Release 1.0.3

mathmech/AUTHORS

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

mathmech/CMakeLists.txt

@@ -1,6 +1,6 @@
 set ("PROJECT_VERSION_MAJOR" 1)
 set ("PROJECT_VERSION_MINOR" 0)
-set ("PROJECT_VERSION_PATCH" 2)
+set ("PROJECT_VERSION_PATCH" 3)
 set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
 
 message (STATUS "Version ${PROJECT_VERSION}")
@@ -15,10 +15,13 @@ set (COMPS mathmech
 
 # install options
 set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
-if (CMAKE_COMPILER_IS_GNUCXX)
+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")
-else ()
+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()

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
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+
+  To protect your rights, we need to make restrictions that forbid
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+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
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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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+  The precise terms and conditions for copying, distribution and
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+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
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+
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+
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+Foundation.
+
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+
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+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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+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
+
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+Also add information on how to contact you by electronic and paper mail.
+
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+    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
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+
+  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

@@ -2,7 +2,7 @@
 # Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
 
 pkgname=mathmech
-pkgver=1.0.2
+pkgver=1.0.3
 pkgrel=1
 pkgdesc="Software package for analysis of molecular dynamics trajectories"
 arch=(any)
@@ -11,7 +11,7 @@ license=('GPL')
 depends=('qt4' 'qwt')
 makedepends=('unzip' 'cmake' 'automoc4')
 source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
-md5sums=('7c80789a74255108581583830258fe1c')
+md5sums=('4eccb72efd4a8a531d7fda1aabc04f62')
 _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
             -DQWT_INCLUDE_PATH=/usr/include/qwt
             -DMM_PREFIX=mm_

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

@@ -1,3 +1,3 @@
 Mathematical Molecular Mechanics is GUI for "mm" program pack
-Version: 1.0.2
+Version: 1.0.3
 License: GPL

mathmech/mathmech/resources/res_icon.rc

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

mathmech/mathmech/src/CMakeLists.txt

@@ -2,12 +2,15 @@
 file (GLOB SOURCES *.cpp)
 file (GLOB HEADERS *.h)
 file (GLOB FORMS *.ui)
+if (CMAKE_SYSTEM_NAME MATCHES Windows)
+  set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
+endif ()
 # set library
 if (CMAKE_COMPILER_IS_GNUCXX)
   set (LIBRARIES m qwt)
 else ()
   set (LIBRARIES qwt)
-endif()
+endif ()
 set (LANGUAGES
      eng
      rus)
@@ -61,7 +64,11 @@ target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRA
 
 # install properties
 install (TARGETS ${PROJECT} DESTINATION bin)
-install (FILES ../mathmech.desktop
+if (CMAKE_SYSTEM_NAME MATCHES Linux)
-        DESTINATION share/applications/)
+  install (FILES ../mathmech.desktop
-install (FILES ../mathmech-logo.png
+          DESTINATION share/applications/)
-        DESTINATION share/pixmaps/)
+  install (FILES ../mathmech-logo.png
+          DESTINATION share/pixmaps/)
+  install (FILES ../mathmech.png
+          DESTINATION share/icons/hicolor/32x32/apps/)
+endif ()

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];
 

mathmech/mathmech/src/mainwindow.ui

@@ -3715,14 +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">

mathmech/mathmech/src/mathmech.pro.user

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 2.8.1, 2013-08-30T03:38:54. -->
+<!-- Written by QtCreator 2.8.1, 2013-08-30T19:09:45. -->
 <qtcreator>
  <data>
   <variable>ProjectExplorer.Project.ActiveTarget</variable>

mathmech/mm_agl/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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

@@ -1,5 +1,5 @@
 mm_agl - program that creates PDB file with chosen agglomerate
-Version: 1.0.2
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_agl/mm_agl.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

mathmech/mm_agl/mm_agl.doxygen

@@ -32,7 +32,7 @@ PROJECT_NAME           = mm_agl
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = V.1.0.2
+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_agl/src/CMakeLists.txt

@@ -19,4 +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/main.c

@@ -61,8 +61,14 @@
  * You may also download compiled executable file for Win_x86.
  *
  * @page Changelog
- * V.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -128,7 +134,7 @@ int main(int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_agl\n");
       sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.2                                                    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/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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: 1.0.2
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_envir/mm_envir.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

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.1.0.2
+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

@@ -19,4 +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.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <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 : 1.0.2                                                    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/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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 : 1.0.2
+Version : 1.0.3
 License : GPL
 
 Usage:

mathmech/mm_radf/mm_radf.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

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.1.0.2
+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

@@ -19,4 +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.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <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 : 1.0.2                                                    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/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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: 1.0.2
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_statgen/mm_statgen.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

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.1.0.2
+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

@@ -19,4 +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.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <ul>
+ * <li> initial release
+ * </ul>
  */ 
 
 #include <math.h>
@@ -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 : 1.0.2                                                    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/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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 : 1.0.2
+Version : 1.0.3
 License : GPL
 
 Usage:

mathmech/mm_trj/mm_trj.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

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.1.0.2
+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

@@ -19,4 +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.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <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 : 1.0.2                                                    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/CMakeLists.txt

@@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
 
 # set project name
 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)

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: 1.0.2
+Version: 1.0.3
 License: GPL
 
 Usage:

mathmech/mm_trj2pdb/mm_trj2pdb.cmake

@@ -1,8 +1,8 @@
 # set directories
 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}

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.1.0.2
+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

@@ -19,4 +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.1.0.2 (2013-07-27)
+ * V.1.0.3 (2013-08-30)
- * * initial release
+ * <ul>
+ * <li> Bug fixes
+ * </ul>
+ * V.1.0.1 (2013-07-27)
+ * <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 : 1.0.2                                                    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/update_ver.sh

@@ -38,11 +38,10 @@ fi
 # work block
 COMPONENTS=(mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb)
 for COMPONENT in ${COMPONENTS[*]}; do
-  sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/src/main.c
+  sed -i "s/Version : $OLDVER/Version : $NEWVER/g" $COMPONENT/src/main.c
-  sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/README
+  sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
-  sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/$COMPONENT.doxygen
+  sed -i "s/V.$OLDVER/V.$NEWVER/g" $COMPONENT/$COMPONENT.doxygen
 done
 
 COMPONENT=mathmech
-sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/src/main.cpp
+sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
-sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/README