Mercurial > repos > chemteam > mdanalysis_dihedral
diff dihedrals.py @ 4:d8178fe9aaff draft
"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 | 554f60da9c8f |
| children | 0493024c3318 |
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--- a/dihedrals.py Wed Apr 03 15:47:36 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:52:20 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -56,7 +58,8 @@ return np.rad2deg(psi) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory]) frame, psi = data.T PSI = np.concatenate(psi, axis=0)