Release 1.1.1

* optimization
Release 1.1.0
2025-07-16 07:10:00 +00:00 · 2013-09-03 18:09:26 +04:00 · 2013-09-03 06:01:23 +04:00 · 2013-09-02 21:35:07 +04:00 · 2013-09-01 14:16:23 +04:00
78 changed files with 3080 additions and 646 deletions
--- a/mathmech/CMakeLists.txt
+++ b/mathmech/CMakeLists.txt
@ -1,6 +1,12 @@
+cmake_minimum_required (VERSION 2.8)
+
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)
+
 set ("PROJECT_VERSION_MAJOR" 1)
-set ("PROJECT_VERSION_MINOR" 0)
-set ("PROJECT_VERSION_PATCH" 3)
+set ("PROJECT_VERSION_MINOR" 1)
+set ("PROJECT_VERSION_PATCH" 1)
 set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})

 message (STATUS "Version ${PROJECT_VERSION}")
@ -16,7 +22,6 @@ set (COMPS mathmech
 # install options
 set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
 OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 OPTION (ADD_DOCS "Add documentation" OFF)
 if (CMAKE_SYSTEM_NAME MATCHES Linux)
  set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")
@ -24,8 +29,13 @@ 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 ()
--- a/mathmech/PKGBUILD
+++ b/mathmech/PKGBUILD
@ -2,35 +2,36 @@
 # Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>

 pkgname=mathmech
-pkgver=1.0.3
+pkgver=1.1.1
 pkgrel=1
 pkgdesc="Software package for analysis of molecular dynamics trajectories"
 arch=(any)
-url="https://github.com/arcan1s/moldyn/mathmech"
+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=('6a7f3dd17ae4ad0498110aaaadea5a2b')
 _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
            -DQWT_INCLUDE_PATH=/usr/include/qwt
+            -DQWT_LIBRARY_PATH=/usr/lib
            -DMM_PREFIX=mm_
+            -DADD_DOCS:BOOL=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
 }
 
--- a/mathmech/create_archive.sh
+++ b/mathmech/create_archive.sh
@ -0,0 +1,18 @@
+#!/bin/bash
+
+FILES="docs mathmech mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb AUTHORS CMakeLists.txt COPYING docs.cmake INSTALL"
+ARCHIVE="mathmech"
+VERSION=`grep -m1 PROJECT_VERSION_MAJOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
+`grep -m1 PROJECT_VERSION_MINOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
+`grep -m1 PROJECT_VERSION_PATCH CMakeLists.txt | awk '{print $3}' | cut -c 1`
+
+# create archive
+if [ -e ${ARCHIVE}-${VERSION}-src.zip ]; then
+  rm -f ${ARCHIVE}-${VERSION}-src.zip
+fi
+zip -9 -y -r -q ${ARCHIVE}-${VERSION}-src.zip ${FILES}
+
+# update md5sum
+MD5SUMS=`md5sum ${ARCHIVE}-${VERSION}-src.zip | awk '{print $1}'`
+sed -i "/md5sums=('[0-9A-Fa-f]*/s/[^'][^)]*/md5sums=('${MD5SUMS}'/" PKGBUILD
+sed -i "s/pkgver=[0-9.]*/pkgver=${VERSION}/" PKGBUILD
--- a/mathmech/docs.cmake
+++ b/mathmech/docs.cmake
@ -0,0 +1,5 @@
+set (PROJECT mathmech)
+# set directory
+set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
+install (DIRECTORY ${PROJECT_DOCS_DIR}
+        DESTINATION share/doc/${PROJECT})
--- a/mathmech/docs/eng/help_agl.html
+++ b/mathmech/docs/eng/help_agl.html
@ -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>
--- a/mathmech/docs/eng/help_envir.html
+++ b/mathmech/docs/eng/help_envir.html
@ -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>
--- a/mathmech/docs/eng/help_radf.html
+++ b/mathmech/docs/eng/help_radf.html
@ -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>
--- a/mathmech/docs/eng/help_statgen.html
+++ b/mathmech/docs/eng/help_statgen.html
@ -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>
--- a/mathmech/docs/eng/help_trj.html
+++ b/mathmech/docs/eng/help_trj.html
@ -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>
--- a/mathmech/docs/eng/help_trj2pdb.html
+++ b/mathmech/docs/eng/help_trj2pdb.html
@ -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>
--- a/mathmech/docs/rus/help_agl.html
+++ b/mathmech/docs/rus/help_agl.html
@ -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>
--- a/mathmech/docs/rus/help_envir.html
+++ b/mathmech/docs/rus/help_envir.html
@ -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>
--- a/mathmech/docs/rus/help_radf.html
+++ b/mathmech/docs/rus/help_radf.html
@ -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>
--- a/mathmech/docs/rus/help_statgen.html
+++ b/mathmech/docs/rus/help_statgen.html
@ -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>
--- a/mathmech/docs/rus/help_trj.html
+++ b/mathmech/docs/rus/help_trj.html
@ -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>
--- a/mathmech/docs/rus/help_trj2pdb.html
+++ b/mathmech/docs/rus/help_trj2pdb.html
@ -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>
--- a/mathmech/mathmech-1.0.3-src.zip
+++ b/mathmech/mathmech-1.0.3-src.zip
--- a/mathmech/mathmech-1.0.3-win32.zip
+++ b/mathmech/mathmech-1.0.3-win32.zip
--- a/mathmech/mathmech-1.1.1-src.zip
+++ b/mathmech/mathmech-1.1.1-src.zip
--- a/mathmech/mathmech-1.1.1-win32.zip
+++ b/mathmech/mathmech-1.1.1-win32.zip
--- a/mathmech/mathmech/CMakeLists.txt
+++ b/mathmech/mathmech/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT mathmech)
--- a/mathmech/mathmech/README
+++ b/mathmech/mathmech/README
@ -1,3 +1,3 @@
 Mathematical Molecular Mechanics is GUI for "mm" program pack
-Version: 1.0.3
+Version: 1.1.1
 License: GPL
--- a/mathmech/mathmech/mathmech.cmake
+++ b/mathmech/mathmech/mathmech.cmake
@ -1,8 +1,6 @@
 # set directories
 set (PROJECT_BINARY_DIR bin)
 set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
-set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
-set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
 set (PROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
 set (PROJECT_TRANSLATION_DIR ${PROJECT_RESOURCE_DIR}/translations)

--- a/mathmech/mathmech/mathmech.desktop
+++ b/mathmech/mathmech/mathmech.desktop
@ -1,3 +1,4 @@
+#!/usr/bin/env xdg-open
 [Desktop Entry]
 Name=Mathematical Molecular Mechanics 
 Comment=GUI for mathmech program pack
--- a/mathmech/mathmech/resources/translations/eng.qm
+++ b/mathmech/mathmech/resources/translations/eng.qm
--- a/mathmech/mathmech/resources/translations/eng.ts
+++ b/mathmech/mathmech/resources/translations/eng.ts
--- a/mathmech/mathmech/resources/translations/rus.qm
+++ b/mathmech/mathmech/resources/translations/rus.qm
--- a/mathmech/mathmech/resources/translations/rus.ts
+++ b/mathmech/mathmech/resources/translations/rus.ts
--- a/mathmech/mathmech/src/CMakeLists.txt
+++ b/mathmech/mathmech/src/CMakeLists.txt
@ -16,17 +16,16 @@ set (LANGUAGES
     rus)
 set (RESOURCES ${PROJECT_RESOURCE_DIR}/resources.qrc)

-message (STATUS "SOURCES: ${SOURCES}")
-message (STATUS "HEADERS: ${HEADERS}")
-message (STATUS "FORMS: ${FORMS}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
+message (STATUS "${PROJECT} FORMS: ${FORMS}")


 # compile
 project (${PROJECT})
 # include_path
 link_directories (${QWT_LIBRARY_PATH})
-include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
-                     ${PROJECT_SOURCE_DIR}
+include_directories (${PROJECT_SOURCE_DIR}
                     ${CMAKE_CURRENT_BINARY_DIR}
                     ${QWT_INCLUDE_PATH})

@ -51,7 +50,7 @@ add_custom_target (
 add_custom_command (
    TARGET translations
    COMMAND ${QT_LRELEASE_EXECUTABLE} ${TRANSLATIONS})
-message (STATUS "TRANSLATIONS: ${TRANSLATIONS_BINARY}")
+message (STATUS "${PROJECT} TRANSLATIONS: ${TRANSLATIONS_BINARY}")

 source_group ("Header Files" FILES ${HEADERS})
 source_group ("Source Files" FILES ${SOURCES})
@ -59,7 +58,6 @@ source_group ("Generated Files" FILES ${MOC_SOURCES})
 source_group ("Resource Files" FILES ${QRC_SOURCES})

 add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURCES} ${QRC_SOURCES} ${TRANSLATIONS})
-
 target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})

 # install properties
--- a/mathmech/mathmech/src/Makefile
+++ b/mathmech/mathmech/src/Makefile
@ -1,6 +1,6 @@
 #############################################################################
 # Makefile for building: mathmech
-# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 26 15:52:26 2013
+# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 3 02:36:06 2013
 # Project:  mathmech.pro
 # Template: app
 # Command: /usr/bin/qmake-qt4 -o Makefile mathmech.pro
@ -54,7 +54,8 @@ SOURCES       = main.cpp \
 		aboutwindow.cpp \
 		statgengraphwindow.cpp \
 		settingswindow.cpp \
-		aglallwindow.cpp moc_mainwindow.cpp \
+		aglallwindow.cpp \
+		helpwindow.cpp moc_mainwindow.cpp \
 		moc_errorwindow.cpp \
 		moc_clear_items.cpp \
 		moc_start_events.cpp \
@ -64,7 +65,8 @@ SOURCES       = main.cpp \
 		moc_aboutwindow.cpp \
 		moc_statgengraphwindow.cpp \
 		moc_settingswindow.cpp \
-		moc_aglallwindow.cpp
+		moc_aglallwindow.cpp \
+		moc_helpwindow.cpp
 OBJECTS       = main.o \
 		mainwindow.o \
 		errorwindow.o \
@ -77,6 +79,7 @@ OBJECTS       = main.o \
 		statgengraphwindow.o \
 		settingswindow.o \
 		aglallwindow.o \
+		helpwindow.o \
 		moc_mainwindow.o \
 		moc_errorwindow.o \
 		moc_clear_items.o \
@ -87,7 +90,8 @@ OBJECTS       = main.o \
 		moc_aboutwindow.o \
 		moc_statgengraphwindow.o \
 		moc_settingswindow.o \
-		moc_aglallwindow.o
+		moc_aglallwindow.o \
+		moc_helpwindow.o
 DIST          = /usr/share/qt4/mkspecs/common/unix.conf \
 		/usr/share/qt4/mkspecs/common/linux.conf \
 		/usr/share/qt4/mkspecs/common/gcc-base.conf \
@ -146,7 +150,7 @@ first: all

 all: Makefile $(TARGET)

-$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h $(OBJECTS)  
+$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h $(OBJECTS)  
 	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)

 Makefile: mathmech.pro  /usr/share/qt4/mkspecs/linux-g++/qmake.conf /usr/share/qt4/mkspecs/common/unix.conf \
@ -219,7 +223,7 @@ qmake:  FORCE

 dist: 
 	@$(CHK_DIR_EXISTS) .tmp/mathmech1.0.0 || $(MKDIR) .tmp/mathmech1.0.0 
-	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0
+	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h helpwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp helpwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui helpwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0


 clean:compiler_clean 
@ -240,9 +244,9 @@ mocclean: compiler_moc_header_clean compiler_moc_source_clean

 mocables: compiler_moc_header_make_all compiler_moc_source_make_all

-compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
+compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
 compiler_moc_header_clean:
-	-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
+	-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
 moc_mainwindow.cpp: mainwindow.h
 	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) mainwindow.h -o moc_mainwindow.cpp

@ -276,6 +280,9 @@ moc_settingswindow.cpp: settingswindow.h
 moc_aglallwindow.cpp: aglallwindow.h
 	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) aglallwindow.h -o moc_aglallwindow.cpp

+moc_helpwindow.cpp: helpwindow.h
+	/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) helpwindow.h -o moc_helpwindow.cpp
+
 compiler_rcc_make_all:
 compiler_rcc_clean:
 compiler_image_collection_make_all: qmake_image_collection.cpp
@ -283,9 +290,9 @@ compiler_image_collection_clean:
 	-$(DEL_FILE) qmake_image_collection.cpp
 compiler_moc_source_make_all:
 compiler_moc_source_clean:
-compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
+compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
 compiler_uic_clean:
-	-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
+	-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
 ui_mainwindow.h: mainwindow.ui
 	/usr/lib/qt4/bin/uic mainwindow.ui -o ui_mainwindow.h

@ -310,6 +317,9 @@ ui_settingswindow.h: settingswindow.ui
 ui_aglallwindow.h: aglallwindow.ui
 	/usr/lib/qt4/bin/uic aglallwindow.ui -o ui_aglallwindow.h

+ui_helpwindow.h: helpwindow.ui
+	/usr/lib/qt4/bin/uic helpwindow.ui -o ui_helpwindow.h
+
 compiler_yacc_decl_make_all:
 compiler_yacc_decl_clean:
 compiler_yacc_impl_make_all:
@ -327,10 +337,11 @@ mainwindow.o: mainwindow.cpp aboutwindow.h \
 		agglwindow.h \
 		aglallwindow.h \
 		atomtypeswindow.h \
+		helpwindow.h \
 		settingswindow.h \
+		statgengraphwindow.h \
 		clear_items.h \
 		start_events.h \
-		statgengraphwindow.h \
 		update_fields.h \
 		mainwindow.h \
 		ui_mainwindow.h
@ -386,6 +397,10 @@ aglallwindow.o: aglallwindow.cpp errorwindow.h \
 		ui_aglallwindow.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o aglallwindow.o aglallwindow.cpp

+helpwindow.o: helpwindow.cpp helpwindow.h \
+		ui_helpwindow.h
+	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o helpwindow.o helpwindow.cpp
+
 moc_mainwindow.o: moc_mainwindow.cpp 
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_mainwindow.o moc_mainwindow.cpp

@ -419,6 +434,9 @@ moc_settingswindow.o: moc_settingswindow.cpp
 moc_aglallwindow.o: moc_aglallwindow.cpp 
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_aglallwindow.o moc_aglallwindow.cpp

+moc_helpwindow.o: moc_helpwindow.cpp 
+	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_helpwindow.o moc_helpwindow.cpp
+
 ####### Install

 install:   FORCE
--- a/mathmech/mathmech/src/helpwindow.cpp
+++ b/mathmech/mathmech/src/helpwindow.cpp
@ -0,0 +1,68 @@
+#include <QDir>
+#include <QFileDialog>
+#include <QKeyEvent>
+#include <QTextStream>
+
+#include "errorwindow.h"
+
+#include "helpwindow.h"
+#include "ui_helpwindow.h"
+
+HelpWindow::HelpWindow(QWidget *parent) :
+  QMainWindow(parent),
+  ui(new Ui::HelpWindow)
+{
+  ui->setupUi(this);
+}
+
+HelpWindow::~HelpWindow()
+{
+  delete ui;
+}
+
+// ESC press event
+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;
+}
--- a/mathmech/mathmech/src/helpwindow.h
+++ b/mathmech/mathmech/src/helpwindow.h
@ -0,0 +1,31 @@
+#ifndef HELPWINDOW_H
+#define HELPWINDOW_H
+
+#include <QMainWindow>
+
+class ErrorWindow;
+
+namespace Ui {
+  class HelpWindow;
+}
+
+class HelpWindow : public QMainWindow
+{
+  Q_OBJECT
+
+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);
+};
+
+#endif /* HELPWINDOW_H */
--- a/mathmech/mathmech/src/helpwindow.ui
+++ b/mathmech/mathmech/src/helpwindow.ui
@ -0,0 +1,416 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>HelpWindow</class>
+ <widget class="QMainWindow" name="HelpWindow">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>598</width>
+    <height>456</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Help</string>
+  </property>
+  <widget class="QWidget" name="centralwidget">
+   <layout class="QGridLayout" name="gridLayout">
+    <item row="0" column="0">
+     <widget class="QToolBox" name="toolBox">
+      <property name="currentIndex">
+       <number>0</number>
+      </property>
+      <widget class="QWidget" name="page_trj">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>580</width>
+         <height>233</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about trj</string>
+       </property>
+       <attribute name="label">
+        <string>trj</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_3">
+        <item row="0" column="0">
+         <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>
+      <widget class="QWidget" name="page_statgen">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about statgen</string>
+       </property>
+       <attribute name="label">
+        <string>statgen</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_4">
+        <item row="0" column="0">
+         <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>
+      <widget class="QWidget" name="page_envir">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about envir</string>
+       </property>
+       <attribute name="label">
+        <string>envir</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_5">
+        <item row="0" column="0">
+         <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>
+      <widget class="QWidget" name="page_radf">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about radf</string>
+       </property>
+       <attribute name="label">
+        <string>radf</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_6">
+        <item row="0" column="0">
+         <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>
+      <widget class="QWidget" name="page_trj2pdb">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>0</y>
+         <width>98</width>
+         <height>88</height>
+        </rect>
+       </property>
+       <property name="toolTip">
+        <string>Help about trj2pdb</string>
+       </property>
+       <attribute name="label">
+        <string>trj2pdb</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayout_7">
+        <item row="0" column="0">
+         <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>
+     </widget>
+    </item>
+    <item row="1" column="0">
+     <layout class="QHBoxLayout" name="horizontalLayout">
+      <item>
+       <spacer name="horizontalSpacer">
+        <property name="orientation">
+         <enum>Qt::Horizontal</enum>
+        </property>
+        <property name="sizeHint" stdset="0">
+         <size>
+          <width>40</width>
+          <height>20</height>
+         </size>
+        </property>
+       </spacer>
+      </item>
+      <item>
+       <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>
+          <height>23</height>
+         </size>
+        </property>
+        <property name="toolTip">
+         <string>Close window</string>
+        </property>
+        <property name="text">
+         <string>Close</string>
+        </property>
+        <property name="autoDefault">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
+     </layout>
+    </item>
+   </layout>
+  </widget>
+ </widget>
+ <tabstops>
+  <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_close</sender>
+   <signal>clicked()</signal>
+   <receiver>HelpWindow</receiver>
+   <slot>close()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>545</x>
+     <y>431</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>598</x>
+     <y>414</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>
--- a/mathmech/mathmech/src/mainwindow.cpp
+++ b/mathmech/mathmech/src/mainwindow.cpp
@ -5,10 +5,11 @@
 #include "agglwindow.h"
 #include "aglallwindow.h"
 #include "atomtypeswindow.h"
+#include "helpwindow.h"
 #include "settingswindow.h"
+#include "statgengraphwindow.h"
 #include "clear_items.h"
 #include "start_events.h"
-#include "statgengraphwindow.h"
 #include "update_fields.h"

 #include "mainwindow.h"
@ -928,9 +929,10 @@ void MainWindow::createActions()
 {
  connect(ui->actionAtom_types_file, SIGNAL(triggered()), this, SLOT(createAtomTypes()));
  connect(ui->actionAgglomerate_file, SIGNAL(triggered()), this, SLOT(createAgglFile()));
-  connect(ui->actionAbout, SIGNAL(triggered()), this, SLOT(aboutWin()));
-  connect(ui->actionSettings, SIGNAL(triggered()), this, SLOT(settingsWinShow()));
  connect(ui->actionAgl_all, SIGNAL(triggered()), this, SLOT(aglallWinShow()));
+  connect(ui->actionHelp, SIGNAL(triggered()), this, SLOT(helpWindow()));
+  connect(ui->actionSettings, SIGNAL(triggered()), this, SLOT(settingsWinShow()));
+  connect(ui->actionAbout, SIGNAL(triggered()), this, SLOT(aboutWin()));
 }

 void MainWindow::createAtomTypes()
@ -967,3 +969,10 @@ void MainWindow::aglallWinShow()
  aglallWin = new AglAllWindow(this, mm_agl_path);
  aglallWin->show();
 }
+
+void MainWindow::helpWindow()
+{
+  HelpWindow *helpWindow;
+  helpWindow = new HelpWindow(this);
+  helpWindow->show();
+}
--- a/mathmech/mathmech/src/mainwindow.h
+++ b/mathmech/mathmech/src/mainwindow.h
@ -86,11 +86,12 @@ private slots:
 // completion
  void on_tabWidget_currentChanged(int index);
 // window signals
-  void createAtomTypes();
-  void createAgglFile();
  void aboutWin();
-  void settingsWinShow();
  void aglallWinShow();
+  void createAgglFile();
+  void createAtomTypes();
+  void settingsWinShow();
+  void helpWindow();

 private:
  Ui::MainWindow *ui;
--- a/mathmech/mathmech/src/mainwindow.ui
+++ b/mathmech/mathmech/src/mainwindow.ui
@ -1352,6 +1352,9 @@
            <property name="toolTip">
             <string>Number of steps of analysis</string>
            </property>
+            <property name="alignment">
+             <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+            </property>
            <property name="minimum">
             <number>1</number>
            </property>
@ -3710,6 +3713,7 @@
    <property name="title">
     <string>Help</string>
    </property>
+    <addaction name="actionHelp"/>
    <addaction name="actionAbout"/>
   </widget>
   <addaction name="menuMenu"/>
@ -3755,6 +3759,14 @@
    <string>agl_all</string>
   </property>
  </action>
+  <action name="actionHelp">
+   <property name="text">
+    <string>&amp;Help</string>
+   </property>
+   <property name="shortcut">
+    <string>F1</string>
+   </property>
+  </action>
 </widget>
 <layoutdefault spacing="6" margin="11"/>
 <tabstops>
--- a/mathmech/mathmech/src/mathmech.pro
+++ b/mathmech/mathmech/src/mathmech.pro
@ -19,7 +19,8 @@ HEADERS += mainwindow.h \
    aboutwindow.h \
    statgengraphwindow.h \
    settingswindow.h \
-    aglallwindow.h
+    aglallwindow.h \
+    helpwindow.h
 FORMS += mainwindow.ui \
    errorwindow.ui \
    atomtypeswindow.ui \
@ -27,7 +28,8 @@ FORMS += mainwindow.ui \
    aboutwindow.ui \
    statgengraphwindow.ui \
    settingswindow.ui \
-    aglallwindow.ui
+    aglallwindow.ui \
+    helpwindow.ui
 SOURCES += main.cpp mainwindow.cpp \
    errorwindow.cpp \
    clear_items.cpp \
@ -38,7 +40,8 @@ SOURCES += main.cpp mainwindow.cpp \
    aboutwindow.cpp \
    statgengraphwindow.cpp \
    settingswindow.cpp \
-    aglallwindow.cpp
+    aglallwindow.cpp \
+    helpwindow.cpp
 TRANSLATIONS += rus.ts \
    eng.ts

--- a/mathmech/mathmech/src/mathmech.pro.user
+++ b/mathmech/mathmech/src/mathmech.pro.user
@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 2.8.1, 2013-08-30T19:09:45. -->
+<!-- Written by QtCreator 2.8.1, 2013-09-03T05:28:10. -->
 <qtcreator>
 <data>
  <variable>ProjectExplorer.Project.ActiveTarget</variable>
--- a/mathmech/mm_agl/CMakeLists.txt
+++ b/mathmech/mm_agl/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}agl)
--- a/mathmech/mm_agl/README
+++ b/mathmech/mm_agl/README
@ -1,5 +1,5 @@
 mm_agl - program that creates PDB file with chosen agglomerate
-Version: 1.0.3
+Version: 1.1.1
 License: GPL

 Usage:
--- a/mathmech/mm_agl/mm_agl.doxygen
+++ b/mathmech/mm_agl/mm_agl.doxygen
@ -32,7 +32,7 @@ PROJECT_NAME           = mm_agl
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.

-PROJECT_NUMBER         = V.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_agl/mm_agl.pdf
+++ b/mathmech/mm_agl/mm_agl.pdf
--- a/mathmech/mm_agl/src/CMakeLists.txt
+++ b/mathmech/mm_agl/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_agl/src/main.c
+++ b/mathmech/mm_agl/src/main.c
@ -61,13 +61,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -134,7 +144,7 @@ int main(int argc, char *argv[])
    {
      sprintf (tmp_str, "                                     mm_agl\n");
      sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/mm_envir/CMakeLists.txt
+++ b/mathmech/mm_envir/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}envir)
--- a/mathmech/mm_envir/README
+++ b/mathmech/mm_envir/README
@ -1,5 +1,5 @@
 mm_envir - program that searchs environment for chosen molecule by geometric criterion
-Version: 1.0.3
+Version: 1.1.1
 License: GPL

 Usage:
--- a/mathmech/mm_envir/mm_envir.doxygen
+++ b/mathmech/mm_envir/mm_envir.doxygen
@ -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.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_envir/mm_envir.pdf
+++ b/mathmech/mm_envir/mm_envir.pdf
--- a/mathmech/mm_envir/src/CMakeLists.txt
+++ b/mathmech/mm_envir/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_envir/src/main.c
+++ b/mathmech/mm_envir/src/main.c
@ -63,13 +63,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -136,7 +146,7 @@ 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 : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/mm_radf/CMakeLists.txt
+++ b/mathmech/mm_radf/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}radf)
--- a/mathmech/mm_radf/README
+++ b/mathmech/mm_radf/README
@ -1,17 +1,17 @@
 mm_radf - program that calculates radial distribution function (RDF) or radial-angles 
-distribution function
+distribution function (RADF)
 Version : 1.0.3
 License : GPL

 Usage:
-mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
-                   [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+  mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+                      [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]

 Parametrs:
  -i          - mask of input files
  -s          - trajectory steps (integer)
  -c          - cell size (float), A
-  -a          - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
+  -a5         - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
                (will enable RDF calculation for center mass automaticaly)
  -o          - output file name
  -r          - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
--- a/mathmech/mm_radf/mm_radf.doxygen
+++ b/mathmech/mm_radf/mm_radf.doxygen
@ -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.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_radf/mm_radf.pdf
+++ b/mathmech/mm_radf/mm_radf.pdf
--- a/mathmech/mm_radf/src/CMakeLists.txt
+++ b/mathmech/mm_radf/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_radf/src/add_main.c
+++ b/mathmech/mm_radf/src/add_main.c
@ -127,7 +127,7 @@ int printing_head (const char *output, const int log, const int quiet, const int
  FILE *f_out;
  
  f_out = fopen (output, "w");
-  fprintf (f_out, "radf ::: V.1.0.1 ::: 2013-07-23\n\n");
+  fprintf (f_out, "radf ::: V.1.1.1\n\n");
  fprintf (f_out, "CONFIGURATION\n");
  
  fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix);
--- a/mathmech/mm_radf/src/main.c
+++ b/mathmech/mm_radf/src/main.c
@ -25,13 +25,13 @@
 * @section How-To-Use How to use
 * Usage:
 * <pre>
- * mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
- *                    [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+ * mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+ *                     [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
 * Parametrs:
 *    -i          - mask of input files
 *    -s          - trajectory steps (integer)
 *    -c          - cell size (float), A
- *    -a          - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
+ *    -at         - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
 *                  (will enable RDF calculation for center mass automaticaly)
 *    -o          - output file name
 *    -r          - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
@ -70,13 +70,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -153,7 +163,7 @@ 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 : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/mm_statgen/CMakeLists.txt
+++ b/mathmech/mm_statgen/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}statgen)
--- a/mathmech/mm_statgen/README
+++ b/mathmech/mm_statgen/README
@ -1,5 +1,5 @@
 mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
-Version: 1.0.3
+Version: 1.1.1
 License: GPL

 Usage:
--- a/mathmech/mm_statgen/mm_statgen.doxygen
+++ b/mathmech/mm_statgen/mm_statgen.doxygen
@ -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.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_statgen/mm_statgen.pdf
+++ b/mathmech/mm_statgen/mm_statgen.pdf
--- a/mathmech/mm_statgen/src/CMakeLists.txt
+++ b/mathmech/mm_statgen/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_statgen/src/add_main.c
+++ b/mathmech/mm_statgen/src/add_main.c
@ -92,7 +92,7 @@ int printing_head (const char *output, const int log, const int quiet,
  FILE *f_out;
  
  f_out = fopen (output, "w");
-  fprintf (f_out, "statgen ::: V.1.0.1 ::: 2013-07-23\n\n");
+  fprintf (f_out, "statgen ::: V.1.1.1\n\n");
  fprintf (f_out, "CONFIGURATION\n");
  
  fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
--- a/mathmech/mm_statgen/src/main.c
+++ b/mathmech/mm_statgen/src/main.c
@ -66,13 +66,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -168,7 +178,7 @@ 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 : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/mm_statgen/src/summary_stat.c
+++ b/mathmech/mm_statgen/src/summary_stat.c
@ -71,11 +71,11 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
    x = type_agl[0] + type_agl[1];
    type[0] = type_agl[0];
    type[1] = type_agl[1];
-    fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
+    fprintf (f_out, "LINEAR=%.5f\nCYCLE=%.5f\n--------------------\n", type[0]/x, type[1]/x);
 // branched
    type[0] = type_agl[2];
    type[1] = type_agl[3];
-    fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
+    fprintf (f_out, "NOT BRANCHED=%.5f\nBRANCHED=%.5f\n--------------------\n", type[0]/x, type[1]/x);
 // n_cycle
    x = 0;
    for (i=4; i<max_depth+2; i++)
@ -83,7 +83,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
    for (i=4; i<max_depth+2; i++)
    {
      type[0] = type_agl[i];
-      fprintf (f_out, "CYCLE_'%2i'=%7.5f\n", i-1, type[0]/x);
+      fprintf (f_out, "CYCLE_'%2i'=%.5f\n", i-1, type[0]/x);
    }
  }
  
--- a/mathmech/mm_trj/CMakeLists.txt
+++ b/mathmech/mm_trj/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}trj)
--- a/mathmech/mm_trj/README
+++ b/mathmech/mm_trj/README
@ -3,8 +3,8 @@ Version : 1.0.3
 License : GPL

 Usage:
-mm_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]
-                                                            [ -l LOGFILE ] [ -q ] [ -h ]
+  mm_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]
+                                                              [ -l LOGFILE ] [ -q ] [ -h ]

 Parametrs:
  -i          - input file name
--- a/mathmech/mm_trj/mm_trj.doxygen
+++ b/mathmech/mm_trj/mm_trj.doxygen
@ -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.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_trj/mm_trj.pdf
+++ b/mathmech/mm_trj/mm_trj.pdf
--- a/mathmech/mm_trj/src/CMakeLists.txt
+++ b/mathmech/mm_trj/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_trj/src/main.c
+++ b/mathmech/mm_trj/src/main.c
@ -63,13 +63,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -133,7 +143,7 @@ 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 : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/mm_trj2pdb/CMakeLists.txt
+++ b/mathmech/mm_trj2pdb/CMakeLists.txt
@ -1,8 +1,8 @@
 cmake_minimum_required (VERSION 2.8)

-cmake_policy(SET CMP0003 OLD)
-cmake_policy(SET CMP0011 NEW)
-cmake_policy(SET CMP0015 NEW)
+cmake_policy (SET CMP0003 OLD)
+cmake_policy (SET CMP0011 NEW)
+cmake_policy (SET CMP0015 NEW)

 # set project name
 set (PROJECT ${MM_PREFIX}trj2pdb)
--- a/mathmech/mm_trj2pdb/README
+++ b/mathmech/mm_trj2pdb/README
@ -1,5 +1,5 @@
 mm_trj2pdb - program that creates PDB file from trajetory snapshot
-Version: 1.0.3
+Version: 1.1.1
 License: GPL

 Usage:
--- a/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen
+++ b/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen
@ -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.1.0.3
+PROJECT_NUMBER         = V.1.1.1

 # 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/mathmech/mm_trj2pdb/mm_trj2pdb.pdf
+++ b/mathmech/mm_trj2pdb/mm_trj2pdb.pdf
--- a/mathmech/mm_trj2pdb/src/CMakeLists.txt
+++ b/mathmech/mm_trj2pdb/src/CMakeLists.txt
@ -1,25 +1,24 @@
 # set files
-aux_source_directory (. SOURCES)
+file (GLOB SOURCES *.c)
+file (GLOB HEADERS *.h)

 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
  set (ADDITIONAL_LIB m)
 else ()
  set (ADDITIONAL_LIB)
-endif()
+endif ()

 # message
-message (STATUS "SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
+message (STATUS "${PROJECT} HEADERS: ${HEADERS}")

 # link libraries and compile
-add_executable (${PROJECT} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES} ${HEADERS})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})

 # install properties
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
 if (ADD_DOCS)
  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
 endif ()
--- a/mathmech/mm_trj2pdb/src/main.c
+++ b/mathmech/mm_trj2pdb/src/main.c
@ -59,13 +59,23 @@
 * You may also download compiled executable file for Win_x86.
 *
 * @page Changelog
+ * V.1.1.1 (2013-09-03)
+ * <ul>
+ * <li>optimization
+ * </ul>
+ * V.1.1.0 (2013-09-02)
+ * <ul>
+ * <li>added help window
+ * <li>added help docs
+ * <li>small bug fixes
+ * </ul>
 * V.1.0.3 (2013-08-30)
 * <ul>
- * <li> Bug fixes
+ * <li>bug fixes
 * </ul>
 * V.1.0.1 (2013-07-27)
 * <ul>
- * <li> initial release
+ * <li>initial release
 * </ul>
 */ 

@ -125,7 +135,7 @@ 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 : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.1                                                    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);
--- a/mathmech/update_ver.sh
+++ b/mathmech/update_ver.sh
@ -2,8 +2,8 @@
 func_help() {
  echo -e "\nUsage: update_ver.sh -o OLDVER -n NEWVER"
  echo -e "\nRequired parameters:"
-  echo -e "  -o  --oldver      - path to GIT repository"
-  echo -e "  -n  --newver      - time to sleep"
+  echo -e "  -o  --oldver      - old version"
+  echo -e "  -n  --newver      - new version"
  echo -e "\nAdditional parametrs:"
  echo -e "  -h  --help        - show this help and exit"
  exit 1
@ -38,10 +38,21 @@ fi
 # work block
 COMPONENTS=(mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb)
 for COMPONENT in ${COMPONENTS[*]}; do
+# help message
  sed -i "s/Version : $OLDVER/Version : $NEWVER/g" $COMPONENT/src/main.c
+# head in output
+  sed -i "s/V.$OLDVER/V.$NEWVER/g" $COMPONENT/src/add_main.c
+# readme
  sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
+# documentation
  sed -i "s/V.$OLDVER/V.$NEWVER/g" $COMPONENT/$COMPONENT.doxygen
 done
+# update documentation
+./update_docs.sh

 COMPONENT=mathmech
+# about window
+sed -i "s/$OLDVER/$NEWVER/g" $COMPONENT/resources/translations/eng.ts
+sed -i "s/$OLDVER/$NEWVER/g" $COMPONENT/resources/translations/rus.ts
+# readme
 sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
Author	SHA1	Message	Date
arcan1s	473d195ea9	Release 1.1.1 * optimization	2013-09-03 18:09:26 +04:00
arcan1s	6b0a2a47db	Release 1.1.0 + added help window + added help docs + small bug fixes	2013-09-03 06:01:23 +04:00
arcan1s	d7f7a9c2b5	Added documentatiion in russian	2013-09-02 21:35:07 +04:00
arcan1s	cd3857adc1	Added helpwindow fixed wersions edited PKGBUILD edited scripts	2013-09-01 14:16:23 +04:00