Mercurial > repos > chemteam > mdanalysis_distance
comparison distance.py @ 4:312f912de69d draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:52:40 -0400 |
| parents | 2b1434ec8c7e |
| children |
comparison
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| 3:489b25966bb9 | 4:312f912de69d |
|---|---|
| 12 import numpy as np | 12 import numpy as np |
| 13 | 13 |
| 14 | 14 |
| 15 def parse_command_line(argv): | 15 def parse_command_line(argv): |
| 16 parser = argparse.ArgumentParser() | 16 parser = argparse.ArgumentParser() |
| 17 parser.add_argument('--idcd', help='input dcd') | 17 parser.add_argument('--itraj', help='input traj') |
| 18 parser.add_argument('--ipdb', help='input pdb') | 18 parser.add_argument('--istr', help='input str') |
| 19 parser.add_argument('--itrajext', help='input traj ext') | |
| 20 parser.add_argument('--istrext', help='input str ext') | |
| 19 parser.add_argument('--isegid1', help='segid 1') | 21 parser.add_argument('--isegid1', help='segid 1') |
| 20 parser.add_argument('--iresid1', help='resid 1') | 22 parser.add_argument('--iresid1', help='resid 1') |
| 21 parser.add_argument('--iname1', help='name 1') | 23 parser.add_argument('--iname1', help='name 1') |
| 22 parser.add_argument('--isegid2', help='segid 2') | 24 parser.add_argument('--isegid2', help='segid 2') |
| 23 parser.add_argument('--iresid2', help='resid 2') | 25 parser.add_argument('--iresid2', help='resid 2') |
| 32 atom1 = "(segid %s and resid %s and name %s)" % \ | 34 atom1 = "(segid %s and resid %s and name %s)" % \ |
| 33 (args.isegid1, args.iresid1, args.iname1) | 35 (args.isegid1, args.iresid1, args.iname1) |
| 34 atom2 = "(segid %s and resid %s and name %s)" % \ | 36 atom2 = "(segid %s and resid %s and name %s)" % \ |
| 35 (args.isegid2, args.iresid2, args.iname2) | 37 (args.isegid2, args.iresid2, args.iname2) |
| 36 | 38 |
| 37 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") | 39 u = mda.Universe(args.istr, args.itraj, |
| 40 topology_format=args.istrext, format=args.itrajext) | |
| 38 x = u.select_atoms(atom1) | 41 x = u.select_atoms(atom1) |
| 39 y = u.select_atoms(atom2) | 42 y = u.select_atoms(atom2) |
| 40 | 43 |
| 41 with open(args.output, 'w') as f: | 44 with open(args.output, 'w') as f: |
| 42 for t in u.trajectory: | 45 for t in u.trajectory: |