Edited documentation

agl/CMakeLists.txt

@@ -1,7 +1,8 @@
 cmake_minimum_required (VERSION 2.8)
 
-cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0003 OLD)
+cmake_policy(SET CMP0011 NEW)
+cmake_policy(SET CMP0015 NEW)
 
 # set project name
 set (PROJECT agl)
@@ -28,4 +29,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (src)
+add_subdirectory (${${PROJECT}_SOURCE_DIR})

agl/README

@@ -0,0 +1,15 @@
+agl - program that creates PDB file with chosen aglomerate
+Version: 1.0.1
+License: GPL
+
+Usage:
+  agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
+
+Parametrs:
+  -a          - input file with aglomerates (in format statgen)
+  -i          - input file with coordinates
+  -c          - cell size (float), A
+  -o          - output file with coordinates
+  -l          - log enable
+  -q          - quiet enable
+  -h          - show this help and exit

agl/about.dox

@@ -0,0 +1,63 @@
+/*! 
+ * @mainpage agl
+ * @image latex ./logo.png
+ *
+ * @section intro_sec Introduction
+ *
+ * <b>About this program</b>:
+ * <ul>
+ * <li>Program that creates PDB file with chosen aglomerate
+ * </ul>
+ *
+ * <b>Developer</b>:
+ * <ul>
+ * <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
+ *</ul>
+ * <b>License</b>:
+ * <ul>
+ * <li>GPL
+ * </ul>
+ *
+ * @section How-To-Use How to use
+ * Usage:
+ * <pre>
+ * agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
+ *
+ * Parametrs:
+ *    -a          - input file with aglomerates (in format statgen)
+ *    -i          - input file with coordinates
+ *    -c          - cell size (float), A
+ *    -o          - output file with coordinates
+ *    -l          - log enable
+ *    -q          - quiet enable
+ *    -h          - show this help and exit
+ * </pre>
+ * 
+ * @page Install
+ * 
+ * @section Requirements Requirements
+ * The application statgen requires the following external stuff:
+ * - cmake  >= 2.8
+ * - gcc    >= 4.8
+ *
+ * @section How-To How to install
+ *
+ * @subsection Linux Linux
+ * @code
+ * mkdir build && cd build
+ * cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
+ * make
+ * make install
+ * @endcode
+ * 
+ * @subsection Windows Windows
+ * @code
+ * create project file using 'cmake'
+ * compile project
+ * @endcode
+ * You may also download compiled executable file for Win_x86.
+ *
+ * @page Changelog
+ * V.1.0.1 (2013-07-27)
+ * * initial release
+ */ 

agl/agl.cmake

@@ -1,22 +1,32 @@
 # set directories
 set (${PROJECT}_BINARY_DIR bin)
-set (${PROJECT}_SOURCE_DIR src:include)
+set (${PROJECT}_SOURCE_DIR src)
+set (${PROJECT}_INCLUDE_DIR include)
 set (${PROJECT}_LIB_DIR lib)
 
-set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
+# include_path
-set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
+include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
+                     ${${PROJECT}_SOURCE_DIR})
+# library path
+link_directories (${${PROJECT}_LIB_DIR})
+# executable path
 set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
+
+# verbose
 set (CMAKE_VERBOSE_MAKEFILE ON)
 
+# flags
 if ( WITH_DEBUG_MODE )
-  ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
+  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 (STATUS "Flags not enabled")
+  message ("Unknown compiler")
 endif ()

agl/src/CMakeLists.txt

@@ -3,59 +3,27 @@ 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})
+message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
 
-## set files
+# set files
-# main files
+aux_source_directory (. SOURCES)
-set (MAIN_SOURCES main)
+
-# not public srcs
+# set library
-set (PRIVATE_CLASSES)
-# headers only files
-SET (HEADERS_ONLY)
-# public srcs
-set (PUBLIC_CLASSES add_main 
-                    coords 
-                    envir_search 
-                    messages 
-                    print_struct 
-                    set_center)
-# public headers
-set (PUBLIC_HEADERS)
-# shared libraries
 if (CMAKE_COMPILER_IS_GNUCXX)
   set (ADDITIONAL_LIB m)
 else ()
   set (ADDITIONAL_LIB)
 endif()
-set (SOURCES)
-
-# append list
-foreach (class ${PRIVATE_CLASSES})
-  LIST (APPEND SOURCES ${class}.c)
-  LIST (APPEND HEADERS ${class}.h)
-endforeach ()
-
-foreach (class ${HEADERS_ONLY})
-  LIST (APPEND HEADERS ${class}.h)
-endforeach ()
-
-foreach (class ${PUBLIC_CLASSES})
-  LIST (APPEND SOURCES ${class}.c)
-  LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
-  LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
-endforeach ()
 
 # message
 message (STATUS "SOURCES: ${SOURCES}")
 
 # link libraries and compile
-add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 
 # install properties
-INSTALL (TARGETS ${PROJECT} 
+INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-         DESTINATION bin)
 if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} 
+  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-           DESTINATION include/${PROJECT})
 endif ()

agl/src/coords.c

@@ -1,52 +1,67 @@
-/* Library for reading coordinates from input file
+/**
- * 
+ * @file
- * Usage:
- *                    reading_coords (mode, filename, type_interaction, labels, 
- *            cell, &number_of_molecules, &number_of_atoms, true_label_molecule, 
- *                          label_molecule, type_atoms, coords, char_type_atoms)
  */
 
 #include <stdio.h>
 #include <stdlib.h>
 
-
+/**
+ * @fn reading_coords
+ */
 int reading_coords (const int mode, const char *filename, const int type_inter, 
                     const int *label_atom, const float *cell, int *num_mol, 
                     int *num_atoms, int *true_label_mol, int *label_mol, 
                     int *type_atoms, float *coords, char *ch_type_atoms)
-/* filename         - name of file with coordinates
+/**
- * type_inter       - type interaction (number of molecules for interaction) 
+ * @brief function that reads coordinates from special file format
- *                    (number of molecules in aglomerate for agl)
+ * @code
- * label_atom       - types of atom for interaction 
+ * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms, 
- *                    (molecules in aglomerate for agl)
+ *                 true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
- * cell             - cell dimension
+ * @endcode
- * num_mol          - number of molecules for writing coordinates
+ * 
- * num_atoms        - number of atoms for writing coordinates
+ * @param mode            mode of reading; '1' is statgen, '2' is envir or 
- * true_label_mol   - massive of true numbers of molecule for atoms
+ *                        frad, '3' is agl
- * label_mol        - massive of numbers of molecule for atoms
+ * @param filename        input file name
- * type_atoms       - massive of atom types for atoms
+ * @param type_inter      number of needed atoms
- * coords           - massive of coordinates
+ *                        (number of needed molecules)
- * ch_type_atoms    - massive of char types for atoms
+ * @param label_atom      massive of needed atom types
+ *                        (massive of needed molecules)
+ * @param cell            massive of cell size
+ * @param num_mol         number of molecules
+ * @param num_atoms       number of atoms
+ * @param true_label_mol  massive of true numbers of molecule for atoms
+ * @param label_mol       massive of numbers of molecule for atoms
+ * @param type_atoms      massive of atom types
+ * @param coords          massive of coordinates
+ * @param ch_type_atoms   massive of char atom types
+ * 
+ * @return 1              - file $filename does not exist
+ * @return 2              - unknown mode
+ * @return 0              - exit without errors
  */
 {
   char at_symb[32], file_string[256];
   int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
   float cur_coords[3], *not_tr_coords, ref[3];
   FILE *inp;
-/* cur_*, at_symb   - temp variables
+  
- * file_string      - temp string variable
+/* cur_*                  temp variables
- * atoms            - total number of atoms in system
+ * at_symb                temp variable
- * tr_num_atoms     - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
+ * file_string            temp string variable
- * ref_mol          - number of molecule for reference
+ * atoms                  total number of atoms in system
- * not_tr_coords    - not translated coordinates
+ * tr_num_atoms           number of translated atoms (must be 8*num_atoms)
- * ref              - coordinates of reference molecule
+ * ref_mol                number of molecule for reference in translation
- * inp              - file with input data
+ * not_tr_coords          massive of not translated coordinates
+ * ref                    massive of coordinates of reference molecule
+ * inp                    input file
  */
   
+/// <b>Work blocks</b>
+  
   *num_atoms = 0;
   *num_mol = 0;
   
-//   Reading file
+/// <pre>   reading file </pre>
   inp = fopen (filename, "r");
   if (inp == NULL)
     return 1;
@@ -61,10 +76,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
     sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0], 
             &cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
     
+// reading variables according to selected mode
     switch (mode)
     {
       case 0:
-//         for statgen
+// mode == 0 (selected atoms)
         for (j=0; j<type_inter; j++)
           if (cur_at_type == label_atom[j])
           {
@@ -85,7 +101,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
           }
         break;
       case 1:
-//         for envir and frad
+// mode == 1 (all atoms)
         not_tr_coords[3**num_atoms+0] = cur_coords[0];
         not_tr_coords[3**num_atoms+1] = cur_coords[1];
         not_tr_coords[3**num_atoms+2] = cur_coords[2];
@@ -104,7 +120,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
         *num_atoms = *num_atoms + 1;
         break;
       case 2:
-//         for agl
+// mode == 2 (selected molecules)
         for (j=0; j<type_inter; j++)
           if (cur_mol == label_atom[j])
           {
@@ -126,18 +142,18 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
             *num_atoms = *num_atoms + 1;
           }
         break;
-      default: return 1;
+      default: return 2;
     }
   }
   fclose (inp);
   
-//   Translation
+/// <pre>   translation </pre>
   tr_num_atoms = *num_atoms;
   for (i=0; i<*num_atoms; i++)
     for (j=0; j<3; j++)
       coords[3*i+j] = not_tr_coords[3*i+j];
   
-//   Assign initial value to reference coordinates
+// assign initial value to reference coordinates
   ref_mol = label_mol[0];
   for (i=0; i<3; i++)
     ref[i] = coords[3*0+i];
@@ -331,7 +347,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
     }
   }
   
-//   free memory
+/// <pre>   free memory </pre>
   free (not_tr_coords);
   
   return 0;

agl/src/main.c

@@ -46,7 +46,7 @@ int main(int argc, char *argv[])
     if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
     {
       sprintf (tmp_str, "                                        agl\n");
-      sprintf (tmp_str, "%sProgram for create PDB file with choosen aglomerate\n", tmp_str);
+      sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
       sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);

agl/src/messages.c

@@ -1,16 +1,27 @@
-/* Library for printing messages at output
+/**
- *
+ * @file
- * Usage:
- *                                             message (log, mode, text, output)
  */
 
 #include <stdio.h>
 #include <time.h>
 
 
+/**
+ * @fn message
+ */
 int message (const int log, const int mode, const char *text, FILE *output)
-/* mode             - number of message
+/**
- * text             - additional text
+ * @brief function that prints messages to output
+ * @code
+ * message (log, mode, text, output);
+ * @endcode
+ * 
+ * @param log             equal to 1 if print to logfile
+ * @param mode            number of message
+ * @param text            additional text
+ * @param output          output file (may be stdout)
+ * 
+ * @return 0              - exit without errors
  */
 {
   char out[4096];
@@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
   if (log == 1)
   {
     char time_str[256];
+    
     time_t t = time (NULL);
     struct tm* aTm = localtime (&t);
     sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900, 

agl/src/print_struct.c

@@ -1,3 +1,7 @@
+/**
+ * @file
+ */
+
 /* Library for printing structure to pdb file
  * 
  * Usage:
@@ -8,23 +12,37 @@
 #include <stdio.h>
 
 
+/**
+ * @fn print_structure
+ */
 int print_structure (const char *output, const int num_needed_mol, const int *needed_mol, 
                      const int num_atoms, const int *label_mol, const char *ch_type_atoms, 
                      const float *coords)
-/* output           - output file name
+/**
- * num_needed_mol   - number of needed molecules
+ * @brief function that prints structure to pdb file
- * needed_mol       - massive of needed molecules
+ * @code
- * num_atoms        - number of atoms
+ * print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol, 
- * label_mol        - massive of numbers of molecule for atoms
+ *                  char_type_atoms, coords);
- * ch_type_atoms    - massive of char types for atoms
+ * @endcode
- * coords           - massive of coordinates
+ * 
+ * @param output          output file name
+ * @param num_needed_mol  number of needed molecules
+ * @param needed_mol      massive of number of needed molecules
+ * @param num_atoms       number of atoms
+ * @param label_mol       massive of numbers of molecule for atoms
+ * @param ch_type_atoms   massive of char atom types
+ * @param coords          massive of coordinates
+ * 
+ * @return 0              - exit without errors
  */
 {
   int cur_atom, cur_atom_num, cur_mol, i, j;
   FILE *f_out;
-/* cur_atom         - current atom
+  
- * cur_atom_num     - true atom number
+/* cur_atom               current atom
- * cur_mol          - current molecule
+ * cur_atom_num           true atom number
+ * cur_mol                current molecule
+ * f_out                  output file
  */
   
   cur_atom = 1;

en_disp/ca.txt

@@ -0,0 +1,300 @@
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en_disp/no.csv

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en_disp/no.txt

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envir/CMakeLists.txt

@@ -1,7 +1,8 @@
 cmake_minimum_required (VERSION 2.8)
 
-cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0003 OLD)
+cmake_policy(SET CMP0011 NEW)
+cmake_policy(SET CMP0015 NEW)
 
 # set project name
 set (PROJECT envir)
@@ -28,4 +29,4 @@ set (LIBRARIES)
 set (TARGETS "")
 set (HEADERS "")
 
-add_subdirectory (src)
+add_subdirectory (${${PROJECT}_SOURCE_DIR})

envir/README

@@ -1,4 +1,4 @@
-envir - program for search environment for chosen molecule by geometric criterion
+envir - program that searchs environment for chosen molecule by geometric criterion
 Version: 1.0.1
 License: GPL
 

envir/about.dox

@@ -0,0 +1,65 @@
+/*! 
+ * @mainpage envir
+ * @image latex ./logo.png
+ *
+ * @section intro_sec Introduction
+ *
+ * <b>About this program</b>:
+ * <ul>
+ * <li>Program that searchs environment for chosen molecule by geometric criterion
+ * </ul>
+ *
+ * <b>Developer</b>:
+ * <ul>
+ * <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
+ *</ul>
+ * <b>License</b>:
+ * <ul>
+ * <li>GPL
+ * </ul>
+ *
+ * @section How-To-Use How to use
+ * Usage:
+ * <pre>
+ * envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
+ *                                                   [ -l LOGFILE] [ -q ] [ -h ]
+ *
+ * Parametrs:
+ *    -i          - input file with coordinates
+ *    -c          - cell size (float), A
+ *    -o          - output file with coordinates
+ *    -n          - number of molecule for search (integer). Default is 1
+ *    -r          - radius of environment (float). Default is 6.0
+ *    -l          - log enable
+ *    -q          - quiet enable
+ *    -h          - show this help and exit
+ * </pre>
+ * 
+ * @page Install
+ * 
+ * @section Requirements Requirements
+ * The application statgen requires the following external stuff:
+ * - cmake  >= 2.8
+ * - gcc    >= 4.8
+ *
+ * @section How-To How to install
+ *
+ * @subsection Linux Linux
+ * @code
+ * mkdir build && cd build
+ * cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
+ * make
+ * make install
+ * @endcode
+ * 
+ * @subsection Windows Windows
+ * @code
+ * create project file using 'cmake'
+ * compile project
+ * @endcode
+ * You may also download compiled executable file for Win_x86.
+ *
+ * @page Changelog
+ * V.1.0.1 (2013-07-27)
+ * * initial release
+ */ 

envir/envir.cmake

@@ -1,22 +1,32 @@
 # set directories
 set (${PROJECT}_BINARY_DIR bin)
-set (${PROJECT}_SOURCE_DIR src:include)
+set (${PROJECT}_SOURCE_DIR src)
+set (${PROJECT}_INCLUDE_DIR include)
 set (${PROJECT}_LIB_DIR lib)
 
-set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
+# include_path
-set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
+include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
+                     ${${PROJECT}_SOURCE_DIR})
+# library path
+link_directories (${${PROJECT}_LIB_DIR})
+# executable path
 set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
+
+# verbose
 set (CMAKE_VERBOSE_MAKEFILE ON)
 
+# flags
 if ( WITH_DEBUG_MODE )
-  ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
+  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 (STATUS "Flags not enabled")
+  message ("Unknown compiler")
 endif ()

envir/src/CMakeLists.txt

@@ -3,59 +3,27 @@ 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})
+message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
 
-## set files
+# set files
-# main files
+aux_source_directory (. SOURCES)
-set (MAIN_SOURCES main)
+
-# not public srcs
+# set library
-set (PRIVATE_CLASSES add_main 
-                     coords 
-                     envir_search 
-                     messages 
-                     print_struct 
-                     set_center)
-# headers only files
-SET (HEADERS_ONLY)
-# public srcs
-set (PUBLIC_CLASSES)
-# public headers
-set (PUBLIC_HEADERS)
-# shared libraries
 if (CMAKE_COMPILER_IS_GNUCXX)
   set (ADDITIONAL_LIB m)
 else ()
   set (ADDITIONAL_LIB)
 endif()
-set (SOURCES)
-
-# append list
-foreach (class ${PRIVATE_CLASSES})
-  LIST (APPEND SOURCES ${class}.c)
-  LIST (APPEND HEADERS ${class}.h)
-endforeach ()
-
-foreach (class ${HEADERS_ONLY})
-  LIST (APPEND HEADERS ${class}.h)
-endforeach ()
-
-foreach (class ${PUBLIC_CLASSES})
-  LIST (APPEND SOURCES ${class}.c)
-  LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
-  LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
-endforeach ()
 
 # message
 message (STATUS "SOURCES: ${SOURCES}")
 
 # link libraries and compile
-add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
+add_executable (${PROJECT} ${SOURCES})
 target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
 
 # install properties
-INSTALL (TARGETS ${PROJECT} 
+INSTALL (TARGETS ${PROJECT} DESTINATION bin)
-         DESTINATION bin)
 if (ADD_INCLUDE)
-  INSTALL (FILES ${PUBLIC_HEADERS} 
+  INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
-           DESTINATION include/${PROJECT})
 endif ()

envir/src/add_main.c

@@ -1,4 +1,5 @@
-/* Additional library for main.c (envir)
+/**
+ * @file
  */
 
 #include <stdio.h>
@@ -6,7 +7,25 @@
 #include "messages.h"
 
 
+/**
+ * @fn error_checking
+ */
 int error_checking (const float *cell, const char *input, const char *output)
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (cell, input, output);
+ * @endcode
+ * 
+ * @param cell            massive of cell size
+ * @param input           first trajectory step
+ * @param output          last trajectory step
+ * 
+ * @return 11             - error in 'cell'
+ * @return 12             - error in 'input'
+ * @return 13             - error in 'output'
+ * @return 0              - exit without errors
+ */
 {
   if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
     return 11;
@@ -19,8 +38,26 @@ int error_checking (const float *cell, const char *input, const char *output)
 }
 
 
+/**
+ * @fn print_message
+ */
 int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, 
                    const int mode, const char *str)
+/**
+ * @brief function that prints message in log and stdout
+ * @code
+ * print_message (quiet, stdout, log, f_log, 0, str);
+ * @endcode
+ * 
+ * @param quiet           status of quiet-mode
+ * @param std_output      stdout
+ * @param log             status of log-mode
+ * @param f_log           log file
+ * @param mode            number of message in "messages.c"
+ * @param str             additional text in message
+ * 
+ * @return 0              - exit without errors
+ */
 {
   if ((quiet != 1) && (std_output != stderr))
     message (0, mode, str, std_output);
@@ -31,8 +68,28 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 }
 
 
+/**
+ * @fn set_defaults
+ */
 int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output, 
                   int *quiet, float *rad)
+/**
+ * @brief function for set default values of variables
+ * @code
+ * set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
+ *               &type_inter, &quiet);
+ * @endcode
+ * 
+ * @param cell            massive of cell size
+ * @param input           mask of trajectory files
+ * @param log             status of log-mode
+ * @param num_of_mol      number of molecule
+ * @param output          output file name
+ * @param quiet           status of quiet-mode
+ * @param rad             radius of environment sphere
+ * 
+ * @return 0              - exit without errors
+ */
 {
   int i;
   

envir/src/add_main.h

@@ -1,6 +1,20 @@
+/**
+ * @file
+ */
+
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+/**
+ * @fn error_checking
+ */
+/**
+ * @fn print_message
+ */
+/**
+ * @fn set_defaults
+ */
+
 int error_checking (const float *, const char *, const char *);
 int print_message (const int, FILE *, const int, FILE *, const int, const char *);
 int set_defaults (float *, char *, int *, int *, char *, int *, float *);

envir/src/coords.c

@@ -1,52 +1,67 @@
-/* Library for reading coordinates from input file
+/**
- * 
+ * @file
- * Usage:
- *                    reading_coords (mode, filename, type_interaction, labels, 
- *            cell, &number_of_molecules, &number_of_atoms, true_label_molecule, 
- *                          label_molecule, type_atoms, coords, char_type_atoms)
  */
 
 #include <stdio.h>
 #include <stdlib.h>
 
-
+/**
+ * @fn reading_coords
+ */
 int reading_coords (const int mode, const char *filename, const int type_inter, 
                     const int *label_atom, const float *cell, int *num_mol, 
                     int *num_atoms, int *true_label_mol, int *label_mol, 
                     int *type_atoms, float *coords, char *ch_type_atoms)
-/* filename         - name of file with coordinates
+/**
- * type_inter       - type interaction (number of molecules for interaction) 
+ * @brief function that reads coordinates from special file format
- *                    (number of molecules in aglomerate for agl)
+ * @code
- * label_atom       - types of atom for interaction 
+ * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms, 
- *                    (molecules in aglomerate for agl)
+ *                 true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
- * cell             - cell dimension
+ * @endcode
- * num_mol          - number of molecules for writing coordinates
+ * 
- * num_atoms        - number of atoms for writing coordinates
+ * @param mode            mode of reading; '1' is statgen, '2' is envir or 
- * true_label_mol   - massive of true numbers of molecule for atoms
+ *                        frad, '3' is agl
- * label_mol        - massive of numbers of molecule for atoms
+ * @param filename        input file name
- * type_atoms       - massive of atom types for atoms
+ * @param type_inter      number of needed atoms
- * coords           - massive of coordinates
+ *                        (number of needed molecules)
- * ch_type_atoms    - massive of char types for atoms
+ * @param label_atom      massive of needed atom types
+ *                        (massive of needed molecules)
+ * @param cell            massive of cell size
+ * @param num_mol         number of molecules
+ * @param num_atoms       number of atoms
+ * @param true_label_mol  massive of true numbers of molecule for atoms
+ * @param label_mol       massive of numbers of molecule for atoms
+ * @param type_atoms      massive of atom types
+ * @param coords          massive of coordinates
+ * @param ch_type_atoms   massive of char atom types
+ * 
+ * @return 1              - file $filename does not exist
+ * @return 2              - unknown mode
+ * @return 0              - exit without errors
  */
 {
   char at_symb[32], file_string[256];
   int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
   float cur_coords[3], *not_tr_coords, ref[3];
   FILE *inp;
-/* cur_*, at_symb   - temp variables
+  
- * file_string      - temp string variable
+/* cur_*                  temp variables
- * atoms            - total number of atoms in system
+ * at_symb                temp variable
- * tr_num_atoms     - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
+ * file_string            temp string variable
- * ref_mol          - number of molecule for reference
+ * atoms                  total number of atoms in system
- * not_tr_coords    - not translated coordinates
+ * tr_num_atoms           number of translated atoms (must be 8*num_atoms)
- * ref              - coordinates of reference molecule
+ * ref_mol                number of molecule for reference in translation
- * inp              - file with input data
+ * not_tr_coords          massive of not translated coordinates
+ * ref                    massive of coordinates of reference molecule
+ * inp                    input file
  */
   
+/// <b>Work blocks</b>
+  
   *num_atoms = 0;
   *num_mol = 0;
   
-//   Reading file
+/// <pre>   reading file </pre>
   inp = fopen (filename, "r");
   if (inp == NULL)
     return 1;
@@ -61,10 +76,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
     sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0], 
             &cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
     
+// reading variables according to selected mode
     switch (mode)
     {
       case 0:
-//         for statgen
+// mode == 0 (selected atoms)
         for (j=0; j<type_inter; j++)
           if (cur_at_type == label_atom[j])
           {
@@ -85,7 +101,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
           }
         break;
       case 1:
-//         for envir and frad
+// mode == 1 (all atoms)
         not_tr_coords[3**num_atoms+0] = cur_coords[0];
         not_tr_coords[3**num_atoms+1] = cur_coords[1];
         not_tr_coords[3**num_atoms+2] = cur_coords[2];
@@ -104,7 +120,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
         *num_atoms = *num_atoms + 1;
         break;
       case 2:
-//         for agl
+// mode == 2 (selected molecules)
         for (j=0; j<type_inter; j++)
           if (cur_mol == label_atom[j])
           {
@@ -126,18 +142,18 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
             *num_atoms = *num_atoms + 1;
           }
         break;
-      default: return 1;
+      default: return 2;
     }
   }
   fclose (inp);
   
-//   Translation
+/// <pre>   translation </pre>
   tr_num_atoms = *num_atoms;
   for (i=0; i<*num_atoms; i++)
     for (j=0; j<3; j++)
       coords[3*i+j] = not_tr_coords[3*i+j];
   
-//   Assign initial value to reference coordinates
+// assign initial value to reference coordinates
   ref_mol = label_mol[0];
   for (i=0; i<3; i++)
     ref[i] = coords[3*0+i];
@@ -331,7 +347,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
     }
   }
   
-//   free memory
+/// <pre>   free memory </pre>
   free (not_tr_coords);
   
   return 0;

envir/src/coords.h

@@ -1,6 +1,14 @@
+/**
+ * @file
+ */
+
 #ifndef COORDS_H
 #define COORDS_H
 
+/**
+ * @fn reading_coords
+ */
+
 int reading_coords (const int, const char *, const int, const int *, 
                     const float *, int *, int *, int *, int *, int *, float *, 
                     char *);

envir/src/envir_search.c

@@ -1,3 +1,7 @@
+/**
+ * @file
+ */
+
 /* Library for search environment
  * 
  * Usage:
@@ -8,19 +12,32 @@
 #include <math.h>
 
 
+/**
+ * @fn search_envir
+ */
 int search_envir (const int num_of_mol, const int num_mol, const float *centr_coords, 
                   const double rad, int *needed_mol, int *num_needed_mol)
-/* num_of_mol       - number of molecule for search
+/**
- * num_mol          - number of molecules for writing coordinates
+ * @brief function that searchs environment
- * centr_coords     - massive of centered coordinates
+ * @code
- * rad              - criterion
+ * search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol, 
- * needed_mol       - massive of needed molecules
+ *               &num_needed_mol);
- * num_needed_mol   - number of needed molecules
+ * @endcode
+ * 
+ * @param num_of_mol      number of molecule
+ * @param num_mol         number of molecules
+ * @param centr_coords    massive of centered coordinates
+ * @param rad             radius of environment sphere
+ * @param needed_mol      massive of number of needed molecules
+ * @param num_needed_mol  number of needed molecules
+ * 
+ * @return 0              - exit without errors
  */
 {
   float r;
   int i;
-/* r                - radius
+  
+/* r                      radius
  */
   
   *num_needed_mol = 0;

envir/src/envir_search.h

@@ -1,6 +1,14 @@
+/**
+ * @file
+ */
+
 #ifndef ENVIR_SEARCH_H
 #define ENVIR_SEARCH_H
 
+/**
+ * @fn search_envir
+ */
+
 int search_envir (const int, const int, const float *, const double, int *, int *);
 
 #endif /* ENVIR_SEARCH_H */

envir/src/main.c

@@ -1,3 +1,7 @@
+/**
+ * @file
+ */
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -11,7 +15,16 @@
 #include "set_center.h"
 
 
+/**
+ * @fn main
+ */
 int main(int argc, char *argv[])
+/**
+ * @return 1              - error in error_checking
+ * @return 2              - input file does not exist
+ * @return 3              - memory error
+ * @return 0              - exit without errors
+ */
 {
   char tmp_str[2048];
   int error, i, j, *tmp_int;
@@ -21,25 +34,26 @@ int main(int argc, char *argv[])
   float cell[3], *centr_coords, *coords, rad;
   int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol, 
       *needed_mol, quiet, *true_label_mol;
-/* ch_type_atoms    - massive of char types for atoms
+  
- * input            - input file name
+/* ch_type_atoms          massive of char atom types
- * logfile          - log file name
+ * input                  input file name
- * output           - output file name
+ * logfile                log file name
+ * output                 output file name
  * 
- * cell             - cell dimension
+ * cell                   massive of cell size
- * centr_coords     - massive of coordinates of center molecules
+ * centr_coords           massive of centered coordinates
- * coords           - massive of coordinates
+ * coords                 massive of coordinates
- * rad              - criterion
+ * rad                    radius of environment sphere
  * 
- * label_mol        - massive of numbers of molecule for atoms
+ * label_mol              massive of numbers of molecule for atoms
- * log              - status of log-mode
+ * log                    status of log-mode
- * num_atoms        - number of atoms for writing coordinates
+ * num_atoms              number of atoms
- * num_mol          - number of molecules for writing coordinates
+ * num_mol                number of molecules
- * num_needed_mol   - number of needed molecules
+ * num_needed_mol         number of needed molecules
- * num_of_mol       - number of molecule for search
+ * num_of_mol             number of molecule
- * needed_mol       - massive of needed molecules
+ * needed_mol             massive of number of needed molecules
- * quiet            - status of quiet-mode
+ * quiet                  status of quiet-mode
- * true_label_mol   - massive of true numbers of molecule for atoms
+ * true_label_mol         massive of true numbers of molecule for atoms
  */
   
   set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
@@ -134,7 +148,7 @@ int main(int argc, char *argv[])
   if (f_inp == NULL)
   {
     print_message (quiet, stderr, log, f_log, 18, input);
-    return 1;
+    return 2;
   }
   fscanf (f_inp, "%i", &num_atoms);
   fclose (f_inp);
@@ -151,7 +165,7 @@ int main(int argc, char *argv[])
     (true_label_mol == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
-    return 17;
+    return 3;
   }
   sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
 %6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
@@ -178,7 +192,7 @@ int main(int argc, char *argv[])
     (needed_mol == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
-    return 17;
+    return 3;
   }
   
 // analyze

envir/src/messages.c

@@ -1,16 +1,27 @@
-/* Library for printing messages at output
+/**
- *
+ * @file
- * Usage:
- *                                             message (log, mode, text, output)
  */
 
 #include <stdio.h>
 #include <time.h>
 
 
+/**
+ * @fn message
+ */
 int message (const int log, const int mode, const char *text, FILE *output)
-/* mode             - number of message
+/**
- * text             - additional text
+ * @brief function that prints messages to output
+ * @code
+ * message (log, mode, text, output);
+ * @endcode
+ * 
+ * @param log             equal to 1 if print to logfile
+ * @param mode            number of message
+ * @param text            additional text
+ * @param output          output file (may be stdout)
+ * 
+ * @return 0              - exit without errors
  */
 {
   char out[4096];
@@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
   if (log == 1)
   {
     char time_str[256];
+    
     time_t t = time (NULL);
     struct tm* aTm = localtime (&t);
     sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900, 

envir/src/messages.h

@@ -1,6 +1,14 @@
+/**
+ * @file
+ */
+
 #ifndef MESSAGES_H
 #define MESSAGES_H
 
+/**
+ * @fn message
+ */
+
 int message (const int, const int, const char *, FILE *);
 
 #endif /* MESSAGES_H */

envir/src/print_struct.c

@@ -1,3 +1,7 @@
+/**
+ * @file
+ */
+
 /* Library for printing structure to pdb file
  * 
  * Usage:
@@ -8,23 +12,37 @@
 #include <stdio.h>
 
 
+/**
+ * @fn print_structure
+ */
 int print_structure (const char *output, const int num_needed_mol, const int *needed_mol, 
                      const int num_atoms, const int *label_mol, const char *ch_type_atoms, 
                      const float *coords)
-/* output           - output file name
+/**
- * num_needed_mol   - number of needed molecules
+ * @brief function that prints structure to pdb file
- * needed_mol       - massive of needed molecules
+ * @code
- * num_atoms        - number of atoms
+ * print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol, 
- * label_mol        - massive of numbers of molecule for atoms
+ *                  char_type_atoms, coords);
- * ch_type_atoms    - massive of char types for atoms
+ * @endcode
- * coords           - massive of coordinates
+ * 
+ * @param output          output file name
+ * @param num_needed_mol  number of needed molecules
+ * @param needed_mol      massive of number of needed molecules
+ * @param num_atoms       number of atoms
+ * @param label_mol       massive of numbers of molecule for atoms
+ * @param ch_type_atoms   massive of char atom types
+ * @param coords          massive of coordinates
+ * 
+ * @return 0              - exit without errors
  */
 {
   int cur_atom, cur_atom_num, cur_mol, i, j;
   FILE *f_out;
-/* cur_atom         - current atom
+  
- * cur_atom_num     - true atom number
+/* cur_atom               current atom
- * cur_mol          - current molecule
+ * cur_atom_num           true atom number
+ * cur_mol                current molecule
+ * f_out                  output file
  */
   
   cur_atom = 1;

envir/src/print_struct.h

@@ -1,6 +1,14 @@
+/**
+ * @file
+ */
+
 #ifndef PRINT_STRUCTURE_H
 #define PRINT_STRUCTURE_H
 
+/**
+ * @fn print_structure
+ */
+
 int print_structure (const char *, const int, const int *, const int, const int *, 
                      const char *, const float *);
 

envir/src/set_center.c

@@ -1,3 +1,7 @@
+/**
+ * @file
+ */
+
 /* Library for search center mass of molecules
  * 
  * Usage:
@@ -6,18 +10,30 @@
  */
 
 
+/**
+ * @fn set_center
+ */
 int set_center (const int num_atoms, const int num_mol, const int *label_mol, 
                 const float *coords, float *centr_coords)
-/* num_atoms        - number of atoms for writing coordinates
+/**
- * num_mol          - number of molecules for writing coordinates
+ * @brief function that searchs center mass of molecules
- * label_mol        - massive of numbers of molecule for atoms
+ * @code
- * coords           - massive of coordinates
+ * set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
- * coords           - massive of coordinates of center molecules
+ * @endcode
+ * 
+ * @param num_atoms       number of atoms
+ * @param num_mol         number of molecules
+ * @param label_mol       massive of numbers of molecule for atoms
+ * @param coords          massive of coordinates
+ * @param centr_coords    massive of centered coordinates
+ * 
+ * @return 0              - exit without errors
  */
 {
   int at_in_mol, cur_mol, i, j, k;
-/* at_int_mol       - number of atoms in molecule
+  
- * cur_mol          - current molecule
+/* at_int_mol             number of atoms in molecule
+ * cur_mol                current molecule
  */
   
   for (i=0; i<8*num_mol; i++)

envir/src/set_center.h

@@ -1,6 +1,14 @@
+/**
+ * @file
+ */
+
 #ifndef SET_CENTER_H
 #define SET_CENTER_H
 
+/**
+ * @fn set_center
+ */
+
 int set_center (const int, const int, const int *, const float *, float *);
 
 #endif /* SET_CENTER_H */

statgen/README

@@ -1,4 +1,4 @@
-statgen - program for analyze molecular dynamic trajectories
+statgen - program that analyzes molecular dynamic trajectories using topological analysis
 Version: 1.0.1
 License: GPL
 

statgen/about.dox

@@ -1,7 +1,14 @@
-/*! @mainpage statgen
+/*! 
+ * @mainpage statgen 
+ * @image latex ./logo.png
  *
  * @section intro_sec Introduction
  * 
+ * <b>About this program</b>:
+ * <ul>
+ * <li>Program that analyzes molecular dynamic trajectories using topological analysis
+ * </ul>
+ *
  * <b>Developer</b>:
  * <ul>
  * <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>

statgen/src/add_main.c

@@ -119,6 +119,7 @@ int printing_head (const char *output, const int log, const int quiet,
   return 0;
 }
 
+
 /**
  * @fn print_message
  */

statgen/src/coords.c

@@ -15,9 +15,8 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
 /**
  * @brief function that reads coordinates from special file format
  * @code
- * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, 
+ * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms, 
- *                 &num_atoms, true_label_mol, label_mol, type_atoms, 
+ *                 true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
- *                 coords, ch_type_atoms);
  * @endcode
  * 
  * @param mode            mode of reading; '1' is statgen, '2' is envir or 

statgen/src/graph.c

@@ -23,6 +23,7 @@ int check_cycle (const int N, const int *pn)
  */
 {
   int cycle, i;
+  
 /* cycle                  number of cycle
  */
   
@@ -58,6 +59,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
  */
 {
   int cur_N, cycle, i, j, k, n, p, *vertex;
+  
 /* cur_N                  current number of elements in submatrix
  * cycle                  if (cycle == 1) that cycle exist
  * n                      number of samples
@@ -147,6 +149,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
  */
 {
   int depth, i, j, *n_cycle, p, *pn;
+  
 /* depth                  depth of search for check_cycle_size
  * n_cycle                number of cycle
  * p                      current weight

statgen/src/main.c

@@ -18,7 +18,16 @@
 #include "summary_stat.h"
 
 
+/**
+ * @fn main
+ */
 int main (int argc, char *argv[])
+/**
+ * @return 1              - error in error_checking
+ * @return 2              - input file does not exist
+ * @return 3              - memory error
+ * @return 0              - exit without errors
+ */
 {
   char filename[256], tmp_str[2048];
   int error, i, index, j, k, label[2];
@@ -30,6 +39,7 @@ int main (int argc, char *argv[])
   int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms, 
       num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to, 
       *true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
+  
 /* input                  mask of trajectory files
  * logfile                log file name
  * output                 output file name
@@ -232,7 +242,7 @@ int main (int argc, char *argv[])
   if (f_inp == NULL)
   {
     print_message (quiet, stderr, log, f_log, 18, filename);
-    return 1;
+    return 2;
   }
   fscanf (f_inp, "%i", &num_atoms);
   fclose (f_inp);
@@ -260,7 +270,7 @@ int main (int argc, char *argv[])
     (stat_all == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
-    return 17;
+    return 3;
   }
 // set type_agl to zero
   for (i=0; i<max_depth+2; i++)
@@ -327,7 +337,7 @@ int main (int argc, char *argv[])
       (stat_all == NULL))
     {
       print_message (quiet, stderr, log, f_log, 19, argv[0]);
-      return 18;
+      return 3;
     }
     print_message (quiet, stdout, log, f_log, 9, argv[0]);
     

statgen/src/stat_print.c

@@ -17,9 +17,9 @@ int printing_agl (const char *input, const char *output, const int *connect,
 /**
  * @brief function that prints aglomerates to output file
  * @code
- * printing_agl (input_file, output_file, number_of_molecules, 
+ * printing_agl (input_file, output_file, number_of_molecules, true_label_molecules, 
- *          true_label_molecules, num_of_molecules_in_aglomerates, aglomerates, 
+ *               num_of_molecules_in_aglomerates, aglomerates, statistic, max_depth, 
- *                                    statistic, max_depth, type_of_aglomerate);
+ *               type_of_aglomerate);
  * @endcode
  * 
  * @param input           input file name
@@ -39,6 +39,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
 {
   int error, i, *iso, j, k, *label_matrix, *matrix;
   FILE *f_out;
+  
 /* iso                    isomorphic graph in database
  * label_matrix           massive of indexes of molecule
  * matrix                 connectivity graph

statgen/src/stat_select.c

@@ -15,8 +15,8 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
 /**
  * @brief function that creates connectivity matrix
  * @code
- * create_matrix (number_of_molecules, number_of_atoms, label_molecule,
+ * create_matrix (number_of_molecules, number_of_atoms, label_molecule, type_atoms, 
- *        type_atoms, coords, number_of_interactions, criteria, connect_matrix);
+ *                coords, number_of_interactions, criteria, connect_matrix);
  * @endcode
  * 
  * @param num_mol         number of molecules
@@ -34,6 +34,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
 {
   float r;
   int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
+  
 /* r                      radius
  * cur_num_inter          current number of true interactions
  * num_inter              needed number of true interactions

statgen/src/stat_sort.c

@@ -13,8 +13,8 @@ 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, 
+ * proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_aglomerates, 
- *  num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
+ *              aglomerates, statistic, summary_statistic);
  * @endcode
  * 
  * @param num_mol         number of molecules
@@ -29,6 +29,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
  */
 {
   int i, j, k, p, *bin;
+  
   /* p                    weight / graph index
    * bin                  binary massive of labels
    */

statgen/src/summary_stat.c

@@ -30,6 +30,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
   float conc, p, pn, type[2], x, y;
   int i, index;
   FILE *f_out;
+  
 /* conc                   concentrate of aglomerates
  * p                      probability of aglomerates
  * pn                     weight probability of aglomerates

statgen/statgen.doxygen

@@ -38,7 +38,7 @@ PROJECT_NUMBER         = V.1.0.1
 # 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 for analyze molecular dynamic trajectories"
+PROJECT_BRIEF          = "Program that analyzes molecular dynamic trajectories using topological analysis"
 
 # 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 
@@ -52,7 +52,7 @@ PROJECT_LOGO           = /home/arcanis/Documents/github/moldyn/statgen/logo.png
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = /home/arcanis/Documents/github/moldyn/statgen/docs
+OUTPUT_DIRECTORY       = ./docs
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
 # 4096 sub-directories (in 2 levels) under the output directory of each output 
@@ -680,7 +680,6 @@ INPUT_ENCODING         = UTF-8
 # *.f90 *.f *.for *.vhd *.vhdl
 
 FILE_PATTERNS          = *.c \
-                         *.h \
                          *.dox
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories