Mercurial > repos > chemteam > gmx_check
comparison merge_top.py @ 0:26467f738ed4 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author | chemteam |
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date | Tue, 12 Jul 2022 12:48:09 +0000 |
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-1:000000000000 | 0:26467f738ed4 |
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1 import argparse | |
2 | |
3 import parmed as pmd | |
4 | |
5 | |
6 def merge_gro_files(prot_gro, lig_gro, cmplx_gro): | |
7 prot = pmd.load_file(prot_gro) | |
8 lig = pmd.load_file(lig_gro) | |
9 cmplx = prot + lig | |
10 cmplx.save(cmplx_gro) | |
11 | |
12 | |
13 def merge_top_files(prot_top, lig_top, cmplx_top): | |
14 with open(lig_top, 'r') as f: | |
15 lig_top_sections = f.read().split('\n[') | |
16 | |
17 # open ligand topology | |
18 for n in range(len(lig_top_sections)): | |
19 if 'atomtypes' in lig_top_sections[n][:10]: | |
20 lig_atomtypes = lig_top_sections[n] | |
21 del lig_top_sections[n] | |
22 break | |
23 else: | |
24 lig_atomtypes = None | |
25 lig_top_updated = '\n['.join(lig_top_sections) | |
26 | |
27 # open protein topology | |
28 with open(prot_top, 'r') as f: | |
29 prot_top_combined = f.read() | |
30 if lig_atomtypes: | |
31 prot_top_sections = prot_top_combined.split('[ moleculetype ]\n') | |
32 prot_top_combined = (prot_top_sections[0] + | |
33 '; Include ligand atomtypes\n[' + | |
34 lig_atomtypes + | |
35 '\n[ moleculetype ]\n' + | |
36 prot_top_sections[1]) | |
37 prot_top_sections = prot_top_combined.split('; Include water topology') | |
38 prot_top_combined = (prot_top_sections[0] + | |
39 '; Include ligand topology\n' + | |
40 lig_top_updated + | |
41 '\n; Include water topology' + | |
42 prot_top_sections[1]) | |
43 prot_top_combined += 'base 1\n' | |
44 | |
45 # save complex topology | |
46 with open(cmplx_top, 'w') as f: | |
47 f.write(prot_top_combined) | |
48 | |
49 | |
50 def main(): | |
51 parser = argparse.ArgumentParser( | |
52 description='Perform SMD runs for dynamic undocking') | |
53 parser.add_argument('--lig-top', help='Ligand TOP file.') | |
54 parser.add_argument('--prot-top', help='Protein TOP file.') | |
55 parser.add_argument('--lig-gro', help='Ligand GRO file.') | |
56 parser.add_argument('--prot-gro', help='Protein GRO file.') | |
57 parser.add_argument('--complex-top', help='Complex TOP file.') | |
58 parser.add_argument('--complex-gro', help='Complex GRO file.') | |
59 args = parser.parse_args() | |
60 merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro) | |
61 merge_top_files(args.prot_top, args.lig_top, args.complex_top) | |
62 | |
63 | |
64 if __name__ == "__main__": | |
65 main() |