diff hbonds.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/hbonds.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
+import MDAnalysis.analysis.hbonds
+
+import pandas as pd
+
+
+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('--isegid2', help='segid 2')
+    parser.add_argument('--idistance', help='cutoff distance')
+    parser.add_argument('--iangle', help='ctoff angle')
+    parser.add_argument('--output', help='output')
+    parser.add_argument('--ofreq_output', help='frequency output')
+    parser.add_argument('--onumber_output', help='number of hbond output')
+    parser.add_argument('--otime_output', help='time steps output')
+    return parser.parse_args()
+
+
+args = parse_command_line(sys.argv)
+
+selection1 = "segid %s" % args.isegid1
+selection2 = "segid %s" % args.isegid2
+distance = float(args.idistance)
+angle = float(args.iangle)
+
+u = mda.Universe(args.istr, args.itraj,
+                 topology_format=args.istrext, format=args.itrajext)
+
+h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(
+    u, selection1, selection2, distance=distance, angle=angle)
+h.run()
+h.generate_table()
+
+df = pd.DataFrame.from_records(h.table)
+df.to_csv(args.output, sep='\t')
+
+t1 = list(h.count_by_type())
+t2 = list(h.count_by_time())
+t3 = list(h.timesteps_by_type())
+
+with open(args.ofreq_output, 'w') as f:
+    f.write("donor_index\tacceptor_index\t\
+            donor_resname\tdonor_resid\tdonor_atom\t\
+            hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
+            acceptor_atom\tfrequency\n")
+    writer = csv.writer(f, delimiter='\t')
+    writer.writerows(t1)
+
+
+with open(args.onumber_output, 'w') as f1:
+    f1.write("time_step\tno_of_h_bonds\n")
+    writer = csv.writer(f1, delimiter='\t')
+    writer.writerows(t2)
+
+with open(args.otime_output, 'w') as f2:
+    f2.write("donor_index\tacceptor_index\t\
+             donor_resname\tdonor_resid\tdonor_atom\t\
+             hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\
+             acceptor_atom\ttime_step\n")
+    writer = csv.writer(f2, delimiter='\t')
+    writer.writerows(t3)