--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmxtras_add_restraints.py	Thu Jan 27 18:17:05 2022 +0000
@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+import argparse
+END_OF_MOL = ('[ moleculetype ]', '[ system ]')
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Add restriction to gromacs topology file')
+    parser.add_argument(
+                        '--top_file', default=None,
+                        help="Topology file input")
+    parser.add_argument(
+                        '--res_file', default=None,
+                        help='Restraint input')
+    parser.add_argument(
+                        '--molecule', default=None,
+                        help='Target Molecule Name you restrained')
+    parser.add_argument(
+                        '--out', default=None,
+                        help='Path to output')
+    args = parser.parse_args()
+    with open(args.out, 'w') as fh_out:
+        with open(args.top_file, 'r') as fh:
+            # for now, we will avoid using 'for line in fh:',
+            # since we have multiple places where we might want
+            # to read the next line
+            while True:
+                line = fh.readline()
+                if not line:
+                    # eof
+                    break
+                # always write out the line
+                fh_out.write(line)
+                # check if line matches molecule, then check if
+                # molecule name matches args.molecule
+                if line.strip().startswith('[ moleculetype ]'):
+                    not_found_molecule = True
+                    while not_found_molecule:
+                        line = fh.readline()
+                        if not line:
+                            # eof
+                            break
+                        # always write this line
+                        fh_out.write(line)
+                        if not line.strip().startswith(';') or (line.strip()
+                           and not line.strip().startswith(';')):
+                            # this line should be the name line,
+                            fields = line.strip().split()
+                            if fields[0] == args.molecule:
+                                # found our molecule!
+                                while True:
+                                    line = fh.readline()
+                                    if not line:
+                                        # eof
+                                        break
+                                    if line.strip().startswith(END_OF_MOL):
+                                        fh_out.write("\n#ifdef POSRES\n")
+                                        with open(args.res_file, 'r') as fh_re:
+                                            for line2 in fh_re:
+                                                fh_out.write(line2)
+                                        fh_out.write("#endif\n\n")
+                                        fh_out.write(line)
+                                        not_found_molecule = False
+                                        break
+                                    fh_out.write(line)
+                            else:
+                                break
+
+
+if __name__ == "__main__":
+    __main__()