Mercurial > repos > chemteam > mdanalysis_rdf
annotate hbonds.py @ 6:fb2b84481239 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
| author | chemteam |
|---|---|
| date | Wed, 20 May 2020 16:56:07 +0000 |
| parents | aabf6858f293 |
| children |
| rev | line source |
|---|---|
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3
fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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1 #!/usr/bin/env python |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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2 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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3 import argparse |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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4 import csv |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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5 import sys |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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6 |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
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changeset
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7 import MDAnalysis as mda |
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3
fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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8 import MDAnalysis.analysis.hbonds |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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9 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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10 import pandas as pd |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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11 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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12 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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13 def parse_command_line(argv): |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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14 parser = argparse.ArgumentParser() |
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4
aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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15 parser.add_argument('--itraj', help='input traj') |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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16 parser.add_argument('--istr', help='input str') |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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17 parser.add_argument('--itrajext', help='input traj ext') |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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18 parser.add_argument('--istrext', help='input str ext') |
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3
fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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19 parser.add_argument('--isegid1', help='segid 1') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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20 parser.add_argument('--isegid2', help='segid 2') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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21 parser.add_argument('--idistance', help='cutoff distance') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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22 parser.add_argument('--iangle', help='ctoff angle') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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23 parser.add_argument('--output', help='output') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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24 parser.add_argument('--ofreq_output', help='frequency output') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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25 parser.add_argument('--onumber_output', help='number of hbond output') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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26 parser.add_argument('--otime_output', help='time steps output') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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27 return parser.parse_args() |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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28 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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29 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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30 args = parse_command_line(sys.argv) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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31 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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32 selection1 = "segid %s" % args.isegid1 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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33 selection2 = "segid %s" % args.isegid2 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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34 distance = float(args.idistance) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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35 angle = float(args.iangle) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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36 |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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37 u = mda.Universe(args.istr, args.itraj, |
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aabf6858f293
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
3
diff
changeset
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38 topology_format=args.istrext, format=args.itrajext) |
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3
fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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39 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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40 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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41 u, selection1, selection2, distance=distance, angle=angle) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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42 h.run() |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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43 h.generate_table() |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
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44 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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45 df = pd.DataFrame.from_records(h.table) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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46 df.to_csv(args.output, sep='\t') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
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47 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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48 t1 = list(h.count_by_type()) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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49 t2 = list(h.count_by_time()) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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50 t3 = list(h.timesteps_by_type()) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
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51 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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52 with open(args.ofreq_output, 'w') as f: |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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53 f.write("donor_index\tacceptor_index\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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54 donor_resname\tdonor_resid\tdonor_atom\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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55 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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56 acceptor_atom\tfrequency\n") |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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57 writer = csv.writer(f, delimiter='\t') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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58 writer.writerows(t1) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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59 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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60 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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61 with open(args.onumber_output, 'w') as f1: |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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62 f1.write("time_step\tno_of_h_bonds\n") |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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63 writer = csv.writer(f1, delimiter='\t') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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64 writer.writerows(t2) |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
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65 |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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66 with open(args.otime_output, 'w') as f2: |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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67 f2.write("donor_index\tacceptor_index\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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68 donor_resname\tdonor_resid\tdonor_atom\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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69 hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\ |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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70 acceptor_atom\ttime_step\n") |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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71 writer = csv.writer(f2, delimiter='\t') |
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fdc0c1615372
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff
changeset
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72 writer.writerows(t3) |