Mercurial > repos > chemteam > gmx_merge_topology_files

annotate merge_top.py @ 17:930a403f7389 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 7120a24dbb365d0a06595018a3b6f27dad0961e0"
author chemteam
date Mon, 14 Mar 2022 10:36:01 +0000
parents 06ea4e040d45
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
1 import argparse
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
2
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
3 import parmed as pmd
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
4
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
5
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
6 def merge_gro_files(prot_gro, lig_gro, cmplx_gro):
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
7 prot = pmd.load_file(prot_gro)
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
8 lig = pmd.load_file(lig_gro)
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
9 cmplx = prot + lig
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
10 cmplx.save(cmplx_gro)
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
11
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
12
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
13 def merge_top_files(prot_top, lig_top, cmplx_top):
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
14 with open(lig_top, 'r') as f:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
15 lig_top_sections = f.read().split('\n[')
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
16
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
17 # open ligand topology
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
18 for n in range(len(lig_top_sections)):
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
19 if 'atomtypes' in lig_top_sections[n][:10]:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
20 lig_atomtypes = lig_top_sections[n]
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
21 del lig_top_sections[n]
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
22 break
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
23 else:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
24 lig_atomtypes = None
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
25 lig_top_updated = '\n['.join(lig_top_sections)
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
26
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
27 # open protein topology
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
28 with open(prot_top, 'r') as f:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
29 prot_top_combined = f.read()
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
30 if lig_atomtypes:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
31 prot_top_sections = prot_top_combined.split('[ moleculetype ]\n')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
32 prot_top_combined = (prot_top_sections[0] +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
33 '; Include ligand atomtypes\n[' +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
34 lig_atomtypes +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
35 '\n[ moleculetype ]\n' +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
36 prot_top_sections[1])
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
37 prot_top_sections = prot_top_combined.split('; Include water topology')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
38 prot_top_combined = (prot_top_sections[0] +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
39 '; Include ligand topology\n' +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
40 lig_top_updated +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
41 '\n; Include water topology' +
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
42 prot_top_sections[1])
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
43 prot_top_combined += 'base 1\n'
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
44
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
45 # save complex topology
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
46 with open(cmplx_top, 'w') as f:
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
47 f.write(prot_top_combined)
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
48
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
49
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
50 def main():
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
51 parser = argparse.ArgumentParser(
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
52 description='Perform SMD runs for dynamic undocking')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
53 parser.add_argument('--lig-top', help='Ligand TOP file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
54 parser.add_argument('--prot-top', help='Protein TOP file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
55 parser.add_argument('--lig-gro', help='Ligand GRO file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
56 parser.add_argument('--prot-gro', help='Protein GRO file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
57 parser.add_argument('--complex-top', help='Complex TOP file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
58 parser.add_argument('--complex-gro', help='Complex GRO file.')
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
59 args = parser.parse_args()
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
60 merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro)
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
61 merge_top_files(args.prot_top, args.lig_top, args.complex_top)
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
62
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
63
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
64 if __name__ == "__main__":
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
chemteam
parents: 0
diff changeset
65 main()