--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pca_cosine.py	Wed Apr 03 15:47:56 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))