Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
comparison ramachandran_plots.py @ 1:ce0728b92289 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:50:22 -0400 |
| parents | d710c7f00ae6 |
| children | 8bd0e29927da |
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| 0:d710c7f00ae6 | 1:ce0728b92289 |
|---|---|
| 17 import seaborn as sns | 17 import seaborn as sns |
| 18 | 18 |
| 19 | 19 |
| 20 def parse_command_line(argv): | 20 def parse_command_line(argv): |
| 21 parser = argparse.ArgumentParser() | 21 parser = argparse.ArgumentParser() |
| 22 parser.add_argument('--idcd', help='input dcd') | 22 parser.add_argument('--itraj', help='input traj') |
| 23 parser.add_argument('--ipdb', help='input pdb') | 23 parser.add_argument('--istr', help='input str') |
| 24 parser.add_argument('--itrajext', help='input traj ext') | |
| 25 parser.add_argument('--istrext', help='input str ext') | |
| 24 parser.add_argument('--isegid1', help='segid 1') | 26 parser.add_argument('--isegid1', help='segid 1') |
| 25 parser.add_argument('--iresid1', help='resid 1') | 27 parser.add_argument('--iresid1', help='resid 1') |
| 26 parser.add_argument('--iname1', help='name 1') | 28 parser.add_argument('--iname1', help='name 1') |
| 27 parser.add_argument('--isegid2', help='segid 2') | 29 parser.add_argument('--isegid2', help='segid 2') |
| 28 parser.add_argument('--iresid2', help='resid 2') | 30 parser.add_argument('--iresid2', help='resid 2') |
| 92 | 94 |
| 93 dihe = calc_dihedrals(A, B, C, D) | 95 dihe = calc_dihedrals(A, B, C, D) |
| 94 return np.rad2deg(dihe) | 96 return np.rad2deg(dihe) |
| 95 | 97 |
| 96 | 98 |
| 97 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") | 99 u = mda.Universe(args.istr, args.itraj, |
| 100 topology_format=args.istrext, format=args.itrajext) | |
| 98 | 101 |
| 99 phi_trajdata = np.array( | 102 phi_trajdata = np.array( |
| 100 [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) | 103 [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) |
| 101 psi_trajdata = np.array( | 104 psi_trajdata = np.array( |
| 102 [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) | 105 [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) |
| 106 | |
| 107 print(phi_trajdata, psi_trajdata) | |
| 103 | 108 |
| 104 phi_frame, phi_series = phi_trajdata.T | 109 phi_frame, phi_series = phi_trajdata.T |
| 105 psi_frame, psi_series = psi_trajdata.T | 110 psi_frame, psi_series = psi_trajdata.T |
| 106 | 111 |
| 107 phi_series = np.concatenate(phi_series, axis=0) | 112 phi_series = np.concatenate(phi_series, axis=0) |