- removed *.pdf

+ release agl 1.0.1
* modified shared library (messages.c)
* small bug fixes

agl/src/Makefile

@@ -4,7 +4,7 @@ CC=gcc
 CFLAGS=-c -Wall -fPIC
 LDFLAGS=-lm
 SOURCES_DIR=src
-SOURCES=main.c add_main.c coords.c messages.c print_struct.c set_center.c read_agl.c
+SOURCES=main.c add_main.c coords.c messages.c print_struct.c read_agl.c select_mol.c set_center.c
 OBJECTS=$(SOURCES:.c=.o)
 EXECUTABLE=agl
 

agl/src/add_main.c

@@ -1,13 +1,34 @@
-/* Additional library for main.c (agl)
+/**
+ * @file
  */
 
 #include <stdio.h>
 
-// #include "messages.h"
+#include "messages.h"
 
 
+/**
+ * @fn error_checking
+ */
 int error_checking (const char *aglinp, const float *cell, const char *input, 
                     const char *output)
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (aglinp, cell, input, output);
+ * @endcode
+ * 
+ * @param aglinp          aglomerate file name
+ * @param cell            massive of cell size
+ * @param input           input file name
+ * @param output          output file name
+ * 
+ * @return 11             - error in 'cell'
+ * @return 12             - error in 'input'
+ * @return 13             - error in 'output'
+ * @return 14             - error in 'aglinp'
+ * @return 0              - exit without errors
+ */
 {
   if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
     return 11;
@@ -22,8 +43,26 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
 }
 
 
+/**
+ * @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);
@@ -34,8 +73,25 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 }
 
 
-int set_defaults (char aglinp, float *cell, char *input, int *log, int *num_of_mol, 
-                  char *output, int *quiet, float *rad)
+/**
+ * @fn set_defaults
+ */
+int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output, int *quiet)
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (aglinp, cell, input, &log, output, &quiet);
+ * @endcode
+ * 
+ * @param aglinp          aglomerate file name
+ * @param cell            massive of cell size
+ * @param input           mask of trajectory files
+ * @param log             status of log-mode
+ * @param output          output file name
+ * @param quiet           status of quiet-mode
+ * 
+ * @return 0              - exit without errors
+ */
 {
   int i;
   
@@ -44,10 +100,8 @@ int set_defaults (char aglinp, float *cell, char *input, int *log, int *num_of_m
     cell[i] = 0.0;
   input[0] = '#';
   *log = 0;
-  *num_of_mol = 1;
   output[0] = '#';
   *quiet = 0;
-  *rad = 6.0;
   
   return 0;
 }

agl/src/add_main.h

@@ -0,0 +1,22 @@
+/**
+ * @file
+ */
+
+#ifndef ADD_MAIN_H
+#define ADD_MAIN_H
+
+/**
+ * @fn error_checking
+ */
+/**
+ * @fn print_message
+ */
+/**
+ * @fn set_defaults
+ */
+
+int error_checking (const char *, const float *, const char *, const char *);
+int print_message (const int, FILE *, const int, FILE *, const int, const char *);
+int set_defaults (char *, float *, char *, int *, char *, int *);
+
+#endif /* ADD_MAIN_H */

agl/src/coords.h

@@ -0,0 +1,16 @@
+/**
+ * @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 *);
+
+#endif /* COORDS_H */

agl/src/main.c

@@ -1,45 +1,62 @@
+/**
+ * @file
+ */
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-// #include "add_main.h"
-// #include "coords.h"
-// #include "messages.h"
-// #include "print_struct.h"
-// #include "read_agl.h"
+#include "add_main.h"
+#include "coords.h"
+#include "messages.h"
+#include "print_struct.h"
+#include "read_agl.h"
+#include "select_mol.h"
+#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;
+  int error, i, *tmp_int;
   FILE *f_inp, *f_log;
   
   char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
-  float cell[3], *coords;
+  float cell[3], *centr_coords, *coords;
   int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet, 
       *true_label_mol;
-/* ch_type_atoms    - massive of char types for atoms
- * aglinp           - input file with aglomerate name
- * input            - input file name
- * logfile          - log file name
- * output           - output file name
+  
+/* aglinp                 aglomerate file name
+ * ch_type_atoms          massive of char atom types
+ * input                  input file name
+ * logfile                log file name
+ * output                 output file name
  * 
- * cell             - cell dimension
- * coords           - massive of coordinates
+ * cell                   massive of cell size
+ * centr_coords           massive of centered coordinates
+ * coords                 massive of coordinates
  * 
- * label_mol        - massive of numbers of molecule for atoms
- * log              - status of log-mode
- * num_atoms        - number of atoms for writing coordinates
- * num_mol          - number of molecules for writing coordinates
- * num_needed_mol   - number of needed molecules
- * needed_mol       - massive of needed molecules
- * quiet            - status of quiet-mode
- * true_label_mol   - massive of true numbers of molecule for atoms
+ * label_mol              massive of numbers of molecule for atoms
+ * log                    status of log-mode
+ * num_atoms              number of atoms
+ * num_mol                number of molecules
+ * num_needed_mol         number of needed molecules
+ * needed_mol             massive of number of needed molecules
+ * quiet                  status of quiet-mode
+ * true_label_mol         massive of true numbers of molecule for atoms
  */
   
-  set_defaults (aglinp, cell, input, &log, &num_of_mol, output, &quiet, &rad);
+  set_defaults (aglinp, cell, input, &log, output, &quiet);
   
   for (i=1; i<argc; i++)
   {
@@ -64,38 +81,38 @@ int main(int argc, char *argv[])
       return 0;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
-//       input file
+// input file
     {
       strcpy (aglinp, argv[i+1]);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
-//       input file
+// input file
     {
       strcpy (input, argv[i+1]);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
-//       cell size
+// cell size
     {
       sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
-//       output file
+// output file
     {
       strcpy (output, argv[i+1]);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
-//       log mode
+// log mode
     {
       log = 1;
       strcpy (logfile, argv[i+1]);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
-//       quiet mode
+// quiet mode
     {
       quiet = 1;
     }
@@ -117,14 +134,14 @@ int main(int argc, char *argv[])
   
   print_message (quiet, stdout, log, f_log, 2, argv[0]);
   
-//   processing
-//   initial variables
+// processing
+// initial variables
   print_message (quiet, stdout, log, f_log, 3, input);
   f_inp = fopen (input, "r");
   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);
@@ -134,7 +151,7 @@ int main(int argc, char *argv[])
   needed_mol = (int *) malloc (num_atoms * sizeof (int));
   tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
   true_label_mol = (int *) malloc (num_atoms * sizeof (int));
-//   error checking
+// error checking
   if ((ch_type_atoms == NULL) ||
     (coords == NULL) || 
     (label_mol == NULL) || 
@@ -143,7 +160,7 @@ 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, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
 %6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n", 
@@ -152,43 +169,57 @@ int main(int argc, char *argv[])
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
   
-//   reading aglomerate
+// reading aglomerate
   print_message (quiet, stdout, log, f_log, 7, aglinp);
   error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
   
   if (error == 0)
   {
-    sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", num_needed_mol);
+    sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol);
     print_message (quiet, stdout, log, f_log, 8, tmp_str);
-//     reading coordinates
+// reading coordinates
     print_message (quiet, stdout, log, f_log, 7, input);
-    error = reading_coords (1, input, num_needed_mol, needed_mol, cell, &num_mol, 
+    error = reading_coords (2, input, num_needed_mol, needed_mol, cell, &num_mol, 
                             &num_atoms, true_label_mol, label_mol, tmp_int, coords, 
                             ch_type_atoms);
+    centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
+    if (centr_coords == NULL)
+    {
+      print_message (quiet, stderr, log, f_log, 19, argv[0]);
+      return 3;
+    }
     
-//     analyze
+// analyze
     if (error == 0)
     {
       sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", 
               ' ', num_mol, ' ', num_atoms);
       print_message (quiet, stdout, log, f_log, 8, tmp_str);
-      error = 
+      error = 1;
+      error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
+      if (error == 0)
+      {
+        print_message (quiet, stderr, log, f_log, 20, argv[0]);
+        error = 1;
+        error = select_molecule (centr_coords, num_needed_mol, needed_mol);
         if (error == 0)
         {
-          print_message (quiet, stderr, log, f_log, 21, argv[0]);
+          print_message (quiet, stderr, log, f_log, 4, argv[0]);
+          error = 1;
           error = print_structure (output, num_needed_mol, needed_mol, num_atoms, 
-                                  label_mol, ch_type_atoms, coords);
+                                   label_mol, ch_type_atoms, coords);
           print_message (quiet, stderr, log, f_log, 12, output);
         }
       }
     }
   }
   
-  print_message (quiet, stdout, log, f_log, 13, argv[0]);
+  print_message (quiet, stderr, log, f_log, 13, argv[0]);
   
   print_message (quiet, stdout, log, f_log, 15, argv[0]);
-//   free memory
+// free memory
   free (ch_type_atoms);
+  free (centr_coords);
   free (coords);
   free (label_mol);
   free (needed_mol);

agl/src/messages.c

@@ -52,6 +52,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "Initialization of variables from file '%s'\n", text);
       break;
     case 4:
+      sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
       break;
     case 5:
       sprintf (out, "Initial parametrs: \n%s", text);

agl/src/messages.h

@@ -0,0 +1,14 @@
+/**
+ * @file
+ */
+
+#ifndef MESSAGES_H
+#define MESSAGES_H
+
+/**
+ * @fn message
+ */
+
+int message (const int, const int, const char *, FILE *);
+
+#endif /* MESSAGES_H */

agl/src/print_struct.c

@@ -2,13 +2,6 @@
  * @file
  */
 
-/* Library for printing structure to pdb file
- * 
- * Usage:
- *              print_structure (output, num_needed_mol, needed_mol, num_atoms, 
- *                                           label_mol, char_type_atoms, coords)
- */
-
 #include <stdio.h>
 
 

agl/src/print_struct.h

@@ -0,0 +1,15 @@
+/**
+ * @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 *);
+
+#endif /* PRINT_STRUCTURE_H */

agl/src/read_agl.c

@@ -1,3 +1,6 @@
+/**
+ * @file
+ */
 /* Library for reading aglomerate from statgen-file
  *
  * Usage:
@@ -7,17 +10,32 @@
 #include <stdio.h>
 
 
+/**
+ * @fn reading_agl
+ */
 int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
-/* aglinp           - input file with aglomerate
- * num_needed_mol   - number of needed molecules
- * agl_class        - aglomerate class
- * needed_mol       - massive of needed molecules
+/**
+ * @brief function that reads aglomerate from statgen-formated file
+ * @code
+ * reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
+ * @endcode
+ * 
+ * @param aglinp          aglomerate file name
+ * @param num_needed_mol  number of needed molecules
+ * @param agl_class       aglomerate class
+ * @param needed_mol      massive of numbed of needed molecules
+ * 
+ * @return 0              - exit without errors
  */
 {
   char connect[256], tmp_str[256];
   int i;
   FILE *f_agl;
   
+/* connect                - connectivity matrix for molecule
+ * f_agl                  - aglomerate file
+ */
+  
   f_agl = fopen (aglinp, "r");
   
   fgets (tmp_str, 256, f_agl);

agl/src/read_agl.h

@@ -0,0 +1,14 @@
+/**
+ * @file
+ */
+
+#ifndef READ_AGL_H
+#define READ_AGL_H
+
+/**
+ * @fn reading_agl
+ */
+
+int reading_agl (const char *, int *, char *, int *);
+
+#endif /* READ_AGL_H */

agl/src/select_mol.c

@@ -1,59 +1,69 @@
-/* Library for select molecules in translations
- * 
- * Usage:
- * 
+/**
+ * @file
  */
 
 #include <math.h>
 
 
-int select_molecule (const int num_atoms, const int *label_mol, const int *true_label_mol, const float *coords, const int num_needed_mol, int *needed_mol)
+/**
+ * @fn select_molecule
+ */
+int select_molecule (const float *centr_coords, const int num_needed_mol, int *needed_mol)
+/**
+ * @brief function that selects molecules from array of translated molecules
+ * @code
+ * select_molecule (centr_coords, num_needed_mol, needed_mol);
+ * @endcode
+ * 
+ * @param centr_coords    massive of centered coordinates
+ * @param num_needed_mol  number of needed molecules
+ * @param needed_mol      massive of number of needed molecules
+ * 
+ * @return 0              - exit without errors
+ */
 {
   float r, ref[3], rmin;
-  int i, j, k, *old_needed_mol;
+  int i, j, jmin;
   
-  old_needed_mol = (int *) malloc (num_needed_mol * sizeof (int));
-  if (old_needed_mol == NULL)
-    return 1;
+/* r                      radius
+ * ref                    coordinated of center mass
+ * rmin                   minimal radius
+ * jmin                   index of the nearest molecule
+ */
   
-//   set first molecule
-  ref_mol = old_needed_mol[0];
+// set first molecule
   needed_mol[0] = 0;
-  k = 1;
   for (i=0; i<3; i++)
-    ref[i] = coords[3*0+i];
+    ref[i] = centr_coords[3*8*0+0+i];
   
+// work block
   for (i=1; i<num_needed_mol; i++)
-    for (j=0; j<8*num_atoms; j++)
-      if (old_needed_mol[i] == true_label_mol[label_mol[j]])
+  {
+    rmin = sqrt (pow ((centr_coords[3*8*i+0+0] - ref[0]), 2) + \
+                 pow ((centr_coords[3*8*i+0+1] - ref[1]), 2) + \
+                 pow ((centr_coords[3*8*i+0+2] - ref[2]), 2));
+    jmin = 0;
+    for (j=1; j<8; j++)
+    {
+      r = sqrt (pow ((centr_coords[3*8*i+j+0] - ref[0]), 2) + \
+                pow ((centr_coords[3*8*i+j+1] - ref[1]), 2) + \
+                pow ((centr_coords[3*8*i+j+2] - ref[2]), 2));
+      if (r < rmin)
       {
-        if (j < num_atoms)
-          cur_mol = 0;
-        else
-          cur_mol = ((j - num_atoms) % 7) + 1;
-    //     for (j=0; j<3; j++)
-    //       centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
+        rmin = r;
+        jmin = j;
       }
-  
-  for (i=1; i<num_needed_mol; i++)
-    for (j=0; j<num_atoms; j++)
-      if (old_needed_mol[i] == true_label_mol[label_mol[j]])
-      {
-        if (ref_mol != true_label_mol[label_mol[j]])
-        {
-          ref_i = j;
-          rmin = sqrt (pow ((coords[3*j+0] - ref[0]), 2) + \
-                 pow ((coords[3*j+1] - ref[1]), 2) + \
-                 pow ((coords[3*j+2] - ref[2]), 2));
-          ref_mol = true_label_mol[label_mol[j]];
-        }
-        else
-        {
-          
-        }
-      }
-  
-  free (old_needed_mol);
+    }
+    
+// add molecule
+    needed_mol[i] = 8 * i + jmin;
+// update ref
+    for (j=0; j<3; j++)
+    {
+      ref[j] += centr_coords[3*8*i+jmin+j];
+      ref[j] = ref[j] / 2;
+    }
+  }
   
   return 0;
 }

agl/src/select_mol.h

@@ -0,0 +1,14 @@
+/**
+ * @file
+ */
+
+#ifndef SELECT_MOL_H
+#define SELECT_MOL_H
+
+/**
+ * @fn select_molecule
+ */
+
+int select_molecule (const float *, const int, int *);
+
+#endif /* SELECT_MOL_H */

agl/src/set_center.c

@@ -0,0 +1,61 @@
+/**
+ * @file
+ */
+
+
+/**
+ * @fn set_center
+ */
+int set_center (const int num_atoms, const int num_mol, const int *label_mol, 
+                const float *coords, float *centr_coords)
+/**
+ * @brief function that searchs center mass of molecules
+ * @code
+ * set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
+ * @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
+ */
+  
+  for (i=0; i<8*num_mol; i++)
+    for (j=0; j<3; j++)
+      centr_coords[i*3+j] = 0.0;
+  
+  for (i=0; i<8*num_atoms; i++)
+  {
+    if (i < num_atoms)
+      cur_mol = 0;
+    else
+      cur_mol = ((i - num_atoms) % 7) + 1;
+    for (j=0; j<3; j++)
+      centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
+  }
+  
+  at_in_mol = 0;
+  cur_mol = 0;
+  for (i=0; i<num_atoms; i++)
+    if (cur_mol != label_mol[i])
+    {
+      for (j=0; j<8; j++)
+        for (k=0; k<3; k++)
+          centr_coords[3*(8*cur_mol+j)+k] = centr_coords[3*(8*cur_mol+j)+k] / at_in_mol;
+      at_in_mol = 0;
+      cur_mol = label_mol[i];
+    }
+    else
+      at_in_mol++;
+  
+  return 0;
+}

agl/src/set_center.h

@@ -0,0 +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 */

envir/src/add_main.c

@@ -18,8 +18,8 @@ int error_checking (const float *cell, const char *input, const char *output)
  * @endcode
  * 
  * @param cell            massive of cell size
- * @param input           first trajectory step
- * @param output          last trajectory step
+ * @param input           input file name
+ * @param output          output file name
  * 
  * @return 11             - error in 'cell'
  * @return 12             - error in 'input'
@@ -74,7 +74,7 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 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
+ * @brief function that sets default values of variables
  * @code
  * set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
  *               &type_inter, &quiet);

envir/src/envir_search.c

@@ -2,13 +2,6 @@
  * @file
  */
 
-/* Library for search environment
- * 
- * Usage:
- *      search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol, 
- *                                                              &num_needed_mol)
- */
-
 #include <math.h>
 
 

envir/src/main.c

@@ -27,7 +27,7 @@ int main(int argc, char *argv[])
  */
 {
   char tmp_str[2048];
-  int error, i, j, *tmp_int;
+  int error, i, *tmp_int;
   FILE *f_inp, *f_log;
   
   char *ch_type_atoms, input[256], logfile[256], output[256];
@@ -177,7 +177,7 @@ int main(int argc, char *argv[])
   
 // reading coordinates
   print_message (quiet, stdout, log, f_log, 7, input);
-  error = reading_coords (1, input, tmp_int, tmp_int, cell, &num_mol, &num_atoms, 
+  error = reading_coords (1, input, tmp_int[0], tmp_int, cell, &num_mol, &num_atoms, 
                           true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
   centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
   needed_mol = (int *) malloc (num_mol * sizeof (int));
@@ -198,15 +198,18 @@ int main(int argc, char *argv[])
 // analyze
   if (error == 0)
   {
+    error = 1;
     error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
     if (error == 0)
     {
       print_message (quiet, stderr, log, f_log, 20, argv[0]);
+      error = 1;
       error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol, 
                             &num_needed_mol);
       if (error == 0)
       {
         print_message (quiet, stderr, log, f_log, 21, argv[0]);
+        error = 1;
         error = print_structure (output, num_needed_mol, needed_mol, num_atoms, 
                                  label_mol, ch_type_atoms, coords);
         print_message (quiet, stderr, log, f_log, 12, output);

envir/src/messages.c

@@ -52,6 +52,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "Initialization of variables from file '%s'\n", text);
       break;
     case 4:
+      sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
       break;
     case 5:
       sprintf (out, "Initial parametrs: \n%s", text);

envir/src/print_struct.c

@@ -2,13 +2,6 @@
  * @file
  */
 
-/* Library for printing structure to pdb file
- * 
- * Usage:
- *              print_structure (output, num_needed_mol, needed_mol, num_atoms, 
- *                                           label_mol, char_type_atoms, coords)
- */
-
 #include <stdio.h>
 
 

envir/src/set_center.c

@@ -2,13 +2,6 @@
  * @file
  */
 
-/* Library for search center mass of molecules
- * 
- * Usage:
- *          set_center (num_of_atoms, num_of_molecules, label_molecules, coords, 
- *                                                                 centr_coords)
- */
-
 
 /**
  * @fn set_center

statgen/src/add_main.c

@@ -156,7 +156,7 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth, 
                   int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
 /**
- * @brief function for set default values of variables
+ * @brief function that sets default values of variables
  * @code
  * set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
  *               &type_inter, &quiet);

statgen/src/messages.c

@@ -52,6 +52,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "Initialization of variables from file '%s'\n", text);
       break;
     case 4:
+      sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
       break;
     case 5:
       sprintf (out, "Initial parametrs: \n%s", text);