Mercurial > repos > chemteam > mdanalysis_rdf

comparison hbonds.py @ 3:49dac57d004a draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:47:16 -0400
parents
children 36babbdd7818
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2:57a3d6f94bcd 3:49dac57d004a
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import sys
6
7 import MDAnalysis.analysis.hbonds
8
9 import pandas as pd
10
11
12 def parse_command_line(argv):
13 parser = argparse.ArgumentParser()
14 parser.add_argument('--idcd', help='input dcd')
15 parser.add_argument('--ipdb', help='input pdb')
16 parser.add_argument('--isegid1', help='segid 1')
17 parser.add_argument('--isegid2', help='segid 2')
18 parser.add_argument('--idistance', help='cutoff distance')
19 parser.add_argument('--iangle', help='ctoff angle')
20 parser.add_argument('--output', help='output')
21 parser.add_argument('--ofreq_output', help='frequency output')
22 parser.add_argument('--onumber_output', help='number of hbond output')
23 parser.add_argument('--otime_output', help='time steps output')
24 return parser.parse_args()
25
26
27 args = parse_command_line(sys.argv)
28
29 selection1 = "segid %s" % args.isegid1
30 selection2 = "segid %s" % args.isegid2
31 distance = float(args.idistance)
32 angle = float(args.iangle)
33
34 u = MDAnalysis.Universe(
35 args.ipdb, args.idcd, topology_format="PDB", format="DCD")
36
37 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(
38 u, selection1, selection2, distance=distance, angle=angle)
39 h.run()
40 h.generate_table()
41
42 df = pd.DataFrame.from_records(h.table)
43 df.to_csv(args.output, sep='\t')
44
45 t1 = list(h.count_by_type())
46 t2 = list(h.count_by_time())
47 t3 = list(h.timesteps_by_type())
48
49 with open(args.ofreq_output, 'w') as f:
50 f.write("donor_index\tacceptor_index\t\
51 donor_resname\tdonor_resid\tdonor_atom\t\
52 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
53 acceptor_atom\tfrequency\n")
54 writer = csv.writer(f, delimiter='\t')
55 writer.writerows(t1)
56
57
58 with open(args.onumber_output, 'w') as f1:
59 f1.write("time_step\tno_of_h_bonds\n")
60 writer = csv.writer(f1, delimiter='\t')
61 writer.writerows(t2)
62
63 with open(args.otime_output, 'w') as f2:
64 f2.write("donor_index\tacceptor_index\t\
65 donor_resname\tdonor_resid\tdonor_atom\t\
66 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
67 acceptor_atom\ttime_step\n")
68 writer = csv.writer(f2, delimiter='\t')
69 writer.writerows(t3)