comparison hbonds.py @ 1:5c38e38dbc35 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

0:469ad3ea5a5f

import argparse
import csv
import sys

import MDAnalysis.analysis.hbonds

import pandas as pd


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('--isegid2', help='segid 2')
    parser.add_argument('--idistance', help='cutoff distance')
    parser.add_argument('--iangle', help='ctoff angle')
    parser.add_argument('--output', help='output')

selection1 = "segid %s" % args.isegid1
selection2 = "segid %s" % args.isegid2
distance = float(args.idistance)
angle = float(args.iangle)

u = MDAnalysis.Universe(
    args.ipdb, args.idcd, topology_format="PDB", format="DCD")

h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(
    u, selection1, selection2, distance=distance, angle=angle)
h.run()
h.generate_table()

1:5c38e38dbc35

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')

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()