Mercurial > repos > chemteam > mdanalysis_hbonds

comparison rdf.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 5efd0c95f97e
comparison
equal deleted inserted replaced
0:469ad3ea5a5f 1:5c38e38dbc35
14 import numpy as np 14 import numpy as np
15 15
16 16
17 def parse_command_line(argv): 17 def parse_command_line(argv):
18 parser = argparse.ArgumentParser() 18 parser = argparse.ArgumentParser()
19 parser.add_argument('--idcd', help='input dcd') 19 parser.add_argument('--itraj', help='input traj')
20 parser.add_argument('--ipdb', help='input pdb') 20 parser.add_argument('--istr', help='input str')
21 parser.add_argument('--itrajext', help='input traj ext')
22 parser.add_argument('--istrext', help='input str ext')
21 parser.add_argument('--isegid1', help='segid 1') 23 parser.add_argument('--isegid1', help='segid 1')
22 parser.add_argument('--iresid1', help='resid 1') 24 parser.add_argument('--iresid1', help='resid 1')
23 parser.add_argument('--iname1', help='name 1') 25 parser.add_argument('--iname1', help='name 1')
24 parser.add_argument('--isegid2', help='segid 2') 26 parser.add_argument('--isegid2', help='segid 2')
25 parser.add_argument('--iresid2', help='resid 2') 27 parser.add_argument('--iresid2', help='resid 2')
40 (args.isegid2, args.iresid2, args.iname2) 42 (args.isegid2, args.iresid2, args.iname2)
41 bins = int(args.inbins) 43 bins = int(args.inbins)
42 start = float(args.istart) 44 start = float(args.istart)
43 end = float(args.iend) 45 end = float(args.iend)
44 46
45 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") 47 u = mda.Universe(args.istr, args.itraj,
48 topology_format=args.istrext, format=args.itrajext)
46 x = u.select_atoms(atom1) 49 x = u.select_atoms(atom1)
47 y = u.select_atoms(atom2) 50 y = u.select_atoms(atom2)
48 51
49 rdf = InterRDF(x, y, nbins=bins, range=(start, end)) 52 rdf = InterRDF(x, y, nbins=bins, range=(start, end))
50 rdf.run() 53 rdf.run()