90,7 +90,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
if (error > 0)
return 1;
// print class of aglomerate
// print class of agglomerate
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
for (j=0; j<max_depth; j++)
{

8
mathmech/mm_statgen/src/stat_sort.c
View File

@ -13,14 +13,14 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
/**
* @brief function that processes connectivity matrix
* @code
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_aglomerates,
* aglomerates, statistic, summary_statistic);
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_agglomerates,
* agglomerates, statistic, summary_statistic);
* @endcode
*
* @param num_mol number of molecules
* @param connect connectivity graph for all molecules
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param num_mol_agl massive of number of molecules in agglomerates
* @param agl massive of agglomerates
* @param stat massive of statistic
* @param stat_all massive of summary statistic
*

12
mathmech/mm_statgen/src/summary_stat.c
View File

@ -14,14 +14,14 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
* @brief function that prints summary statistic
* @code
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
* type_of_aglomerate, summary_statistic);
* type_of_agglomerate, summary_statistic);
* @endcode
*
* @param filename output file name
* @param step number of steps
* @param num_mol number of molecules
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
* @param type_agl massive of number of agglomerate types
* @param stat_all massive of summary statistic
*
* @return 0 - exit without errors
@ -31,9 +31,9 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
int i, index;
FILE *f_out;
/* conc concentrate of aglomerates
* p probability of aglomerates
* pn weight probability of aglomerates
/* conc concentrate of agglomerates
* p probability of agglomerates
* pn weight probability of agglomerates
* f_out output file
*/
@ -66,7 +66,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
if (max_depth > 0)
{
// types of aglomerates
// types of agglomerates
// linear and cycle
x = type_agl[0] + type_agl[1];
type[0] = type_agl[0];

4
mathmech/mm_trj/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_trj)
set (PROJECT ${MM_PREFIX}trj)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

2
mathmech/mm_trj/README
View File

@ -1,5 +1,5 @@
mm_trj - program that generates trajectory files
Version : 1.0.1
Version : 1.0.2
License : GPL
Usage:

16
mathmech/mm_trj/mm_trj.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

2
mathmech/mm_trj/mm_trj.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj/mm_trj.pdf
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Binary file not shown.

7
mathmech/mm_trj/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

4
mathmech/mm_trj/src/main.c
View File

@ -63,7 +63,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -127,7 +127,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_trj\n");
sprintf (tmp_str, "%sProgram that generates trajectory files\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_trj/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

4
mathmech/mm_trj2pdb/CMakeLists.txt
View File

@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT mm_trj2pdb)
set (PROJECT ${MM_PREFIX}trj2pdb)
# set additional cmake file
include (${PROJECT}.cmake)
@ -29,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${${PROJECT}_SOURCE_DIR})
add_subdirectory (${PROJECT_SOURCE_DIR})

2
mathmech/mm_trj2pdb/README
View File

@ -1,5 +1,5 @@
mm_trj2pdb - program that creates PDB file from trajetory snapshot
Version: 1.0.1
Version: 1.0.2
License: GPL
Usage:

16
mathmech/mm_trj2pdb/mm_trj2pdb.cmake
View File

@ -1,16 +1,16 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

2
mathmech/mm_trj2pdb/mm_trj2pdb.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj2pdb
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.1
PROJECT_NUMBER = V.1.0.2
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj2pdb/mm_trj2pdb.pdf
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Binary file not shown.

7
mathmech/mm_trj2pdb/src/CMakeLists.txt
View File

@ -1,10 +1,3 @@
set ("${PROJECT}_VERSION_MAJOR" 1)
set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
# set files
aux_source_directory (. SOURCES)

4
mathmech/mm_trj2pdb/src/main.c
View File

@ -59,7 +59,7 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* V.1.0.2 (2013-07-27)
* * initial release
*/
@ -119,7 +119,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_trj2pdb\n");
sprintf (tmp_str, "%sProgram for create PDB file from trajectory snapshot\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_trj2pdb/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);