From 1db71b413081978fab707bd455dfd5d68dfb49b2 Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Mon, 17 Dec 2012 14:39:32 +0400
Subject: [PATCH] Added mol2rtp

---
 mol2rtp/README    | 24 +++++++++++++
 mol2rtp/mol2rtp.c | 88 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 112 insertions(+)
 create mode 100644 mol2rtp/README
 create mode 100644 mol2rtp/mol2rtp.c

diff --git a/mol2rtp/README b/mol2rtp/README
new file mode 100644
index 0000000..b16d5f5
--- /dev/null
+++ b/mol2rtp/README
@@ -0,0 +1,24 @@
+                    mol2rtp 
+Version:                                       1.0
+Author:                Evgeniy Alexeev aka arcanis
+Email:                         esalexeev@gmail.com
+
+
+mol2rtp convert *.mol2 file in GROMACS topology
+file (*.rtp).
+
+Usage:           
+                    mol2rtp [MOL2.FILE] [RTP.FILE]
+For example:
+                      mol2rtp exmpl.mol2 exmpl.rtp
+
+NOTE: You must edit molecular mechanics atom types 
+in output *.rtp-file, because atom types in *.mol2
+file don't match GROMACS atom types.
+
+
+Compile:
+                          gcc mol2rtp.c -o mol2rtp
+Dependence:
+    * gcc
+    * lib: string.h, stdlib.c, stdio.h
diff --git a/mol2rtp/mol2rtp.c b/mol2rtp/mol2rtp.c
new file mode 100644
index 0000000..1ea8ae4
--- /dev/null
+++ b/mol2rtp/mol2rtp.c
@@ -0,0 +1,88 @@
+#include<stdio.h>
+#include<stdlib.h>
+#include<string.h>
+
+
+void main(int argc, char *argv[])
+{
+  int i, j, n_bonds, n_angles, num[2];
+  char q[256], label[512][4], type[4];
+  double charge;
+  FILE *inp, *out;
+
+
+  if (argc == 1)
+  {
+    printf ("Error: Parametrs is not enable!\n");
+    printf ("Usage --help or -h for help\n");
+    exit(0);
+  }
+  if ((argv[1][0] == '-' && argv[1][1] == '-' && argv[1][2] == 'h' && argv[1][3] == 'e' && argv[1][4] == 'l', argv[1][5] == 'p') || (argv[1][0] == '-' && argv[1][1] == 'h'))
+  {
+    printf ("mol2rtp convert *.mol2 file in GROMACS topology file *.rtp\n");
+    printf ("NOTE: You must edit MM atom type in *.rtp file\n");
+    printf ("Usage:    mol2rtp [MOL2.FILE] [RTP.FILE]\n");
+    printf ("Evgeniy Alexeev aka arcanis\n");
+    printf ("email: esalexeev@gmail.com\n");
+    exit(0);
+  }
+  else
+    if (argc == 2)
+    {
+      printf ("Error: Parametrs is not enable!\n");
+      printf ("Usage --help or -h for help\n");
+      exit(0);
+    }
+
+
+  printf ("mol2rtp V.1.0\n");
+  inp = fopen (argv[1], "r+");
+  if (inp == NULL)
+  {
+    printf ("File %s is not found!\n", argv[1]);
+    exit(0);
+  }
+  out = fopen (argv[2], "w+");
+
+
+  fgets (q, 255, inp);
+  fgets (q, 255, inp);
+  fscanf (inp, "%i", &n_bonds);
+  fscanf (inp, "%i", &n_angles);
+  for (i=0; i<5; i++)
+    fgets (q, 255, inp);
+
+
+  printf ("Enter molecule name: ");
+  scanf ("%s", q);
+  fprintf (out, "[ %s ]\n [ atoms ]\n", q);
+  for (i=0; i<n_bonds; i++)
+  {
+    fgets( q, 255, inp);
+    charge = atof (&q[69]);
+    for (j=0; j<4; j++)
+    {
+      type[j] = q[j+47];
+      label[i][j] = q[j+8];
+    }
+
+    fprintf (out, "  %c%c%c%c   %c%c%c%c   %5.2f%5i\n", label[i][0], label[i][1], label[i][2], label[i][3], type[0], type[1], type[2], type[3], charge, i);
+  }
+
+
+  fprintf (out, " [ bonds ]\n");
+  fgets (q, 255, inp);
+  for (i=0; i<n_angles; i++)
+  {
+    fscanf (inp, "%i", &j);
+    fscanf (inp, "%i", &num[0]);
+    fscanf (inp, "%i", &num[1]);
+    fscanf (inp, "%i", &j);
+
+    fprintf (out, "  %c%c%c%c    %c%c%c%c\n", label[num[0]-1][0], label[num[0]-1][1], label[num[0]-1][2], label[num[0]-1][3], label[num[1]-1][0], label[num[1]-1][1], label[num[1]-1][2], label[num[1]-1][3]);
+  }
+
+
+  fclose (inp);
+  fclose (out);
+}