Mercurial > repos > chemteam > mdanalysis_hbonds

comparison distance.py @ 1:5c38e38dbc35 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:51:36 -0400
parents 469ad3ea5a5f
children
comparison
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0:469ad3ea5a5f 1:5c38e38dbc35
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: