comparison dihedrals.py @ 1:5c38e38dbc35 draft

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

0:469ad3ea5a5f

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')

    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)

1:5c38e38dbc35

import numpy as np


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')

    D = u.select_atoms(atom4).positions
    psi = calc_dihedrals(A, B, C, D)
    return np.rad2deg(psi)


u = mda.Universe(args.istr, args.itraj,
                 topology_format=args.istrext, format=args.itrajext)
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)