Mercurial > repos > chemteam > mdanalysis_extract_rmsd

comparison hbonds.py @ 0:743bd6aa3c7a draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:41:41 -0400
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-1:000000000000 0:743bd6aa3c7a
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import sys
6
7 import MDAnalysis as mda
8 import MDAnalysis.analysis.hbonds
9
10 import pandas as pd
11
12
13 def parse_command_line(argv):
14 parser = argparse.ArgumentParser()
15 parser.add_argument('--itraj', help='input traj')
16 parser.add_argument('--istr', help='input str')
17 parser.add_argument('--itrajext', help='input traj ext')
18 parser.add_argument('--istrext', help='input str ext')
19 parser.add_argument('--isegid1', help='segid 1')
20 parser.add_argument('--isegid2', help='segid 2')
21 parser.add_argument('--idistance', help='cutoff distance')
22 parser.add_argument('--iangle', help='ctoff angle')
23 parser.add_argument('--output', help='output')
24 parser.add_argument('--ofreq_output', help='frequency output')
25 parser.add_argument('--onumber_output', help='number of hbond output')
26 parser.add_argument('--otime_output', help='time steps output')
27 return parser.parse_args()
28
29
30 args = parse_command_line(sys.argv)
31
32 selection1 = "segid %s" % args.isegid1
33 selection2 = "segid %s" % args.isegid2
34 distance = float(args.idistance)
35 angle = float(args.iangle)
36
37 u = mda.Universe(args.istr, args.itraj,
38 topology_format=args.istrext, format=args.itrajext)
39
40 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(
41 u, selection1, selection2, distance=distance, angle=angle)
42 h.run()
43 h.generate_table()
44
45 df = pd.DataFrame.from_records(h.table)
46 df.to_csv(args.output, sep='\t')
47
48 t1 = list(h.count_by_type())
49 t2 = list(h.count_by_time())
50 t3 = list(h.timesteps_by_type())
51
52 with open(args.ofreq_output, 'w') as f:
53 f.write("donor_index\tacceptor_index\t\
54 donor_resname\tdonor_resid\tdonor_atom\t\
55 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
56 acceptor_atom\tfrequency\n")
57 writer = csv.writer(f, delimiter='\t')
58 writer.writerows(t1)
59
60
61 with open(args.onumber_output, 'w') as f1:
62 f1.write("time_step\tno_of_h_bonds\n")
63 writer = csv.writer(f1, delimiter='\t')
64 writer.writerows(t2)
65
66 with open(args.otime_output, 'w') as f2:
67 f2.write("donor_index\tacceptor_index\t\
68 donor_resname\tdonor_resid\tdonor_atom\t\
69 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
70 acceptor_atom\ttime_step\n")
71 writer = csv.writer(f2, delimiter='\t')
72 writer.writerows(t3)