Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
diff ramachandran_plots.py @ 0:d710c7f00ae6 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author | chemteam |
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date | Wed, 03 Apr 2019 15:46:32 -0400 |
parents | |
children | ce0728b92289 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramachandran_plots.py Wed Apr 03 15:46:32 2019 -0400 @@ -0,0 +1,121 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys +from collections import namedtuple + +import MDAnalysis as mda +from MDAnalysis.lib.distances import calc_dihedrals + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np + +import seaborn as sns + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--isegid3', help='segid 3') + parser.add_argument('--iresid3', help='resid 3') + parser.add_argument('--iname3', help='name 3') + parser.add_argument('--isegid4', help='segid 4') + parser.add_argument('--iresid4', help='resid 4') + parser.add_argument('--iname4', help='name 4') + parser.add_argument('--isegid5', help='segid 1') + parser.add_argument('--iresid5', help='resid 1') + parser.add_argument('--iname5', help='name 1') + parser.add_argument('--isegid6', help='segid 2') + parser.add_argument('--iresid6', help='resid 2') + parser.add_argument('--iname6', help='name 2') + parser.add_argument('--isegid7', help='segid 3') + parser.add_argument('--iresid7', help='resid 3') + parser.add_argument('--iname7', help='name 3') + parser.add_argument('--isegid8', help='segid 4') + parser.add_argument('--iresid8', help='resid 4') + parser.add_argument('--iname8', help='name 4') + parser.add_argument('--output', help='output') + parser.add_argument('--oramachandran_plot', help='dihedral plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +Dihedral = namedtuple( + 'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4']) + +# order of dihedral atom is the crystallographic definition +# (see glycanstructure.org) + +# phi +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid2, args.iresid2, args.iname2) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid3, args.iresid3, args.iname3) +atom4 = "(segid %s and resid %s and name %s)" % \ + (args.isegid4, args.iresid4, args.iname4) + +dihe_phi = Dihedral(atom1, atom2, atom3, atom4) + +# psi +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid5, args.iresid5, args.iname5) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid6, args.iresid6, args.iname6) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid7, args.iresid7, args.iname7) +atom4 = "(segid %s and resid %s and name %s)" % \ + (args.isegid8, args.iresid8, args.iname8) + +dihe_psi = Dihedral(atom1, atom2, atom3, atom4) + + +def calc_torsion(dihedral): + """atom 1 -4 are valid atom selections. torsion in degrees is returned""" + A = u.select_atoms(dihedral.atom1).positions + B = u.select_atoms(dihedral.atom2).positions + C = u.select_atoms(dihedral.atom3).positions + D = u.select_atoms(dihedral.atom4).positions + + dihe = calc_dihedrals(A, B, C, D) + return np.rad2deg(dihe) + + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") + +phi_trajdata = np.array( + [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) +psi_trajdata = np.array( + [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) + +phi_frame, phi_series = phi_trajdata.T +psi_frame, psi_series = psi_trajdata.T + +phi_series = np.concatenate(phi_series, axis=0) +psi_series = np.concatenate(psi_series, axis=0) + +zip(phi_frame, phi_series, psi_series) + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(zip(phi_frame, phi_series, psi_series)) + +with sns.axes_style("white"): + h = sns.jointplot(x=phi_series, y=psi_series, kind="kde", legend=True) + h.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)') + h.ax_joint.set_xlim(-180, 180) + h.ax_joint.set_ylim(-180, 180) + plt.savefig(args.oramachandran_plot, format='png')