From 631e0f8860430909e330a8308628803c33fc8143 Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Tue, 25 Jun 2013 14:18:27 +0400
Subject: [PATCH] Added envir

---
 envir/envir.c | 219 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 219 insertions(+)
 create mode 100644 envir/envir.c

diff --git a/envir/envir.c b/envir/envir.c
new file mode 100644
index 0000000..4cabf0f
--- /dev/null
+++ b/envir/envir.c
@@ -0,0 +1,219 @@
+/*                               envir
+ * Version:                                                                 1.0
+ * License:                                                                 GPL
+ * Author:                                          Evgeniy Alexeev aka arcanis
+ * Email:                                                   esalexeev@gmail.com
+ *
+ * 'envir' is a program for search environment for chosen molecule by geometric 
+ * criterion
+ *
+ * Usage: 
+ *    envir -i FILENAME -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] [ -h ]
+ *
+ * Compile:
+ *                                                     gcc envir.c -o envir -lm
+ * Dependence:
+ *      * gcc
+ *      * libs: stdio.h, stdlib.h, string.h, math.h
+ */
+
+#include<stdio.h>
+#include<stdlib.h>
+#include<string.h>
+#include<math.h>
+
+
+char atom_type[5000][30][2];
+double centr_coord[5000][3], coord[5000][30][3], rad;
+int at_in_mol[5000], mol, needed_mol[50], num_of_mol;
+/* at_in_mol          - number of atoms in molecules
+ * atom_type          - massive of atom names
+ * centr_coord        - coordinates of molecule mass center
+ * coord              - coordinates of atoms
+ * mol                - number of molecule in system
+ * needed_mol         - massive of mulecules found
+ * num_of_mol         - number of molecule for search
+ * rad                - geometric criterion
+ */ 
+
+
+void printing(char output_file[])
+{
+  int cur_mol=0, i, j=1;
+  FILE *out;
+
+  out = fopen (output_file, "w+");
+  while (needed_mol[cur_mol] != 10000)
+  {
+    for (i=0; i<at_in_mol[needed_mol[cur_mol]]; i++)
+    {
+      fprintf(out, "ATOM  %5i %c%c MOL  %4i    %8.3f%8.3f%8.3f\n", j, atom_type[needed_mol[cur_mol]][i][0], \
+          atom_type[needed_mol[cur_mol]][i][1], cur_mol+1, coord[needed_mol[cur_mol]][i][0], \
+          coord[needed_mol[cur_mol]][i][1], coord[needed_mol[cur_mol]][i][2]);
+      j++;
+    }
+    cur_mol++;
+  }
+  fclose (out);
+}
+
+
+void search()
+{
+  double r;
+  int i, k=0;
+
+  for (i=0; i<50; i++)
+    needed_mol[i] = 10000;
+
+  for (i=0; i<mol; i++)
+  {
+    r = sqrt(pow((centr_coord[i][0]-centr_coord[num_of_mol-1][0]), 2) + \
+        pow((centr_coord[i][1]-centr_coord[num_of_mol-1][1]), 2) + \
+        pow((centr_coord[i][2]-centr_coord[num_of_mol-1][2]), 2));
+    if (r < rad)
+    {
+      needed_mol[k] = i;
+      k++;
+    }
+  }
+}
+
+
+void set_center()
+{
+  int i, j, k;
+
+  for (i=0; i<mol; i++)
+    for (j=0; j<3; j++)
+      centr_coord[i][j] = 0;
+
+  for (i=0; i<mol; i++)
+    for (j=0; j<at_in_mol[i]; j++)
+      for (k=0; k<3; k++)
+        centr_coord[i][k] += coord[i][j][k] / at_in_mol[i];
+}
+
+
+void reading(char input_file[])
+{
+  char tmp[256];
+  int atom_num, cur_mol=0, i, summ;
+  FILE *inp;
+
+  inp = fopen (input_file, "r+");
+  fscanf (inp, "%i", &summ);
+  fgets (tmp, 256, inp);
+  printf ("Atoms in system: %i\n", summ);
+  for (i=0; i<summ; i++)
+  {
+    fgets (tmp, 256, inp);
+    if (atoi(&tmp[53]) != mol+1)
+    {
+      at_in_mol[mol] = cur_mol;
+      mol++;
+      cur_mol = 0;
+    }
+
+    atom_type[mol][cur_mol][0] = tmp[7];
+    atom_type[mol][cur_mol][1] = tmp[8];
+    coord[mol][cur_mol][0] = atof(&tmp[10]);
+    coord[mol][cur_mol][1] = atof(&tmp[22]);
+    coord[mol][cur_mol][2] = atof(&tmp[34]);
+
+    cur_mol++;
+  }
+  fclose (inp);
+  mol++;
+}
+
+
+int main(int argc, char *argv[])
+{
+  char input_file[256], output_file[256];
+  int error_label=0, i, j;
+  FILE *f;
+
+  printf ("Starting program '%s'\n", argv[0]);
+  mol = 0;
+  rad = 6.0;
+  num_of_mol = 1;
+  
+
+  printf ("\n1) Reading arguments\n");
+  if (argc == 1)
+  {
+    printf ("Arguments are not set\nType 'envir -h' for help message\nExiting\n");
+    return 1;
+  }
+  
+  for (i=1; i<argc; i++)
+  {
+    if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+    {
+      strcpy(input_file, argv[i+1]);
+      f = fopen (argv[i+1], "r+");
+      if (f == NULL)
+      {
+        printf ("File '%s' does not exist!\nExiting\n", argv[i+1]);
+        return 1;
+      }
+      fclose(f);
+      printf ("Set input file to '%s'\n", input_file);
+      i++;
+      error_label++;
+    }
+
+    if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+    {
+      strcpy(output_file, argv[i+1]);
+      printf ("Set output file to '%s'\n", output_file);
+      i++;
+      error_label++;
+    }
+
+    if ((argv[i][0] == '-') && (argv[i][1] == 'n'))
+    {
+      num_of_mol = atoi(argv[i+1]);
+      printf ("Set number of molecule to '%i'\n", num_of_mol);
+      i++;
+    }
+
+    if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+    {
+      rad = atof(argv[i+1]);
+      printf ("Set radius to '%lf' A\n", rad);
+      i++;
+    }
+
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    {
+      printf ("Usage: envir -i FILENAME -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] [ -h ]\n\n");
+      printf ("  -i       - input file with coordinates\n");
+      printf ("  -o       - output file with coordinates\n");
+      printf ("  -n       - number of molecule for search\n");
+      printf ("  -r       - radius of environment\n");
+      printf ("  -h       - show this help and exit\n");
+      return 0;
+    }
+  }
+
+// error check
+  if (error_label < 2)
+  {
+    printf ("Input files aren't set\nType 'en_disp -h' for help message\nExiting\n");
+    return 1;
+  }
+
+  printf ("Reading file '%s'\n", input_file);
+  reading (input_file);
+  printf ("Set center of molecules\n");
+  set_center ();
+  printf ("Search environments\n");
+  search (); 
+  printf ("Printing\n");
+  printing (output_file);
+  printf ("Exiting without errors\n");
+
+  return 0;
+}