diff ramachandran_plots.py @ 3:ad135cf42274 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramachandran_plots.py	Wed Apr 03 15:47:56 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')