Skip to content

Fixes for clustering pipeline #26

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dkoes merged 1 commit into from
Jul 1, 2019
Merged

Fixes for clustering pipeline #26

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions clustering.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -318,15 +318,15 @@ def computeLigandSimilarity(target_names, fname):
ligand_threshold = args.ligand_similarity #this actually is a sim

if args.cpickle:
with open(args.cpickle, 'r') as file:
with open(args.cpickle, 'rb') as file:
(distanceMatrix, target_names,ligandsim) = pickle.load(file)
elif args.pdbfiles:
if args.verbose: print("reading pdbs...")
target_names, targets = readPDBfiles(args.pdbfiles)
if args.verbose: print("calculating distance matrix...")
distanceMatrix = calcDistanceMatrix(targets)
ligandsim = computeLigandSimilarity(target_names, args.pdbfiles) #returns similarity matrix indexed according to target_names
pickle.dump((distanceMatrix, target_names, ligandsim), open(args.pdbfiles+'.pickle','w'),-1)
pickle.dump((distanceMatrix, target_names, ligandsim), open(args.pdbfiles+'.pickle','wb'),-1)
else:
exit('error: need --cpickle or --pdbfiles to compute target distance matrix')
if args.verbose: print('Number of targets: {}'.format(len(target_names)))
Expand Down
2 changes: 1 addition & 1 deletion combine_rows.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,4 +44,4 @@
print("Missing ligand_sim for",targets[i],targets[j])


pickle.dump((m, target_names, lm), open('matrix.pickle','w'),-1)
pickle.dump((m, target_names, lm), open('matrix.pickle','wb'),-1)