Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
view 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 |
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children | ce0728b92289 |
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#!/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')