diff rdf.py @ 0:78aa3659fcd1 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/rdf.py	Mon Aug 24 16:47:23 2020 -0400
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import sys
+
+import MDAnalysis as mda
+from MDAnalysis.analysis.rdf import InterRDF
+
+import matplotlib
+import matplotlib.pyplot as plt
+
+import numpy as np
+
+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('--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('--inbins', help='Number of bins in the histogram')
+    parser.add_argument('--istart', help='Starting Point')
+    parser.add_argument('--iend', help='End point')
+    parser.add_argument('--output', help='output')
+    parser.add_argument('--ordf_plot', help='RDF 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)
+bins = int(args.inbins)
+start = float(args.istart)
+end = float(args.iend)
+
+u = mda.Universe(args.istr, args.itraj,
+                 topology_format=args.istrext, format=args.itrajext)
+x = u.select_atoms(atom1)
+y = u.select_atoms(atom2)
+
+rdf = InterRDF(x, y, nbins=bins, range=(start, end))
+rdf.run()
+bins = rdf.bins
+bins = np.around(bins, decimals=3)
+RDF = rdf.rdf
+zip(bins, RDF)
+
+with open(args.output, 'w') as f:
+    writer = csv.writer(f, delimiter='\t')
+    writer.writerows(zip(bins, RDF))
+
+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]
+    rdf = [xtmp[1] for xtmp in data]
+    plt.plot(time, rdf)
+    plt.xlabel(r'r ($\AA$)')
+    plt.ylabel('g(r)')
+    plt.savefig(args.ordf_plot, format='png')