diff dihedrals.py @ 0:d710c7f00ae6 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/dihedrals.py	Wed Apr 03 15:46:32 2019 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import sys
+
+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
+
+
+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('--output', help='output')
+    parser.add_argument('--odihedral_plot', help='dihedral plot')
+    return parser.parse_args()
+
+
+args = parse_command_line(sys.argv)
+
+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)
+
+
+def psi(u):
+    A = u.select_atoms(atom1).positions
+    B = u.select_atoms(atom2).positions
+    C = u.select_atoms(atom3).positions
+    D = u.select_atoms(atom4).positions
+    psi = calc_dihedrals(A, B, C, D)
+    return np.rad2deg(psi)
+
+
+u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD")
+data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory])
+frame, psi = data.T
+PSI = np.concatenate(psi, axis=0)
+
+zip(frame, PSI)
+
+with open(args.output, 'w') as f:
+    writer = csv.writer(f, delimiter='\t')
+    writer.writerows(zip(frame, PSI))
+
+with open(args.output) as f:
+    g = [xtmp.strip() for xtmp in f]
+    data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
+    time = [xtmp[0] for xtmp in data]
+    dihedral = [xtmp[1] for xtmp in data]
+    plt.plot(time, dihedral)
+    plt.xlabel('Frame No.')
+    plt.ylabel('Dihedral (degrees)')
+    plt.savefig(args.odihedral_plot, format='png')