Mercurial > repos > chemteam > mdanalysis_dihedral

annotate extract_rmsd.py @ 9:976cfd44b921 draft default tip

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 f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author chemteam
date Fri, 13 Nov 2020 19:43:11 +0000
parents f55dd7c08112
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
1 import argparse
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
2 import json
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
3
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
4 import MDAnalysis as m
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
5 from MDAnalysis.analysis import rms
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
6
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
7 import numpy as np
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
8
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
9
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
10 def calc_rmsd(str_files, traj_files, str_format, traj_format, filepath_out,
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
11 group, start, end, step):
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
12 """
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
13 the function will cycle through range 0 to no_t and load all files found.
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
14
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
15 str_files: text file with filepaths for structures, one on each line
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
16 traj_files: text file with filepaths for trajectories, one on each line
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
17 filepath_in: directory where the files are located
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
18 filepath_out: pickle file where results (3D matrix) should be saved to
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
19
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
20 group: atoms for which RMSD should be calculated;
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
21 use the MDAnalysis selection language
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
22
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
23 start: first trajectory frame to calculate RMSD
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
24 end: last trajectory frame to calculate RMSD
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
25 step: how frequently frames are sampled between start and end; obviously,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
26 the larger the step, the quicker the script finishes
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
27 """
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
28
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
29 # open list of files
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
30 with open(str_files) as f1, open(traj_files) as f2:
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
31 str_file_list = f1.read().strip().split('\n')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
32 traj_file_list = f2.read().strip().split('\n')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
33
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
34 if sum(1 for line in f1) != sum(1 for line in f2):
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
35 raise IOError('Number of structure and trajectory files unequal.')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
36
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
37 no_t = len(traj_file_list)
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
38
9
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
39 # hard to find array size before loading files
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
40 universe_coordinate_data = []
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
41
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
42 for traj in range(no_t):
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
43 # We no longer align here, users should do this themselves.
9
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
44 u = m.Universe(str_file_list[traj], traj_file_list[traj],
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
45 format=traj_format, topology_format=str_format)
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
46 u.transfer_to_memory()
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
47 grp = u.select_atoms(group).universe
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
48 coordinates = grp.trajectory.coordinate_array[start:end:step]
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
49 universe_coordinate_data.append(coordinates)
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
50
9
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
51 universe_coordinate_data = np.array(universe_coordinate_data)
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
52 print("All trajs loaded by MDAnalysis")
9
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
53 data = np.zeros((no_t, no_t, universe_coordinate_data.shape[1]))
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
54
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
55 # calculate differences
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
56 for traj1 in range(no_t):
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
57 print("Calculating differences for traj {}".format(traj1))
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
58 for traj2 in range(traj1):
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
59 for frame in range(data.shape[2]):
9
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
60 A = universe_coordinate_data[traj1, frame]
976cfd44b921 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 8
diff changeset
61 B = universe_coordinate_data[traj2, frame]
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
62 r = rms.rmsd(A, B)
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
63 data[traj1, traj2, frame] = r
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
64 data[traj2, traj1, frame] = r
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
65
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
66 with open(filepath_out, 'w') as f:
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
67 json.dump(data.tolist(), f, indent=4, sort_keys=True)
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
68
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
69 print("Done!")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
70 return
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
71
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
72
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
73 def main():
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
74 parser = argparse.ArgumentParser()
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
75 parser.add_argument('--trajs', required=True,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
76 help='File containing trajectory filepaths.')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
77 parser.add_argument("--strs",
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
78 help='File containing structure filepaths.')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
79 parser.add_argument('--traj-format', required=True,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
80 help='Trajectory format.')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
81 parser.add_argument("--str-format", help='Structure format.')
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
82 parser.add_argument('-o', '--outfile',
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
83 help="Path to the output JSON file")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
84 parser.add_argument('--group', help="Atoms for which RMSD should be"
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
85 "calculated in MDAnalysis selection language")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
86 parser.add_argument('--start', type=int,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
87 help="First trajectory frame to calculate RMSD")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
88 parser.add_argument('--end', type=int,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
89 help="Last trajectory frame to calculate RMSD")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
90 parser.add_argument('--step', type=int,
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
91 help="Frame sampling frequency for RMSD calculation")
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
92 args = parser.parse_args()
8
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
93 calc_rmsd(args.strs, args.trajs, args.str_format,
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
94 args.traj_format, args.outfile,
f55dd7c08112 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 7
diff changeset
95 args.group, args.start, args.end, args.step)
7
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
96
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
97
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
98 if __name__ == "__main__":
aaa130695a2b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
99 main()