Mercurial > repos > chemteam > mdanalysis_dihedral

annotate distance.py @ 1:8845c77d62f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
author chemteam
date Thu, 20 Dec 2018 06:46:54 -0500
parents 1abbf9ca75fa
children 4c431a33590e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
2
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
3 import argparse
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
4 import sys
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
5
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
6 import MDAnalysis as mda
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
7
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
8 import matplotlib
1
8845c77d62f2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
9 matplotlib.use('Agg') # noqa
0
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
10 import matplotlib.pyplot as plt
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
11
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
12 import numpy as np
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
13
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
14
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
15 def parse_command_line(argv):
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
16 parser = argparse.ArgumentParser()
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
17 parser.add_argument('--idcd', help='input dcd')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
18 parser.add_argument('--ipdb', help='input pdb')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
19 parser.add_argument('--isegid1', help='segid 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
20 parser.add_argument('--iresid1', help='resid 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
21 parser.add_argument('--iname1', help='name 1')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
22 parser.add_argument('--isegid2', help='segid 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
23 parser.add_argument('--iresid2', help='resid 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
24 parser.add_argument('--iname2', help='name 2')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
25 parser.add_argument('--output', help='output')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
26 parser.add_argument('--odistance_plot', help='odistance plot')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
27 return parser.parse_args()
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
28
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
29
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
30 args = parse_command_line(sys.argv)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
31
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
32 atom1 = "(segid %s and resid %s and name %s)" % \
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
33 (args.isegid1, args.iresid1, args.iname1)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
34 atom2 = "(segid %s and resid %s and name %s)" % \
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
35 (args.isegid2, args.iresid2, args.iname2)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
36
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
37 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
38 x = u.select_atoms(atom1)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
39 y = u.select_atoms(atom2)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
40
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
41 with open(args.output, 'w') as f:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
42 for t in u.trajectory:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
43 r = x.positions - y.positions
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
44 d = np.linalg.norm(r)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
45 f.write(str(t.frame) + '\t ')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
46 f.write(str(d) + '\n')
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
47
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
48 with open(args.output) as f:
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
49 g = [xtmp.strip() for xtmp in f]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
50 data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
51 time = [xtmp[0] for xtmp in data]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
52 distance = [xtmp[1] for xtmp in data]
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
53 plt.plot(time, distance)
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
54 plt.xlabel('Frame No.')
1
8845c77d62f2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
chemteam
parents: 0
diff changeset
55 plt.ylabel(r'Distance ($\AA$)')
0
1abbf9ca75fa planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 6a59f07610c28b07f1d2d2b3badf3a9b8aacce50
chemteam
parents:
diff changeset
56 plt.savefig(args.odistance_plot, format='png')