Mercurial > repos > chemteam > mdanalysis_dihedral

comparison angle.py @ 4:d8178fe9aaff draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:52:20 -0400
parents cc1d22357daf
children 0493024c3318
comparison
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3:554f60da9c8f 4:d8178fe9aaff
14 from numpy.linalg import norm 14 from numpy.linalg import norm
15 15
16 16
17 def parse_command_line(argv): 17 def parse_command_line(argv):
18 parser = argparse.ArgumentParser() 18 parser = argparse.ArgumentParser()
19 parser.add_argument('--idcd', help='input dcd') 19 parser.add_argument('--itraj', help='input traj')
20 parser.add_argument('--ipdb', help='input pdb') 20 parser.add_argument('--istr', help='input str')
21 parser.add_argument('--itrajext', help='input traj ext')
22 parser.add_argument('--istrext', help='input str ext')
21 parser.add_argument('--isegid1', help='segid 1') 23 parser.add_argument('--isegid1', help='segid 1')
22 parser.add_argument('--iresid1', help='resid 1') 24 parser.add_argument('--iresid1', help='resid 1')
23 parser.add_argument('--iname1', help='name 1') 25 parser.add_argument('--iname1', help='name 1')
24 parser.add_argument('--isegid2', help='segid 2') 26 parser.add_argument('--isegid2', help='segid 2')
25 parser.add_argument('--iresid2', help='resid 2') 27 parser.add_argument('--iresid2', help='resid 2')
50 BC = C - B 52 BC = C - B
51 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC))) 53 theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC)))
52 return np.rad2deg(theta) 54 return np.rad2deg(theta)
53 55
54 56
55 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") 57 u = mda.Universe(args.istr, args.itraj,
58 topology_format=args.istrext, format=args.itrajext)
56 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory]) 59 data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory])
57 frame, theta = data.T 60 frame, theta = data.T
58 61
59 with open(args.output, 'w') as f: 62 with open(args.output, 'w') as f:
60 writer = csv.writer(f, delimiter='\t') 63 writer = csv.writer(f, delimiter='\t')