Mercurial > repos > chemteam > mdanalysis_rdf
comparison hbonds.py @ 4:36babbdd7818 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:51:57 -0400 |
| parents | 49dac57d004a |
| children |
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| 3:49dac57d004a | 4:36babbdd7818 |
|---|---|
| 2 | 2 |
| 3 import argparse | 3 import argparse |
| 4 import csv | 4 import csv |
| 5 import sys | 5 import sys |
| 6 | 6 |
| 7 import MDAnalysis as mda | |
| 7 import MDAnalysis.analysis.hbonds | 8 import MDAnalysis.analysis.hbonds |
| 8 | 9 |
| 9 import pandas as pd | 10 import pandas as pd |
| 10 | 11 |
| 11 | 12 |
| 12 def parse_command_line(argv): | 13 def parse_command_line(argv): |
| 13 parser = argparse.ArgumentParser() | 14 parser = argparse.ArgumentParser() |
| 14 parser.add_argument('--idcd', help='input dcd') | 15 parser.add_argument('--itraj', help='input traj') |
| 15 parser.add_argument('--ipdb', help='input pdb') | 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') | |
| 16 parser.add_argument('--isegid1', help='segid 1') | 19 parser.add_argument('--isegid1', help='segid 1') |
| 17 parser.add_argument('--isegid2', help='segid 2') | 20 parser.add_argument('--isegid2', help='segid 2') |
| 18 parser.add_argument('--idistance', help='cutoff distance') | 21 parser.add_argument('--idistance', help='cutoff distance') |
| 19 parser.add_argument('--iangle', help='ctoff angle') | 22 parser.add_argument('--iangle', help='ctoff angle') |
| 20 parser.add_argument('--output', help='output') | 23 parser.add_argument('--output', help='output') |
| 29 selection1 = "segid %s" % args.isegid1 | 32 selection1 = "segid %s" % args.isegid1 |
| 30 selection2 = "segid %s" % args.isegid2 | 33 selection2 = "segid %s" % args.isegid2 |
| 31 distance = float(args.idistance) | 34 distance = float(args.idistance) |
| 32 angle = float(args.iangle) | 35 angle = float(args.iangle) |
| 33 | 36 |
| 34 u = MDAnalysis.Universe( | 37 u = mda.Universe(args.istr, args.itraj, |
| 35 args.ipdb, args.idcd, topology_format="PDB", format="DCD") | 38 topology_format=args.istrext, format=args.itrajext) |
| 36 | 39 |
| 37 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( | 40 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( |
| 38 u, selection1, selection2, distance=distance, angle=angle) | 41 u, selection1, selection2, distance=distance, angle=angle) |
| 39 h.run() | 42 h.run() |
| 40 h.generate_table() | 43 h.generate_table() |