comparison pca_cosine.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('--icomponents', help='number of principle components')
    parser.add_argument('--iindex', help='index of the PC')
    parser.add_argument('--output', help='output')
    parser.add_argument('--cosout', help='cosine output')
    return parser.parse_args()


args = parse_command_line(sys.argv)

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

components = int(args.icomponents)
pca_index = int(args.iindex)

PSF_pca = pca.PCA(u, select='backbone')

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('--icomponents', help='number of principle components')
    parser.add_argument('--iindex', help='index of the PC')
    parser.add_argument('--output', help='output')
    parser.add_argument('--cosout', help='cosine output')
    return parser.parse_args()


args = parse_command_line(sys.argv)

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

components = int(args.icomponents)
pca_index = int(args.iindex)

PSF_pca = pca.PCA(u, select='backbone')