diff gmxtras_add_newmolparam.py @ 0:5521a057ed6a draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmxtras_add_newmolparam.py	Thu Jan 27 18:16:37 2022 +0000
@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+import argparse
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Adds New topologies to gromacs topology file')
+    parser.add_argument(
+                        '--top_file', default=None,
+                        help="Topology file input")
+    parser.add_argument(
+                        '--mol_file', default=None,
+                        help='molecule type and bonded parameters input')
+    parser.add_argument(
+                        '--atom_file', default=None,
+                        help='atomtype and nonbonded parameters input')
+    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:
+            # these two short loop takes care of
+            # adding the atom types and molecule types.
+            for line in fh:
+                fh_out.write(line)
+                if ';name   bond_type' in line:
+                    for contents in open(args.atom_file):
+                        fh_out.write(contents)
+                    break
+            for line in fh:
+                if '[ system ]' in line:
+                    fh_out.write("\n; Begin NewTopologyInfo\n")
+                    for contents in open(args.mol_file):
+                        fh_out.write(contents)
+                    fh_out.write("; end NewTopologyInfo\n\n")
+                    fh_out.write(line)
+                    break
+                fh_out.write(line)
+            for line in fh:
+                fh_out.write(line)
+
+
+if __name__ == "__main__":
+    __main__()