Release 1.0.3

mathmech/AUTHORS

@@ -0,0 +1,3 @@
+Current developers:
+
+Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>

mathmech/CMakeLists.txt

@@ -1,3 +1,10 @@
+set ("PROJECT_VERSION_MAJOR" 1)
+set ("PROJECT_VERSION_MINOR" 0)
+set ("PROJECT_VERSION_PATCH" 3)
+set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
+
+message (STATUS "Version ${PROJECT_VERSION}")
+
 set (COMPS mathmech
            mm_agl
            mm_envir
@@ -6,6 +13,19 @@ set (COMPS mathmech
            mm_trj
            mm_trj2pdb)
 
+# 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")
+  set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
+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()
+
 foreach (COMP ${COMPS})
   add_subdirectory (${COMP})
 endforeach()

mathmech/COPYING

@@ -0,0 +1,341 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+     Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+   Everyone is permitted to copy and distribute verbatim copies
+    of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
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+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
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+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
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+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
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+  Finally, any free program is threatened constantly by software
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+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
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+
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+infringement or for any other reason (not limited to patent issues),
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+
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+certain countries either by patents or by copyrighted interfaces, the
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+
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+
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+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
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+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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+
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+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) 19yy  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) 19yy name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

mathmech/INSTALL

@@ -0,0 +1,19 @@
+CMakeFlags:
+  -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
+  -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
+  -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components
+  -DQWT_INCLUDE_PATH              - path to qwt includes
+  -DQWT_LIBRARY_PATH              - path to qwt library
+
+Install for Linux:
+  mkdir build && cd build
+  cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
+  make
+  make install
+Install for Windows:
+  create project file using 'cmake'
+  compile project
+  copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
+You may also download compiled executable file for Win_x86.

mathmech/PKGBUILD

@@ -0,0 +1,36 @@
+# Author: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
+# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
+
+pkgname=mathmech
+pkgver=1.0.3
+pkgrel=1
+pkgdesc="Software package for analysis of molecular dynamics trajectories"
+arch=(any)
+url="https://github.com/arcan1s/moldyn/mathmech"
+license=('GPL')
+depends=('qt4' 'qwt')
+makedepends=('unzip' 'cmake' 'automoc4')
+source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
+md5sums=('4eccb72efd4a8a531d7fda1aabc04f62')
+_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
+            -DQWT_INCLUDE_PATH=/usr/include/qwt
+            -DMM_PREFIX=mm_
+            -DCMAKE_BUILD_TYPE=Release"
+
+build ()
+{
+  unzip -o -q ${srcdir}/${pkgname}-${pkgver}-src.zip -d ${srcdir}/${pkgname}
+  if [ -d ${srcdir}/${pkgname}/build ]; then
+    rm -rf ${srcdir}/${pkgname}/build
+  fi
+  mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build
+  cmake ${_cmakekeys} ../
+  make
+}
+
+package() 
+{
+  cd ${srcdir}/${pkgname}/build
+  make DESTDIR=${pkgdir} install
+}
+ 

mathmech/mathmech/CMakeLists.txt

@@ -12,7 +12,6 @@ include (${PROJECT}.cmake)
 
 # additional options
 OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)

mathmech/mathmech/INSTALL

@@ -1,7 +1,8 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
-  -DADD_INCLUDE=1                 - install include files (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DQWT_INCLUDE_PATH              - path to qwt includes
+  -DQWT_LIBRARY_PATH              - path to qwt library
 
 Install for Linux:
   mkdir build && cd build
@@ -11,4 +12,5 @@ Install for Linux:
 Install for Windows:
   create project file using 'cmake'
   compile project
+  copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
 You may also download compiled executable file for Win_x86.

mathmech/mathmech/README

@@ -1 +1,3 @@
 Mathematical Molecular Mechanics is GUI for "mm" program pack
+Version: 1.0.3
+License: GPL

mathmech/mathmech/mathmech.desktop

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

mathmech/mathmech/resources/res_icon.rc

@@ -0,0 +1 @@
+IDI_ICON1               ICON    DISCARDABLE     "mathmech.ico" 

mathmech/mathmech/src/CMakeLists.txt

@@ -1,20 +1,16 @@
-set (PROJECT_VERSION_MAJOR 1)
-set (PROJECT_VERSION_MINOR 0)
-set (PROJECT_VERSION_PATCH 0)
-set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${PROJECT_VERSION}")
-
 # set files
 file (GLOB SOURCES *.cpp)
 file (GLOB HEADERS *.h)
 file (GLOB FORMS *.ui)
+if (CMAKE_SYSTEM_NAME MATCHES Windows)
+  set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
+endif ()
 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
   set (LIBRARIES m qwt)
 else ()
   set (LIBRARIES qwt)
-endif()
+endif ()
 set (LANGUAGES
      eng
      rus)
@@ -28,9 +24,11 @@ message (STATUS "FORMS: ${FORMS}")
 # compile
 project (${PROJECT})
 # include_path
+link_directories (${QWT_LIBRARY_PATH})
 include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
                      ${PROJECT_SOURCE_DIR}
-                     ${CMAKE_CURRENT_BINARY_DIR})
+                     ${CMAKE_CURRENT_BINARY_DIR}
+                     ${QWT_INCLUDE_PATH})
 
 find_package (Qt4 REQUIRED)
 include (${QT_USE_FILE})
@@ -46,7 +44,7 @@ foreach (LANGUAGE ${LANGUAGES})
         OUTPUT ${QM}
         COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS}
         MAIN_DEPENDENCY ${TS})
-endforeach()
+endforeach ()
 add_custom_target (
     translations 
     COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS})
@@ -65,4 +63,12 @@ add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURC
 target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
 
 # install properties
-INSTALL (TARGETS ${PROJECT} DESTINATION bin)
+install (TARGETS ${PROJECT} DESTINATION bin)
+if (CMAKE_SYSTEM_NAME MATCHES Linux)
+  install (FILES ../mathmech.desktop
+          DESTINATION share/applications/)
+  install (FILES ../mathmech-logo.png
+          DESTINATION share/pixmaps/)
+  install (FILES ../mathmech.png
+          DESTINATION share/icons/hicolor/32x32/apps/)
+endif ()

mathmech/mathmech/src/aboutwindow.ui

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

mathmech/mathmech/src/agglwindow.ui

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

mathmech/mathmech/src/aglallwindow.ui

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

mathmech/mathmech/src/atomtypeswindow.ui

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

mathmech/mathmech/src/mainwindow.cpp

@@ -19,7 +19,7 @@ MainWindow::MainWindow(QWidget *parent) :
   ui(new Ui::MainWindow),
   clear_items(new Clear_items(this)),
   update_fields(new Update_fields(this))
-{
+{  
   ui->setupUi(this);
   statgen_crit = new float[10];
 
@@ -123,9 +123,19 @@ void MainWindow::on_statgen_checkBox_atoms3_stateChanged(int arg1)
 void MainWindow::on_statgen_checkBox_anal_stateChanged(int arg1)
 {
   if (arg1 == 0)
+  {
     ui->statgen_doubleSpinBox_anal->setDisabled(true);
+    ui->statgen_spinBox_anal->setDisabled(true);
+    ui->statgen_checkBox_graph->setCheckState(Qt::Checked);
+    ui->statgen_checkBox_graph->setEnabled(true);
+  }
   else if (arg1 == 2)
+  {
     ui->statgen_doubleSpinBox_anal->setEnabled(true);
+    ui->statgen_spinBox_anal->setEnabled(true);
+    ui->statgen_checkBox_graph->setCheckState(Qt::Unchecked);
+    ui->statgen_checkBox_graph->setDisabled(true);
+  }
 }
 
 void MainWindow::on_envir_checkBox_log_stateChanged(int arg1)
@@ -664,8 +674,12 @@ void MainWindow::start_events_statgen()
   else
     depth = QString("#");
   float int_step;
+  int imax;
   if (ui->statgen_checkBox_anal->checkState() == 2)
+  {
     int_step = ui->statgen_doubleSpinBox_anal->value();
+    imax = ui->statgen_spinBox_anal->value();
+  }
   QString log;
   if (ui->statgen_checkBox_log->checkState() == 2)
     log = ui->statgen_lineEdit_log->text();
@@ -699,7 +713,7 @@ void MainWindow::start_events_statgen()
                                                  output,
                                                  depth,
                                                  log,
-                                                 int_step);
+                                                 int_step, imax);
   ui->statusBar->showMessage(QApplication::translate("MainWindow", "Done"));
 
   if ((ui->statgen_checkBox_graph->checkState() == 2) && (check == true))

mathmech/mathmech/src/mainwindow.ui

@@ -48,6 +48,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to work directory</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -91,6 +94,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to input file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -134,6 +140,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Input trajectory type</string>
+            </property>
             <item>
              <property name="text">
               <string>GROMACS text</string>
@@ -180,6 +189,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Number of steps in trajectory</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -229,6 +241,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to file with atom types</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -272,6 +287,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Mask of output files</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -315,6 +333,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Maximum number of atom types</string>
+            </property>
             <property name="layoutDirection">
              <enum>Qt::LeftToRight</enum>
             </property>
@@ -353,6 +374,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to log file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -396,6 +420,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Clear window</string>
+            </property>
             <property name="text">
              <string>Clear</string>
             </property>
@@ -431,6 +458,9 @@
               <height>16777215</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Start application</string>
+            </property>
             <property name="text">
              <string>Start</string>
             </property>
@@ -471,6 +501,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to work directory</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -514,6 +547,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Mask of input files</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -570,6 +606,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>First trajectory step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -615,6 +654,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Last trajectory step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -683,6 +725,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, X</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -724,6 +769,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Y</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -765,6 +813,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Z</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -816,6 +867,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom0 type</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -851,6 +905,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom1 type</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -889,6 +946,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom2 type</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -927,6 +987,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom3 type</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -963,6 +1026,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Type of interaction</string>
+            </property>
             <item>
              <property name="text">
               <string>0-0</string>
@@ -984,6 +1050,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Criterion</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1006,6 +1075,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Save this criterion</string>
+            </property>
             <property name="text">
              <string>Save</string>
             </property>
@@ -1022,6 +1094,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Add this interaction</string>
+            </property>
             <property name="text">
              <string>Add</string>
             </property>
@@ -1040,6 +1115,9 @@
             <height>85</height>
            </size>
           </property>
+          <property name="toolTip">
+           <string>Added interactions</string>
+          </property>
           <property name="editTriggers">
            <set>QAbstractItemView::NoEditTriggers</set>
           </property>
@@ -1068,6 +1146,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Remove selected interaction</string>
+            </property>
             <property name="text">
              <string>Remove</string>
             </property>
@@ -1101,6 +1182,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to output file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1147,6 +1231,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Search depth of related graphs</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1185,6 +1272,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to log file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1231,6 +1321,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Step of analysis</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1245,6 +1338,28 @@
             </property>
            </widget>
           </item>
+          <item>
+           <widget class="QSpinBox" name="statgen_spinBox_anal">
+            <property name="enabled">
+             <bool>false</bool>
+            </property>
+            <property name="minimumSize">
+             <size>
+              <width>80</width>
+              <height>23</height>
+             </size>
+            </property>
+            <property name="toolTip">
+             <string>Number of steps of analysis</string>
+            </property>
+            <property name="minimum">
+             <number>1</number>
+            </property>
+            <property name="value">
+             <number>10</number>
+            </property>
+           </widget>
+          </item>
           <item>
            <spacer name="horizontalSpacer_16">
             <property name="orientation">
@@ -1266,6 +1381,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Show graph</string>
+            </property>
             <property name="text">
              <string>Graph</string>
             </property>
@@ -1299,6 +1417,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Clear window</string>
+            </property>
             <property name="text">
              <string>Clear</string>
             </property>
@@ -1334,6 +1455,9 @@
               <height>16777215</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Start application</string>
+            </property>
             <property name="text">
              <string>Start</string>
             </property>
@@ -1374,6 +1498,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to work directory</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1417,6 +1544,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to input file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1479,6 +1609,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, X</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1520,6 +1653,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Y</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1561,6 +1697,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Z</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1600,6 +1739,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to output file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1643,6 +1785,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Number of selected molecule</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1688,6 +1833,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Radius of environment</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1737,6 +1885,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to log file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1780,6 +1931,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Clear window</string>
+            </property>
             <property name="text">
              <string>Clear</string>
             </property>
@@ -1815,6 +1969,9 @@
               <height>16777215</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Start application</string>
+            </property>
             <property name="text">
              <string>Start</string>
             </property>
@@ -1855,6 +2012,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to work directory</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1898,6 +2058,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Mask of input files</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -1954,6 +2117,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>First trajectory step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -1999,6 +2165,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Last trajectory step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2067,6 +2236,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, X</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2108,6 +2280,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Y</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2149,6 +2324,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Z</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2188,6 +2366,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to output file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -2218,6 +2399,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Type of function</string>
+            </property>
             <item>
              <property name="text">
               <string>One atom function</string>
@@ -2263,6 +2447,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom1 type</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2282,6 +2469,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom2 type</string>
+            </property>
             <property name="text">
              <string>atom 2</string>
             </property>
@@ -2323,6 +2513,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom3 type</string>
+            </property>
             <property name="text">
              <string>atom 3</string>
             </property>
@@ -2384,6 +2577,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom1 type</string>
+            </property>
             <property name="text">
              <string>atom 1</string>
             </property>
@@ -2422,6 +2618,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom2 type</string>
+            </property>
             <property name="text">
              <string>atom 2</string>
             </property>
@@ -2463,6 +2662,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>atom3 type</string>
+            </property>
             <property name="text">
              <string>atom 3</string>
             </property>
@@ -2534,6 +2736,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Minimal radius</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2578,6 +2783,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Maximal radius</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2622,6 +2830,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Radius step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2689,6 +2900,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Minimal angle</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2739,6 +2953,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Maximal angle</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2789,6 +3006,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Angle step</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -2821,6 +3041,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Matrix output</string>
+            </property>
             <property name="text">
              <string>Matrix</string>
             </property>
@@ -2850,6 +3073,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to log file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -2893,6 +3119,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Clear window</string>
+            </property>
             <property name="text">
              <string>Clear</string>
             </property>
@@ -2922,6 +3151,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Show graph</string>
+            </property>
             <property name="text">
              <string>Graph</string>
             </property>
@@ -2944,6 +3176,9 @@
               <height>16777215</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Start application</string>
+            </property>
             <property name="text">
              <string>Start</string>
             </property>
@@ -2963,6 +3198,9 @@
        <layout class="QVBoxLayout" name="verticalLayout_5">
         <item>
          <widget class="QComboBox" name="pdb_comboBox_mode">
+          <property name="toolTip">
+           <string>Input file type</string>
+          </property>
           <item>
            <property name="text">
             <string>From agglomerate</string>
@@ -2998,6 +3236,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to work directory</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -3041,6 +3282,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to input file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -3084,6 +3328,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to file with agglomerate</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -3146,6 +3393,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, X</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -3187,6 +3437,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Y</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -3228,6 +3481,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Cell size, Z</string>
+            </property>
             <property name="alignment">
              <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
             </property>
@@ -3267,6 +3523,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to output file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -3313,6 +3572,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Path to log file</string>
+            </property>
            </widget>
           </item>
           <item>
@@ -3356,6 +3618,9 @@
               <height>23</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Clear window</string>
+            </property>
             <property name="text">
              <string>Clear</string>
             </property>
@@ -3391,6 +3656,9 @@
               <height>16777215</height>
              </size>
             </property>
+            <property name="toolTip">
+             <string>Start application</string>
+            </property>
             <property name="text">
              <string>Start</string>
             </property>
@@ -3447,14 +3715,6 @@
    <addaction name="menuMenu"/>
    <addaction name="menuHelp"/>
   </widget>
-  <widget class="QToolBar" name="mainToolBar">
-   <attribute name="toolBarArea">
-    <enum>TopToolBarArea</enum>
-   </attribute>
-   <attribute name="toolBarBreak">
-    <bool>false</bool>
-   </attribute>
-  </widget>
   <widget class="QStatusBar" name="statusBar"/>
   <action name="actionExit">
    <property name="text">
@@ -3467,14 +3727,6 @@
     <string>Ctrl+Q</string>
    </property>
   </action>
-  <action name="actionHelp">
-   <property name="text">
-    <string>&amp;Help</string>
-   </property>
-   <property name="shortcut">
-    <string>F1</string>
-   </property>
-  </action>
   <action name="actionAbout">
    <property name="text">
     <string>About</string>
@@ -3494,17 +3746,15 @@
    <property name="text">
     <string>&amp;Settings</string>
    </property>
+   <property name="shortcut">
+    <string>Ctrl+P</string>
+   </property>
   </action>
   <action name="actionAgl_all">
    <property name="text">
     <string>agl_all</string>
    </property>
   </action>
-  <action name="actionStatgen_all">
-   <property name="text">
-    <string>statgen_all</string>
-   </property>
-  </action>
  </widget>
  <layoutdefault spacing="6" margin="11"/>
  <tabstops>
@@ -3556,6 +3806,7 @@
   <tabstop>statgen_pushButton_log</tabstop>
   <tabstop>statgen_checkBox_anal</tabstop>
   <tabstop>statgen_doubleSpinBox_anal</tabstop>
+  <tabstop>statgen_spinBox_anal</tabstop>
   <tabstop>statgen_checkBox_graph</tabstop>
   <tabstop>statgen_pushButton_clear</tabstop>
   <tabstop>statgen_pushButton_start</tabstop>

mathmech/mathmech/src/mathmech.pro.user

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 2.8.0, 2013-08-28T17:33:30. -->
+<!-- Written by QtCreator 2.8.1, 2013-08-30T19:09:45. -->
 <qtcreator>
  <data>
   <variable>ProjectExplorer.Project.ActiveTarget</variable>

mathmech/mathmech/src/settingswindow.cpp

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

mathmech/mathmech/src/settingswindow.ui

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

mathmech/mathmech/src/start_events.cpp

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

mathmech/mathmech/src/start_events.h

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

mathmech/mathmech/src/statgengraphwindow.cpp

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

mathmech/mathmech/src/statgengraphwindow.h

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

mathmech/mathmech/src/statgengraphwindow.ui

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

mathmech/mm_agl/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_agl)
+set (PROJECT ${MM_PREFIX}agl)
+set (_PROJECT mm_agl)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_agl/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_agl/README

@@ -1,12 +1,12 @@
-mm_agl - program that creates PDB file with chosen aglomerate
+mm_agl - program that creates PDB file with chosen agglomerate
-Version: 1.0.1
+Version: 1.0.3
 License: GPL
 
 Usage:
   mm_agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
-  -a          - input file with aglomerates (in format statgen)
+  -a          - input file with agglomerates (in format statgen)
   -i          - input file with coordinates
   -c          - cell size (float), A
   -o          - output file with coordinates

mathmech/mm_agl/mm_agl.cmake

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

mathmech/mm_agl/mm_agl.doxygen

@@ -32,13 +32,13 @@ PROJECT_NAME           = mm_agl
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = V.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description 
 # for a project that appears at the top of each page and should give viewer 
 # a quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "Program that creates PDB file with chosen aglomerate"
+PROJECT_BRIEF          = "Program that creates PDB file with chosen agglomerate"
 
 # With the PROJECT_LOGO tag one can specify an logo or icon that is 
 # included in the documentation. The maximum height of the logo should not 

mathmech/mm_agl/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_agl/src/add_main.c

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

mathmech/mm_agl/src/main.c

@@ -9,7 +9,7 @@
  *
  * <b>About this program</b>:
  * <ul>
- * <li>Program that creates PDB file with chosen aglomerate
+ * <li>Program that creates PDB file with chosen agglomerate
  * </ul>
  *
  * <b>Developer</b>:
@@ -27,7 +27,7 @@
  * mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
  *
  * Parametrs:
- *    -a          - input file with aglomerates (in format statgen)
+ *    -a          - input file with agglomerates (in format statgen)
  *    -i          - input file with coordinates
  *    -c          - cell size (float), A
  *    -o          - output file name
@@ -61,8 +61,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -100,7 +106,7 @@ int main(int argc, char *argv[])
   int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet, 
       *true_label_mol;
   
-/* aglinp                 aglomerate file name
+/* aglinp                 agglomerate file name
  * ch_type_atoms          massive of char atom types
  * input                  input file name
  * logfile                log file name
@@ -127,14 +133,14 @@ int main(int argc, char *argv[])
     if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
       sprintf (tmp_str, "                                     mm_agl\n");
-      sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
+      sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
       sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
-      sprintf (tmp_str, "%s  -a          - input file with aglomerates (in format statgen)\n", tmp_str);
+      sprintf (tmp_str, "%s  -a          - input file with agglomerates (in format statgen)\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - input file with coordinates\n", tmp_str);
       sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);
       sprintf (tmp_str, "%s  -o          - output file name\n", tmp_str);
@@ -238,13 +244,13 @@ int main(int argc, char *argv[])
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
   
-// reading aglomerate
+// reading agglomerate
   print_message (quiet, stdout, log, f_log, 7, aglinp);
   error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
   
   if (error == 0)
   {
-    sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol);
+    sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol);
     print_message (quiet, stdout, log, f_log, 8, tmp_str);
 // reading coordinates
     print_message (quiet, stdout, log, f_log, 7, input);

mathmech/mm_agl/src/messages.c

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

mathmech/mm_agl/src/read_agl.c

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

mathmech/mm_envir/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_envir)
+set (PROJECT ${MM_PREFIX}envir)
+set (_PROJECT mm_envir)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_envir/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_envir/README

@@ -1,5 +1,5 @@
 mm_envir - program that searchs environment for chosen molecule by geometric criterion
-Version: 1.0.1
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_envir/mm_envir.cmake

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

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.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # 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 

mathmech/mm_envir/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_envir/src/main.c

@@ -63,8 +63,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -130,7 +136,7 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_envir\n");
       sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    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);

mathmech/mm_envir/src/messages.c

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

mathmech/mm_radf/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_radf)
+set (PROJECT ${MM_PREFIX}radf)
+set (_PROJECT mm_radf)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_radf/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_radf/README

@@ -1,6 +1,6 @@
 mm_radf - program that calculates radial distribution function (RDF) or radial-angles 
 distribution function
-Version : 1.0.1
+Version : 1.0.3
 License : GPL
 
 Usage:

mathmech/mm_radf/mm_radf.cmake

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

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.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # 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 

mathmech/mm_radf/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_radf/src/main.c

@@ -70,8 +70,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -147,7 +153,7 @@ int main(int argc, char *argv[])
       sprintf (tmp_str, "                                    mm_radf\n");
       sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
       sprintf (tmp_str, "%sdistribution function\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    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);

mathmech/mm_radf/src/messages.c

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

mathmech/mm_statgen/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_statgen)
+set (PROJECT ${MM_PREFIX}statgen)
+set (_PROJECT mm_statgen)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_statgen/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_statgen/README

@@ -1,5 +1,5 @@
 mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
-Version: 1.0.1
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_statgen/mm_statgen.cmake

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

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.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # 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 

mathmech/mm_statgen/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_statgen/src/main.c

@@ -66,8 +66,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -116,7 +122,7 @@ int main (int argc, char *argv[])
  * coords                 massive of coordinates
  * crit                   massive of criteria
  * 
- * agl                    massive of aglomerates
+ * agl                    massive of agglomerates
  * connect                connectivity graph for all molecules
  * from                   first trajectory step
  * label_atom             massive of atom types for interactions
@@ -125,14 +131,14 @@ int main (int argc, char *argv[])
  * max_depth              maximum depth for check cycles in graph analyze
  * num_atoms              number of atoms
  * num_mol                number of molecules
- * num_mol_agl            massive of number of molecules in aglomerates
+ * num_mol_agl            massive of number of molecules in agglomerates
  * num_of_inter           number of different interactions
  * stat                   massive of statistic
  * stat_all               massive of summary statistic
  * step                   $(to - from + 1)
  * to                     last trajectory step
  * true_label_mol         massive of true numbers of molecule for atoms
- * type_agl               massive of number of aglomerate types
+ * type_agl               massive of number of agglomerate types
  * type_atoms             massive of atom types
  * type_inter             number of atoms for interactions
  * quiet                  status of quiet-mode
@@ -162,7 +168,7 @@ int main (int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_statgen\n");
       sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    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);

mathmech/mm_statgen/src/messages.c

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

mathmech/mm_statgen/src/stat_print.c

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

mathmech/mm_statgen/src/stat_sort.c

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

mathmech/mm_statgen/src/summary_stat.c

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

mathmech/mm_trj/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_trj)
+set (PROJECT ${MM_PREFIX}trj)
+set (_PROJECT mm_trj)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_trj/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_trj/README

@@ -1,5 +1,5 @@
 mm_trj - program that generates trajectory files
-Version : 1.0.1
+Version : 1.0.3
 License : GPL
 
 Usage:

mathmech/mm_trj/mm_trj.cmake

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

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.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # 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 

mathmech/mm_trj/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_trj/src/main.c

@@ -63,8 +63,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -127,7 +133,7 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                    mm_trj\n");
       sprintf (tmp_str, "%sProgram that generates trajectory files\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    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);

mathmech/mm_trj/src/messages.c

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

mathmech/mm_trj2pdb/CMakeLists.txt

@@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT mm_trj2pdb)
+set (PROJECT ${MM_PREFIX}trj2pdb)
+set (_PROJECT mm_trj2pdb)
 # set additional cmake file
-include (${PROJECT}.cmake)
+include (${_PROJECT}.cmake)
-
-
-# additional options
-OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
-OPTION (ADD_INCLUDE "Add include files" OFF)
 
 # set libraries
 set (LIBRARIES)
@@ -29,4 +25,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${${PROJECT}_SOURCE_DIR})
+add_subdirectory (${PROJECT_SOURCE_DIR})

mathmech/mm_trj2pdb/INSTALL

@@ -1,7 +1,9 @@
 CMakeFlags:
   -DCMAKE_INSTALL_PREFIX=         - install prefix (default is '/usr/local')
   -DADD_INCLUDE=1                 - install include files (default is disable)
+  -DADD_DOCS=1                    - install documentation (default is disable)
   -DWITH_DEBUG_MODE=1             - compile with flag '-g' (default is disable)
+  -DMM_PREFIX                     - prefix for mm components (test flag)
 
 Install for Linux:
   mkdir build && cd build

mathmech/mm_trj2pdb/README

@@ -1,5 +1,5 @@
 mm_trj2pdb - program that creates PDB file from trajetory snapshot
-Version: 1.0.1
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_trj2pdb/mm_trj2pdb.cmake

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

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.1.0.1
+PROJECT_NUMBER         = V.1.0.3
 
 # 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 

mathmech/mm_trj2pdb/src/CMakeLists.txt

@@ -1,10 +1,3 @@
-set ("${PROJECT}_VERSION_MAJOR" 1)
-set ("${PROJECT}_VERSION_MINOR" 0)
-set ("${PROJECT}_VERSION_PATCH" 1)
-set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
-
-message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
-
 # set files
 aux_source_directory (. SOURCES)
 
@@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 INSTALL (TARGETS ${PROJECT} DESTINATION bin)
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-endif ()
+endif ()
+if (ADD_DOCS)
+  INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
+endif ()

mathmech/mm_trj2pdb/src/main.c

@@ -59,8 +59,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
+ * V.1.0.3 (2013-08-30)
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
  * V.1.0.1 (2013-07-27)
- * * initial release
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -119,7 +125,7 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_trj2pdb\n");
       sprintf (tmp_str, "%sProgram for create PDB file from trajectory snapshot\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.3                                                    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);

mathmech/mm_trj2pdb/src/messages.c

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

mathmech/update_docs.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+COMPONENTS=( mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb )
+for COMPONENT in ${COMPONENTS[*]}; do
+  cd $COMPONENT
+  doxygen $COMPONENT.doxygen
+  cp logo.png docs/latex
+  cd docs/latex && make && cd ../../../
+  mv $COMPONENT/docs/latex/refman.pdf $COMPONENT/$COMPONENT.pdf
+  rm -rf $COMPONENT/docs
+done