- removed *.pdf

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

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