diff ramachandran_plots.py @ 0:0f270722aca6 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramachandran_plots.py	Mon Aug 24 16:27:56 2020 -0400
@@ -0,0 +1,112 @@
+#!/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
+import matplotlib.pyplot as plt
+import matplotlib.ticker as ticker
+
+
+import numpy as np
+
+import seaborn as sns
+
+
+import yaml
+
+matplotlib.use('Agg')  # noqa
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    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('--iyml', help='input in yml format')
+    parser.add_argument('--output', help='output')
+    parser.add_argument('--oramachandran_plot', help='dihedral plot')
+    return parser.parse_args()
+
+
+args = parse_command_line(sys.argv)
+
+with open(args.iyml) as file:
+    params = yaml.load(file, Loader=yaml.FullLoader)
+
+Dihedral = namedtuple(
+    'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4'])
+
+for k, v in params.items():
+    for a in ['phi', 'psi']:
+        assert (a in v), "Key %s is missing in inputs: %s " % (a, k)
+        atoms = []
+        for b in ['atom1', 'atom2', 'atom3', 'atom4']:
+            assert (b in v[a]), "Key %s is missing in inputs: %s %s" % (
+                b, k, a)
+            for c in ['segid', 'resid', 'name']:
+                assert (c in v[a][b]), \
+                        "Key %s is missing in inputs: %s %s %s " % (c, k, a, b)
+            atoms.append("(segid %s and resid %s and name %s)" %
+                         (v[a][b]['segid'], v[a][b]['resid'], v[a][b]['name']))
+        print(atoms)
+        if a == 'phi':
+            dihe_phi = Dihedral(atoms[0], atoms[1], atoms[2], atoms[3])
+        if a == 'psi':
+            dihe_psi = Dihedral(atoms[0], atoms[1], atoms[2], atoms[3])
+
+# order of dihedral atom is the crystallographic definition
+# (see glycanstructure.org)
+
+assert(dihe_phi), "phi dihedral doesn't exist"
+assert(dihe_psi), "psi dihedral doesn't exist"
+
+
+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.istr, args.itraj,
+                 topology_format=args.istrext, format=args.itrajext)
+
+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])
+
+print(phi_trajdata, psi_trajdata)
+
+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", space=0, 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)
+    h.ax_joint.xaxis.set_major_locator(ticker.MultipleLocator(60))
+    h.ax_joint.yaxis.set_major_locator(ticker.MultipleLocator(60))
+    plt.savefig(args.oramachandran_plot, format='png', bbox_inches='tight')