diff --git a/mathmech/CMakeLists.txt b/mathmech/CMakeLists.txt index d62b36b..0a557d0 100644 --- a/mathmech/CMakeLists.txt +++ b/mathmech/CMakeLists.txt @@ -1,6 +1,6 @@ set ("PROJECT_VERSION_MAJOR" 1) -set ("PROJECT_VERSION_MINOR" 0) -set ("PROJECT_VERSION_PATCH" 3) +set ("PROJECT_VERSION_MINOR" 1) +set ("PROJECT_VERSION_PATCH" 0) set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}) message (STATUS "Version ${PROJECT_VERSION}") diff --git a/mathmech/PKGBUILD b/mathmech/PKGBUILD index acf09d9..93efb79 100644 --- a/mathmech/PKGBUILD +++ b/mathmech/PKGBUILD @@ -2,7 +2,7 @@ # Maintainer: Evgeniy "arcanis" Alexeev pkgname=mathmech -pkgver=1.0.3 +pkgver=1.1.0 pkgrel=1 pkgdesc="Software package for analysis of molecular dynamics trajectories" arch=(any) diff --git a/mathmech/README.doc b/mathmech/README.doc new file mode 100644 index 0000000..f62e22c Binary files /dev/null and b/mathmech/README.doc differ diff --git a/mathmech/mathmech/README b/mathmech/mathmech/README index 3e5348f..d89eb64 100644 --- a/mathmech/mathmech/README +++ b/mathmech/mathmech/README @@ -1,3 +1,3 @@ Mathematical Molecular Mechanics is GUI for "mm" program pack -Version: 1.0.3 +Version: 1.1.0 License: GPL diff --git a/mathmech/mathmech/resources/translations/eng.ts b/mathmech/mathmech/resources/translations/eng.ts index 9faa2c6..fc871c2 100644 --- a/mathmech/mathmech/resources/translations/eng.ts +++ b/mathmech/mathmech/resources/translations/eng.ts @@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> <p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Mathematical Molecular Mechanics</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Version:</span> 1.0.3</p> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Version:</span> 1.1.0</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">License:</span> GPL</p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Author:</span> Evgeniy Alekseev</p> diff --git a/mathmech/mathmech/resources/translations/rus.ts b/mathmech/mathmech/resources/translations/rus.ts index 5fd3e9b..5fc7f32 100644 --- a/mathmech/mathmech/resources/translations/rus.ts +++ b/mathmech/mathmech/resources/translations/rus.ts @@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> <p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Mathematical Molecular Mechanics</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Версия:</span> 1.0.3</p> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Версия:</span> 1.1.0</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Лицензия:</span> GPL</p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Автор:</span> Evgeniy Alekseev</p> diff --git a/mathmech/mathmech/src/mainwindow.ui b/mathmech/mathmech/src/mainwindow.ui index 695e181..5380274 100644 --- a/mathmech/mathmech/src/mainwindow.ui +++ b/mathmech/mathmech/src/mainwindow.ui @@ -1352,6 +1352,9 @@ Number of steps of analysis + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + 1 diff --git a/mathmech/mathmech/src/mathmech.pro.user b/mathmech/mathmech/src/mathmech.pro.user index e0f0208..8f5c685 100644 --- a/mathmech/mathmech/src/mathmech.pro.user +++ b/mathmech/mathmech/src/mathmech.pro.user @@ -1,6 +1,6 @@ - + ProjectExplorer.Project.ActiveTarget diff --git a/mathmech/mm_agl/README b/mathmech/mm_agl/README index e0ddd25..01a73c1 100644 --- a/mathmech/mm_agl/README +++ b/mathmech/mm_agl/README @@ -1,5 +1,5 @@ mm_agl - program that creates PDB file with chosen agglomerate -Version: 1.0.3 +Version: 1.1.0 License: GPL Usage: diff --git a/mathmech/mm_agl/mm_agl.doxygen b/mathmech/mm_agl/mm_agl.doxygen index 69bd1f7..c72e767 100644 --- a/mathmech/mm_agl/mm_agl.doxygen +++ b/mathmech/mm_agl/mm_agl.doxygen @@ -32,7 +32,7 @@ PROJECT_NAME = mm_agl # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = V.1.0.3 +PROJECT_NUMBER = V.1.1.0 # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer diff --git a/mathmech/mm_agl/mm_agl.pdf b/mathmech/mm_agl/mm_agl.pdf index 58c462e..2be6f5a 100644 Binary files a/mathmech/mm_agl/mm_agl.pdf and b/mathmech/mm_agl/mm_agl.pdf differ diff --git a/mathmech/mm_agl/src/main.c b/mathmech/mm_agl/src/main.c index 03b4795..46f9ce6 100644 --- a/mathmech/mm_agl/src/main.c +++ b/mathmech/mm_agl/src/main.c @@ -134,7 +134,7 @@ int main(int argc, char *argv[]) { sprintf (tmp_str, " mm_agl\n"); sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str); - sprintf (tmp_str, "%sVersion : 1.0.3 License : GPL\n", tmp_str); + sprintf (tmp_str, "%sVersion : 1.1.0 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); diff --git a/mathmech/mm_envir/README b/mathmech/mm_envir/README index 6da3681..faed53e 100644 --- a/mathmech/mm_envir/README +++ b/mathmech/mm_envir/README @@ -1,5 +1,5 @@ mm_envir - program that searchs environment for chosen molecule by geometric criterion -Version: 1.0.3 +Version: 1.1.0 License: GPL Usage: diff --git a/mathmech/mm_envir/mm_envir.doxygen b/mathmech/mm_envir/mm_envir.doxygen index 295b016..032e61a 100644 --- a/mathmech/mm_envir/mm_envir.doxygen +++ b/mathmech/mm_envir/mm_envir.doxygen @@ -32,7 +32,7 @@ PROJECT_NAME = mm_envir # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = V.1.0.3 +PROJECT_NUMBER = V.1.1.0 # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer diff --git a/mathmech/mm_envir/mm_envir.pdf b/mathmech/mm_envir/mm_envir.pdf index 6eec094..8362440 100644 Binary files a/mathmech/mm_envir/mm_envir.pdf and b/mathmech/mm_envir/mm_envir.pdf differ diff --git a/mathmech/mm_envir/src/main.c b/mathmech/mm_envir/src/main.c index f4f1c35..8e55b5b 100644 --- a/mathmech/mm_envir/src/main.c +++ b/mathmech/mm_envir/src/main.c @@ -136,7 +136,7 @@ int main(int argc, char *argv[]) { sprintf (tmp_str, " mm_envir\n"); sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str); - sprintf (tmp_str, "%sVersion : 1.0.3 License : GPL\n", tmp_str); + sprintf (tmp_str, "%sVersion : 1.1.0 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); diff --git a/mathmech/mm_radf/README b/mathmech/mm_radf/README index f7086af..31a3525 100644 --- a/mathmech/mm_radf/README +++ b/mathmech/mm_radf/README @@ -4,14 +4,14 @@ Version : 1.0.3 License : GPL Usage: -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 ] + mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -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) -c - cell size (float), A - -a - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' + -a5 - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' (will enable RDF calculation for center mass automaticaly) -o - output file name -r - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0' diff --git a/mathmech/mm_radf/mm_radf.doxygen b/mathmech/mm_radf/mm_radf.doxygen index 6ce1ec9..5c96559 100644 --- a/mathmech/mm_radf/mm_radf.doxygen +++ b/mathmech/mm_radf/mm_radf.doxygen @@ -32,7 +32,7 @@ PROJECT_NAME = mm_radf # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = V.1.0.3 +PROJECT_NUMBER = V.1.1.0 # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer diff --git a/mathmech/mm_radf/mm_radf.pdf b/mathmech/mm_radf/mm_radf.pdf index 13e8296..533dfcb 100644 Binary files a/mathmech/mm_radf/mm_radf.pdf and b/mathmech/mm_radf/mm_radf.pdf differ diff --git a/mathmech/mm_radf/src/add_main.c b/mathmech/mm_radf/src/add_main.c index 8f89ed7..bd68dd2 100644 --- a/mathmech/mm_radf/src/add_main.c +++ b/mathmech/mm_radf/src/add_main.c @@ -127,7 +127,7 @@ 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.1.0.3\n\n"); + fprintf (f_out, "radf ::: V.1.1.0\n\n"); fprintf (f_out, "CONFIGURATION\n"); fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix); diff --git a/mathmech/mm_radf/src/main.c b/mathmech/mm_radf/src/main.c index 7faee40..9b64a52 100644 --- a/mathmech/mm_radf/src/main.c +++ b/mathmech/mm_radf/src/main.c @@ -25,13 +25,13 @@ * @section How-To-Use How to use * Usage: * 
- * 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 ]
+ * mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -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)
  *    -c          - cell size (float), A
- *    -a          - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
+ *    -at         - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
  *                  (will enable RDF calculation for center mass automaticaly)
  *    -o          - output file name
  *    -r          - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
@@ -153,7 +153,7 @@ int main(int argc, char *argv[])
       sprintf (tmp_str, "                                    mm_radf\n");
       sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
       sprintf (tmp_str, "%sdistribution function\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.0                                                    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);
diff --git a/mathmech/mm_statgen/README b/mathmech/mm_statgen/README
index de1503d..015569a 100644
--- a/mathmech/mm_statgen/README
+++ b/mathmech/mm_statgen/README
@@ -1,5 +1,5 @@
 mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
-Version: 1.0.3
+Version: 1.1.0
 License: GPL
 
 Usage:
diff --git a/mathmech/mm_statgen/mm_statgen.doxygen b/mathmech/mm_statgen/mm_statgen.doxygen
index b50b5b2..b44e3d1 100644
--- a/mathmech/mm_statgen/mm_statgen.doxygen
+++ b/mathmech/mm_statgen/mm_statgen.doxygen
@@ -32,7 +32,7 @@ PROJECT_NAME           = mm_statgen
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = V.1.0.3
+PROJECT_NUMBER         = V.1.1.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description 
 # for a project that appears at the top of each page and should give viewer 
diff --git a/mathmech/mm_statgen/mm_statgen.pdf b/mathmech/mm_statgen/mm_statgen.pdf
index 35bcf02..044c596 100644
Binary files a/mathmech/mm_statgen/mm_statgen.pdf and b/mathmech/mm_statgen/mm_statgen.pdf differ
diff --git a/mathmech/mm_statgen/src/add_main.c b/mathmech/mm_statgen/src/add_main.c
index 205bdf0..2e88247 100644
--- a/mathmech/mm_statgen/src/add_main.c
+++ b/mathmech/mm_statgen/src/add_main.c
@@ -92,7 +92,7 @@ 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.1.0.3\n\n");
+  fprintf (f_out, "statgen ::: V.1.1.0\n\n");
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
diff --git a/mathmech/mm_statgen/src/main.c b/mathmech/mm_statgen/src/main.c
index 28b7d3f..447e12a 100644
--- a/mathmech/mm_statgen/src/main.c
+++ b/mathmech/mm_statgen/src/main.c
@@ -168,7 +168,7 @@ int main (int argc, char *argv[])
     {
       sprintf (tmp_str, "                                     mm_statgen\n");
       sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.3                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.1.0                                                    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);
diff --git a/mathmech/mm_statgen/src/summary_stat.c b/mathmech/mm_statgen/src/summary_stat.c
index 6b0eecd..3f6575e 100644
--- a/mathmech/mm_statgen/src/summary_stat.c
+++ b/mathmech/mm_statgen/src/summary_stat.c
@@ -71,11 +71,11 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
     x = type_agl[0] + type_agl[1];
     type[0] = type_agl[0];
     type[1] = type_agl[1];
-    fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
+    fprintf (f_out, "LINEAR=%.5f\nCYCLE=%.5f\n--------------------\n", type[0]/x, type[1]/x);
 // branched
     type[0] = type_agl[2];
     type[1] = type_agl[3];
-    fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
+    fprintf (f_out, "NOT BRANCHED=%.5f\nBRANCHED=%.5f\n--------------------\n", type[0]/x, type[1]/x);
 // n_cycle
     x = 0;
     for (i=4; i