+ added dependecies

+ added oxygen docs building
+ added versioning
* some optimization

mathmech/CMakeLists.txt

@@ -10,6 +10,7 @@ set (PROJECT_VERSION_MAJOR 1)
 set (PROJECT_VERSION_MINOR 2)
 set (PROJECT_VERSION_PATCH 0)
 set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
+configure_file (${CMAKE_SOURCE_DIR}/version.h.in ${CMAKE_CURRENT_BINARY_DIR}/version.h)
 
 message (STATUS "Version ${PROJECT_VERSION}")
 
@@ -25,6 +26,7 @@ set (COMPS mathmech
 set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
 option (WITH_DEBUG_MODE "Build with debug mode" OFF)
 option (ADD_DOCS "Add documentation" OFF)
+option (ADD_INCLUDE "Add include files" 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")
@@ -33,6 +35,25 @@ elseif (CMAKE_SYSTEM_NAME MATCHES Windows)
   set (QWT_LIBRARY_PATH "C:/Qwt-6.1.0/lib" CACHE STRING "Path to qwt library")
 endif ()
 
+# verbose
+set (CMAKE_VERBOSE_MAKEFILE ON)
+
+# flags
+if ( WITH_DEBUG_MODE )
+  add_definitions ( -DDEBUG_MODE=1 )
+endif ()
+if ( CMAKE_COMPILER_IS_GNUCXX )
+  set (ADD_CXX_FLAGS  "-Wall")
+  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
+  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
+  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
+elseif ( MSVC )
+  set (ADD_CXX_FLAGS  "/W4")
+  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
+else ()
+  message ("Unknown compiler")
+endif ()
+
 # set libraries
 set (LIBRARIES mm)
 foreach (LIBRARY ${LIBRARIES})

mathmech/PKGBUILD

@@ -2,7 +2,7 @@
 # Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
 
 pkgname=mathmech
-pkgver=1.1.1
+pkgver=1.2.0
 pkgrel=1
 pkgdesc="Software package for analysis of molecular dynamics trajectories"
 arch=(any)
@@ -11,7 +11,7 @@ license=('GPL')
 depends=('qt4' 'qwt')
 makedepends=('cmake' 'automoc4')
 source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
-md5sums=('6a7f3dd17ae4ad0498110aaaadea5a2b')
+md5sums=('e7d983f602fcfd3f390e72ef684fe5e2')
 _cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
             -DQWT_INCLUDE_PATH=/usr/include/qwt
             -DQWT_LIBRARY_PATH=/usr/lib

mathmech/agl/README

@@ -1,6 +1,4 @@
 agl - program that creates PDB file with chosen agglomerate
-Version: 1.2.0
-License: GPL
 
 Usage:
   agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]

mathmech/agl/agl.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/agl/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/agl/src/main.c

@@ -8,6 +8,7 @@
 #include <string.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/coords.h>
 #include <mathmech/messages.h>
 #include <mathmech/print_struct.h>
@@ -65,7 +66,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/create_archive.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-FILES="docs mathmech mm agl envir radf statgen trj trj2pdb AUTHORS CHANGELOG CMakeLists.txt COPYING docs.cmake INSTALL"
+FILES="docs mathmech mm agl envir radf statgen trj trj2pdb AUTHORS CHANGELOG CMakeLists.txt COPYING docs.cmake doxygen.conf.in INSTALL version.h.in"
 ARCHIVE="mathmech"
 VERSION=`grep -m1 PROJECT_VERSION_MAJOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
 `grep -m1 PROJECT_VERSION_MINOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\

mathmech/docs.cmake

@@ -1,3 +1,14 @@
-# set directory
+# standart documentation
 set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs/)
 install (DIRECTORY ${PROJECT_DOCS_DIR} DESTINATION share/doc/${PROJECT_NAME})
+
+# doxygen documentation
+find_package (Doxygen)
+  if (DOXYGEN_FOUND)
+    set (DOXYGEN_INPUT ${CMAKE_SOURCE_DIR})
+    configure_file (${CMAKE_SOURCE_DIR}/doxygen.conf.in ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
+    add_custom_target (oxygen-docs ALL COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
+    install (DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/docs/ DESTINATION share/doc/${PROJECT_NAME})
+  else (DOXYGEN_FOUND)
+    message (STATUS "WARNING: Doxygen not found - Reference manual will not be created")
+endif ()

mathmech/envir/README

@@ -1,6 +1,4 @@
 envir - program that searchs environment for chosen molecule by geometric criterion
-Version: 1.2.0
-License: GPL
 
 Usage:
   envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 

mathmech/envir/envir.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/envir/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/envir/src/main.c

@@ -8,6 +8,7 @@
 #include <string.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/coords.h>
 #include <mathmech/envir_search.h>
 #include <mathmech/messages.h>
@@ -65,7 +66,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/mathmech/CMakeLists.txt

@@ -3,12 +3,8 @@ set (SUBPROJECT mathmech)
 # set additional cmake file
 include (${SUBPROJECT}.cmake)
 
-
-# additional options
-option (WITH_DEBUG_MODE "Build with debug mode" OFF)
-
 # additional targets
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (${SUBPROJECT_SOURCE_DIR})
+add_subdirectory (${SUBPROJECT_SOURCE_DIR})

mathmech/mathmech/README

@@ -1,3 +1 @@
 Mathematical Molecular Mechanics is GUI for "mm" program pack
-Version: 1.2.0
-License: GPL

mathmech/mathmech/mathmech.cmake

@@ -6,22 +6,3 @@ set (SUBPROJECT_TRANSLATION_DIR ${SUBPROJECT_RESOURCE_DIR}/translations)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/mathmech/resources/translations/eng.ts

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <!DOCTYPE TS>
-<TS version="2.0" language="en">
+<TS version="2.1" language="en">
 <context>
     <name>AboutWindow</name>
     <message>
@@ -29,7 +29,6 @@ p, li { white-space: pre-wrap; }
 &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Liberation Serif&apos;; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
 &lt;p align=&quot;center&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Mathematical Molecular Mechanics&lt;/span&gt;&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
-&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Version:&lt;/span&gt; 1.2.0&lt;/p&gt;
 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;License:&lt;/span&gt; GPL&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Author:&lt;/span&gt; Evgeniy Alekseev&lt;/p&gt;
@@ -852,7 +851,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="184"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -913,7 +912,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the maximum number of different atom types and the log file if this needed.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
@@ -973,7 +972,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;For the variation of geometric criteria you need specify the criteria step changes and the number of steps.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="266"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -1022,7 +1021,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the log file if this needed.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
@@ -1078,7 +1077,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the matrix output, the log file and the graph generate if this needed.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="224"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -1139,7 +1138,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;For the variation of geometric criteria you need specify the criteria step changes and the number of steps.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Run application.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt; {3C?} {4.0/?} {3.?} {40/?} {1&quot;?} {10p?} {400;?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {600;?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {4.?} {0-0:2.4,0-1:3.0&amp;?} {0-0 ?} {2.4 ?} {0-1 ?} {3.0 ?} {3)?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {1;?} {12p?} {0p?} {0p?} {0p?} {0;?} {0p?} {1.1.0&amp;?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {1)?} {1)?} {1)?} {1)?} {1.0000,2.0000,3.0000)?} {1,2,3,4)?} {0, 0 ?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {001)?} {2 ?} {0000001 0000001 ?} {7 ?} {7 ?} {2=?} {1.3.4.?} {1 ?} {1.3.4.?} {0000001=?} {2,3,4,5,?} {1 ?} {7 ?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {2 ?} {0000001 0000002 000003.00 004.00000 0005.00000&lt;?} {7 ?} {7 ?} {9 ?} {2 ?} {9 ?} {5 ?} {10 ?} {5 ?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0.10000)?} {0.10000)?} {0.10000)?} {0.10000)?} {03=?} {0.10000)?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {1;?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {12p?} {12p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {1;?} {12p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {0p?} {0p?} {0p?} {0;?} {0p?} {0p?} {12p?} {0p?} {0p?} {0;?} {0p?}</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="297"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -1196,7 +1195,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Set the matrix output, the log file and the graph generate if this needed.&lt;/li&gt;
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     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="337"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -1271,7 +1270,7 @@ p, li { white-space: pre-wrap; }
         <source>Help about trj2pdb</source>
         <translation>Help about trj2pdb</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="378"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;

mathmech/mathmech/resources/translations/rus.ts

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <!DOCTYPE TS>
-<TS version="2.0" language="ru_RU">
+<TS version="2.1" language="ru_RU">
 <context>
     <name>AboutWindow</name>
     <message>
@@ -29,7 +29,6 @@ p, li { white-space: pre-wrap; }
 &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Liberation Serif&apos;; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
 &lt;p align=&quot;center&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Mathematical Molecular Mechanics&lt;/span&gt;&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
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 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Лицензия:&lt;/span&gt; GPL&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
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@@ -852,7 +851,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;При необходимости указать файл лога.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Запустить приложение.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="184"/>
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 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -913,7 +912,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;При необходимости указать максимальное число различных типов атомов и файл лога.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Запустить приложение.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
@@ -973,7 +972,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Для вариации геометрических критериев необходимо указать шаг изменения критериев и число шагов.&lt;/li&gt;
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Запустить приложение.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="266"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
@@ -1022,7 +1021,7 @@ p, li { white-space: pre-wrap; }
 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;При необходимости указать файл лога.&lt;/li&gt;
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     </message>
-    <message utf8="true">
+    <message>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
@@ -1078,7 +1077,7 @@ p, li { white-space: pre-wrap; }
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 &lt;li align=&quot;justify&quot; style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Запустить приложение.&lt;/li&gt;&lt;/ol&gt;&lt;/body&gt;&lt;/html&gt;</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="224"/>
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     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="297"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
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-    <message utf8="true">
+    <message>
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         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
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@@ -1271,7 +1270,7 @@ p, li { white-space: pre-wrap; }
         <source>Help about trj2pdb</source>
         <translation>Справка по trj2pdb</translation>
     </message>
-    <message utf8="true">
+    <message>
         <location filename="../../../build/mathmech/src/ui_helpwindow.h" line="378"/>
         <source>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
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mathmech/mm/README

@@ -1,3 +1 @@
 libmm is a library for "mm" project
-Version: 1.2.0
-License: GPL

mathmech/mm/mm.cmake

@@ -5,22 +5,3 @@ set (SUBPROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
 # include_path
 include_directories (${SUBPROJECT_INCLUDE_DIR}
                      ${SUBPROJECT_SOURCE_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/mm/src/CMakeLists.txt

@@ -15,8 +15,11 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_library (${SUBPROJECT} SHARED ${SOURCES} ${HEADERS})
+set_target_properties (${SUBPROJECT} PROPERTIES SOVERSION ${PROJECT_VERSION})
 target_link_libraries (${SUBPROJECT} ${ADDITIONAL_LIB})
 
 # install properties
 install (TARGETS ${SUBPROJECT} DESTINATION lib)
-install (DIRECTORY ${SUBPROJECT_INCLUDE_DIR}/ DESTINATION include/)
+if (ADD_INCLUDE)
+  install (DIRECTORY ${SUBPROJECT_INCLUDE_DIR}/ DESTINATION include/)
+endif ()

mathmech/radf/README

@@ -1,7 +1,5 @@
 radf - program that calculates radial distribution function (RDF) or radial-angles 
 distribution function (RADF)
-Version : 1.1.1
-License : GPL
 
 Usage:
   radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 

mathmech/radf/radf.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/radf/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/radf/src/add_main.c

@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 
+#include <version.h>
 #include <mathmech/messages.h>
 
 
@@ -127,7 +128,7 @@ int printing_head (const char *output, const int log, const int quiet, const int
   FILE *f_out;
   
   f_out = fopen (output, "w");
-  fprintf (f_out, "radf ::: V.1.2.0\n\n");
+  fprintf (f_out, "radf ::: V.%s\n\n", PROJ_VERSION);
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix);

mathmech/radf/src/main.c

@@ -8,6 +8,7 @@
 #include <string.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/coords.h>
 #include <mathmech/messages.h>
 #include <mathmech/radf.h>
@@ -75,7 +76,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/statgen/README

@@ -1,6 +1,4 @@
 statgen - program that analyzes molecular dynamic trajectories using topological analysis
-Version: 1.2.0
-License: GPL
 
 Usage:
   statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] 

mathmech/statgen/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/statgen/src/add_main.c

@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 
+#include <version.h>
 #include <mathmech/messages.h>
 
 
@@ -92,7 +93,7 @@ int printing_head (const char *output, const int log, const int quiet,
   FILE *f_out;
   
   f_out = fopen (output, "w");
-  fprintf (f_out, "statgen ::: V.1.2.0\n\n");
+  fprintf (f_out, "statgen ::: V.%s\n\n", PROJ_VERSION);
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);

mathmech/statgen/src/main.c

@@ -9,6 +9,7 @@
 #include <time.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/coords.h>
 #include <mathmech/messages.h>
 #include <mathmech/stat_print.h>
@@ -94,7 +95,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/statgen/statgen.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/trj/README

@@ -1,6 +1,4 @@
 trj - program that generates trajectory files
-Version : 1.1.1
-License : GPL
 
 Usage:
   trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]

mathmech/trj/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/trj/src/main.c

@@ -8,6 +8,7 @@
 #include <string.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/atom_types.h>
 #include <mathmech/messages.h>
 #include <mathmech/print_trj.h>
@@ -62,7 +63,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/trj/trj.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/trj2pdb/README

@@ -1,6 +1,4 @@
 trj2pdb - program that creates PDB file from trajetory snapshot
-Version: 1.2.0
-License: GPL
 
 Usage:
   trj2pdb -i FILENAME -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]

mathmech/trj2pdb/src/CMakeLists.txt

@@ -15,6 +15,7 @@ message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
 
 # link libraries and compile
 add_executable (${MM_PREFIX}${SUBPROJECT} ${SOURCES} ${HEADERS})
+add_dependencies (${MM_PREFIX}${SUBPROJECT} ${LIBRARIES})
 target_link_libraries (${MM_PREFIX}${SUBPROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
 
 # install properties

mathmech/trj2pdb/src/main.c

@@ -8,6 +8,7 @@
 #include <string.h>
 
 #include "add_main.h"
+#include <version.h>
 #include <mathmech/coords.h>
 #include <mathmech/messages.h>
 #include <mathmech/print_struct.h>
@@ -58,7 +59,7 @@ 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 : 1.2.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : %s                                                    License : GPL\n", tmp_str, PROJ_VERSION);
       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/trj2pdb/trj2pdb.cmake

@@ -3,26 +3,8 @@ set (SUBPROJECT_BINARY_DIR bin)
 set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # include_path
-include_directories (${SUBPROJECT_SOURCE_DIR})
+include_directories (${SUBPROJECT_SOURCE_DIR}
+                     ${CMAKE_CURRENT_BINARY_DIR}/../)
 
 # executable path
 set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
-
-# verbose
-set (CMAKE_VERBOSE_MAKEFILE ON)
-
-# flags
-if ( WITH_DEBUG_MODE )
-  add_definitions ( -DDEBUG_MODE=1 )
-endif ()
-if ( CMAKE_COMPILER_IS_GNUCXX )
-  set (ADD_CXX_FLAGS  "-Wall")
-  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
-  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
-  set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-elseif ( MSVC )
-  set (ADD_CXX_FLAGS  "/W4")
-  set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
-else ()
-  message ("Unknown compiler")
-endif ()

mathmech/update_ver.sh

@@ -1,58 +0,0 @@
-#!/bin/bash
-func_help() {
-  echo -e "\nUsage: update_ver.sh -o OLDVER -n NEWVER"
-  echo -e "\nRequired parameters:"
-  echo -e "  -o  --oldver      - old version"
-  echo -e "  -n  --newver      - new version"
-  echo -e "\nAdditional parametrs:"
-  echo -e "  -h  --help        - show this help and exit"
-  exit 0
-}
-
-until [ -z $1 ]; do
-  if [ "$1" = "-h" ]; then
-    func_help; fi
-  if [ "$1" = "--help" ]; then
-    func_help; fi
-  if [ "$1" = "-o" ]; then
-    OLDVER="$2"
-    shift; fi
-  if [ "$1" = "--oldver" ]; then
-   OLDVER="$2"
-    shift; fi
-  if [ "$1" = "-n" ]; then
-    NEWVER="$2"
-    shift; fi
-  if [ "$1" = "--newver" ]; then
-    NEWVER="$2"
-    shift; fi
-  shift
-done
-
-if [[ -z "$OLDVER" || -z "$NEWVER" ]]; then
-  echo "Parametrs aren't set"
-  echo "Usage: update_ver.sh -o OLDVER -n NEWVER" 
-  exit 1
-fi
-
-# work block
-COMPONENTS=(agl envir radf statgen trj trj2pdb)
-for COMPONENT in ${COMPONENTS[*]}; do
-# help message
-  sed -i "s/Version : $OLDVER/Version : $NEWVER/g" $COMPONENT/src/main.c
-# head in output
-  sed -i "s/V.$OLDVER/V.$NEWVER/g" $COMPONENT/src/add_main.c
-# readme
-  sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
-done
-
-COMPONENT=mm
-# readme
-sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
-
-COMPONENT=mathmech
-# about window
-sed -i "s/$OLDVER/$NEWVER/g" $COMPONENT/resources/translations/eng.ts
-sed -i "s/$OLDVER/$NEWVER/g" $COMPONENT/resources/translations/rus.ts
-# readme
-sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README

mathmech/version.h.in

@@ -0,0 +1,12 @@
+/**
+ * @file
+ */
+
+#ifndef VERSION_H
+#define VERSION_H
+
+#ifndef PROJ_VERSION
+#define PROJ_VERSION "@PROJECT_VERSION@"
+#endif /* PROJ_VERSION */
+
+#endif /* VERSION_H */