Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
diff pca_cosine.py @ 0:d710c7f00ae6 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author | chemteam |
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date | Wed, 03 Apr 2019 15:46:32 -0400 |
parents | |
children | ce0728b92289 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca_cosine.py Wed Apr 03 15:46:32 2019 -0400 @@ -0,0 +1,46 @@ +#!/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('--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') +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))