comparison 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"
author chemteam
date Thu, 27 Jan 2022 18:16:37 +0000
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-1:000000000000 0:5521a057ed6a
1 #!/usr/bin/env python3
2 import argparse
3
4
5 def __main__():
6 parser = argparse.ArgumentParser(
7 description='Adds New topologies to gromacs topology file')
8 parser.add_argument(
9 '--top_file', default=None,
10 help="Topology file input")
11 parser.add_argument(
12 '--mol_file', default=None,
13 help='molecule type and bonded parameters input')
14 parser.add_argument(
15 '--atom_file', default=None,
16 help='atomtype and nonbonded parameters input')
17 parser.add_argument(
18 '--out', default=None,
19 help='Path to output')
20 args = parser.parse_args()
21 with open(args.out, 'w') as fh_out:
22 with open(args.top_file, 'r') as fh:
23 # these two short loop takes care of
24 # adding the atom types and molecule types.
25 for line in fh:
26 fh_out.write(line)
27 if ';name bond_type' in line:
28 for contents in open(args.atom_file):
29 fh_out.write(contents)
30 break
31 for line in fh:
32 if '[ system ]' in line:
33 fh_out.write("\n; Begin NewTopologyInfo\n")
34 for contents in open(args.mol_file):
35 fh_out.write(contents)
36 fh_out.write("; end NewTopologyInfo\n\n")
37 fh_out.write(line)
38 break
39 fh_out.write(line)
40 for line in fh:
41 fh_out.write(line)
42
43
44 if __name__ == "__main__":
45 __main__()