annotate ramachandran_plots.py @ 6:be5eaea0b2d1 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"

#!/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')