Added prefix 'mm_'

mm_agl/CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT agl)
+set (PROJECT mm_agl)
 # set additional cmake file
 include (${PROJECT}.cmake)
 

mm_agl/README

@@ -1,9 +1,9 @@
-agl - program that creates PDB file with chosen aglomerate
+mm_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 ]
+  mm_agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
   -a          - input file with aglomerates (in format statgen)

mm_agl/mm_agl.doxygen

@@ -26,7 +26,7 @@ DOXYFILE_ENCODING      = UTF-8
 # identify the project. Note that if you do not use Doxywizard you need 
 # to put quotes around the project name if it contains spaces.
 
-PROJECT_NAME           = agl
+PROJECT_NAME           = mm_agl
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 

mm_agl/src/main.c

@@ -2,7 +2,7 @@
  * @file
  */
 /**
- * @mainpage agl
+ * @mainpage mm_agl
  * @image latex ./logo.png
  *
  * @section intro_sec Introduction
@@ -24,7 +24,7 @@
  * @section How-To-Use How to use
  * Usage:
  * <pre>
- * agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
+ * mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
  *
  * Parametrs:
  *    -a          - input file with aglomerates (in format statgen)
@@ -39,7 +39,7 @@
  * @page Install
  * 
  * @section Requirements Requirements
- * The application agl requires the following external stuff:
+ * The application mm_agl requires the following external stuff:
  * - cmake  >= 2.8
  * - gcc    >= 4.8
  *
@@ -126,13 +126,13 @@ int main(int argc, char *argv[])
   {
     if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
-      sprintf (tmp_str, "                                        agl\n");
+      sprintf (tmp_str, "                                     mm_agl\n");
       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);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%sagl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -a          - input file with aglomerates (in format statgen)\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - input file with coordinates\n", tmp_str);

mm_envir/CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT envir)
+set (PROJECT mm_envir)
 # set additional cmake file
 include (${PROJECT}.cmake)
 

mm_envir/README

@@ -1,10 +1,10 @@
-envir - program that searchs environment for chosen molecule by geometric criterion
+mm_envir - program that searchs environment for chosen molecule by geometric criterion
 Version: 1.0.1
 License: GPL
 
 Usage:
-  envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
-                                                 [ -l LOGFILE ] [ -q ] [ -h ]
+  mm_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

mm_envir/mm_envir.doxygen

@@ -26,7 +26,7 @@ DOXYFILE_ENCODING      = UTF-8
 # identify the project. Note that if you do not use Doxywizard you need 
 # to put quotes around the project name if it contains spaces.
 
-PROJECT_NAME           = envir
+PROJECT_NAME           = mm_envir
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 

mm_envir/src/main.c

@@ -2,7 +2,7 @@
  * @file
  */
 /**
- * @mainpage envir
+ * @mainpage mm_envir
  * @image latex ./logo.png
  *
  * @section intro_sec Introduction
@@ -24,7 +24,7 @@
  * @section How-To-Use How to use
  * Usage:
  * <pre>
- * envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
+ * mm_envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] 
  *                                           [ -l LOGFILE ] [ -q ] [ -h ]
  *
  * Parametrs:
@@ -41,7 +41,7 @@
  * @page Install
  * 
  * @section Requirements Requirements
- * The application envir requires the following external stuff:
+ * The application mm_envir requires the following external stuff:
  * - cmake  >= 2.8
  * - gcc    >= 4.8
  *
@@ -128,14 +128,14 @@ int main(int argc, char *argv[])
   {
     if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
-      sprintf (tmp_str, "                                        envir\n");
+      sprintf (tmp_str, "                                     mm_envir\n");
       sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
       sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%senvir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]\n", tmp_str);
-      sprintf (tmp_str, "%s                                          [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]\n", tmp_str);
+      sprintf (tmp_str, "%s                                             [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - input file name\n", tmp_str);
       sprintf (tmp_str, "%s  -c          - cell size (float), A\n", tmp_str);

mm_radf/CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT radf)
+set (PROJECT mm_radf)
 # set additional cmake file
 include (${PROJECT}.cmake)
 

mm_radf/README

@@ -1,11 +1,11 @@
-radf - program that calculates radial distribution function (RDF) or radial-angles 
+mm_radf - program that calculates radial distribution function (RDF) or radial-angles 
 distribution function
 Version : 1.0.1
 License : GPL
 
 Usage:
-radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
-                [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+                   [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
   -i          - mask of input files

mm_radf/mm_radf.doxygen

@@ -26,7 +26,7 @@ DOXYFILE_ENCODING      = UTF-8
 # identify the project. Note that if you do not use Doxywizard you need 
 # to put quotes around the project name if it contains spaces.
 
-PROJECT_NAME           = radf
+PROJECT_NAME           = mm_radf
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 

mm_radf/src/main.c

@@ -2,7 +2,7 @@
  * @file
  */
 /**
- * @mainpage radf
+ * @mainpage mm_radf
  * @image latex ./logo.png
  *
  * @section intro_sec Introduction
@@ -25,8 +25,8 @@
  * @section How-To-Use How to use
  * Usage:
  * <pre>
- * radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
- *                 [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+ * mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+ *                    [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
  * Parametrs:
  *    -i          - mask of input files
  *    -s          - trajectory steps (integer)
@@ -48,7 +48,7 @@
  * @page Install
  * 
  * @section Requirements Requirements
- * The application radf requires the following external stuff:
+ * The application mm_radf requires the following external stuff:
  * - cmake  >= 2.8
  * - gcc    >= 4.8
  *
@@ -144,15 +144,15 @@ int main(int argc, char *argv[])
   {
     if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
-      sprintf (tmp_str, "                                        radf\n");
+      sprintf (tmp_str, "                                    mm_radf\n");
       sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
       sprintf (tmp_str, "%sdistribution function\n", tmp_str);
       sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%sradf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]\n", tmp_str);
-      sprintf (tmp_str, "%s                 [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]\n", tmp_str);
+      sprintf (tmp_str, "%s                    [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - mask of input files\n", tmp_str);
       sprintf (tmp_str, "%s  -s          - trajectory steps (integer)\n", tmp_str);

mm_statgen/CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_policy(SET CMP0011 NEW)
 cmake_policy(SET CMP0015 NEW)
 
 # set project name
-set (PROJECT statgen)
+set (PROJECT mm_statgen)
 # set additional cmake file
 include (${PROJECT}.cmake)
 

mm_statgen/README

@@ -1,10 +1,10 @@
-statgen - program that analyzes molecular dynamic trajectories using topological analysis
+mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
 Version: 1.0.1
 License: GPL
 
 Usage:
-  statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] 
-                                                  [ -l LOGFILE ] [ -q ] [ -h ]
+  mm_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] 
+                                                     [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
   -i          - mask of input files

mm_statgen/mm_statgen.doxygen

@@ -26,7 +26,7 @@ DOXYFILE_ENCODING      = UTF-8
 # identify the project. Note that if you do not use Doxywizard you need 
 # to put quotes around the project name if it contains spaces.
 
-PROJECT_NAME           = statgen
+PROJECT_NAME           = mm_statgen
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 

mm_statgen/src/main.c

@@ -2,7 +2,7 @@
  * @file
  */
 /**
- * @mainpage statgen 
+ * @mainpage mm_statgen 
  * @image latex ./logo.png
  *
  * @section intro_sec Introduction
@@ -24,8 +24,8 @@
  * @section How-To-Use How to use
  * Usage:
  * <pre>
- * statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] 
- *                                                 [ -l LOGFILE ] [ -q ] [ -h ]
+ * mm_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] 
+ *                                                    [ -l LOGFILE ] [ -q ] [ -h ]
  *
  * Parametrs:
  *    -i          - mask of input files
@@ -44,7 +44,7 @@
  * @page Install
  * 
  * @section Requirements Requirements
- * The application statgen requires the following external stuff:
+ * The application mm_statgen requires the following external stuff:
  * - cmake  >= 2.8
  * - gcc    >= 4.8
  *
@@ -160,14 +160,14 @@ int main (int argc, char *argv[])
   {
     if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
-      sprintf (tmp_str, "                                        statgen\n");
+      sprintf (tmp_str, "                                     mm_statgen\n");
       sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
       sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
-      sprintf (tmp_str, "%sstatgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]\n", tmp_str);
-      sprintf (tmp_str, "%s                                                [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
+      sprintf (tmp_str, "%smm_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]\n", tmp_str);
+      sprintf (tmp_str, "%s                                                   [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
       sprintf (tmp_str, "%sParametrs:\n", tmp_str);
       sprintf (tmp_str, "%s  -i          - mask of input files\n", tmp_str);
       sprintf (tmp_str, "%s  -s          - trajectory steps (integer)\n", tmp_str);