Mercurial > repos > chemteam > mdanalysis_endtoend

annotate extract_rmsd.py @ 2:795a5996cdc8 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 19:40:30 +0000
parents ce9dc91ff87f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
1 import argparse
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
2 import json
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
3
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
4 import MDAnalysis as m
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
5 from MDAnalysis.analysis import rms
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
6
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
7 import numpy as np
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
8
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
9
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
10 def calc_rmsd(str_files, traj_files, str_format, traj_format, filepath_out,
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
11 group, start, end, step):
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
12 """
78aa3659fcd1 "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.
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
14
78aa3659fcd1 "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
78aa3659fcd1 "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
78aa3659fcd1 "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
78aa3659fcd1 "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
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
19
78aa3659fcd1 "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;
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
21 use the MDAnalysis selection language
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
22
78aa3659fcd1 "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
78aa3659fcd1 "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
78aa3659fcd1 "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,
78aa3659fcd1 "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
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
27 """
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
28
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
29 # open list of files
78aa3659fcd1 "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:
78aa3659fcd1 "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')
78aa3659fcd1 "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')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
33
78aa3659fcd1 "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):
78aa3659fcd1 "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.')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
36
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
37 no_t = len(traj_file_list)
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
38
2
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
39 # hard to find array size before loading files
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
40 universe_coordinate_data = []
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
41
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
42 for traj in range(no_t):
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
43 # We no longer align here, users should do this themselves.
2
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
44 u = m.Universe(str_file_list[traj], traj_file_list[traj],
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
45 format=traj_format, topology_format=str_format)
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
46 u.transfer_to_memory()
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
47 grp = u.select_atoms(group).universe
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
48 coordinates = grp.trajectory.coordinate_array[start:end:step]
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
49 universe_coordinate_data.append(coordinates)
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
50
2
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
51 universe_coordinate_data = np.array(universe_coordinate_data)
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
52 print("All trajs loaded by MDAnalysis")
2
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
53 data = np.zeros((no_t, no_t, universe_coordinate_data.shape[1]))
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
54
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
55 # calculate differences
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
56 for traj1 in range(no_t):
78aa3659fcd1 "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))
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
58 for traj2 in range(traj1):
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
59 for frame in range(data.shape[2]):
2
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
60 A = universe_coordinate_data[traj1, frame]
795a5996cdc8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
chemteam
parents: 1
diff changeset
61 B = universe_coordinate_data[traj2, frame]
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
62 r = rms.rmsd(A, B)
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
63 data[traj1, traj2, frame] = r
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
64 data[traj2, traj1, frame] = r
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
65
78aa3659fcd1 "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:
78aa3659fcd1 "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)
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
68
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
69 print("Done!")
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
70 return
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
71
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
72
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
73 def main():
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
74 parser = argparse.ArgumentParser()
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
75 parser.add_argument('--trajs', required=True,
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
76 help='File containing trajectory filepaths.')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
77 parser.add_argument("--strs",
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
78 help='File containing structure filepaths.')
78aa3659fcd1 "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,
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
80 help='Trajectory format.')
78aa3659fcd1 "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.')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
82 parser.add_argument('-o', '--outfile',
78aa3659fcd1 "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")
78aa3659fcd1 "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"
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
85 "calculated in MDAnalysis selection language")
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
86 parser.add_argument('--start', type=int,
78aa3659fcd1 "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")
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
88 parser.add_argument('--end', type=int,
78aa3659fcd1 "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")
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
90 parser.add_argument('--step', type=int,
78aa3659fcd1 "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")
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
92 args = parser.parse_args()
1
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
93 calc_rmsd(args.strs, args.trajs, args.str_format,
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
94 args.traj_format, args.outfile,
ce9dc91ff87f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
chemteam
parents: 0
diff changeset
95 args.group, args.start, args.end, args.step)
0
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
96
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
97
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
98 if __name__ == "__main__":
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
parents:
diff changeset
99 main()