Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
view pca_cosine.py @ 5:af9f01ca6a5c draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
author | chemteam |
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date | Wed, 28 Oct 2020 21:41:36 +0000 |
parents | ce0728b92289 |
children |
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#!/usr/bin/env python import argparse import csv import sys import MDAnalysis as mda import MDAnalysis.analysis.pca as pca 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') PSF_pca.run() n_pcs = np.where(PSF_pca.cumulated_variance > 0.95)[0][0] atomgroup = u.select_atoms('backbone') pca_space = PSF_pca.transform(atomgroup, n_components=components) cosine = mda.analysis.pca.cosine_content(pca_space, pca_index) PCA = list(pca_space) with open(args.output, 'w') as f: writer = csv.writer(f, delimiter='\t') writer.writerows(PCA) with open(args.cosout, 'w') as f1: f1.write(str(cosine))