Mercurial > repos > chemteam > mdanalysis_dihedral

diff dihedrals.py @ 3:6773d984e146 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:42:00 -0400
parents 8845c77d62f2
children 4c431a33590e
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line diff
--- a/dihedrals.py	Sun Jan 13 03:17:22 2019 -0500
+++ b/dihedrals.py	Wed Apr 03 15:42:00 2019 -0400
@@ -59,12 +59,13 @@
 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)
+zip(frame, PSI)
 
 with open(args.output, 'w') as f:
     writer = csv.writer(f, delimiter='\t')
-    writer.writerows(zip(frame, psi))
+    writer.writerows(zip(frame, PSI))
 
 with open(args.output) as f:
     g = [xtmp.strip() for xtmp in f]