Mercurial > repos > bgruening > chemfp

comparison nxn_clustering.py @ 7:0d88631bb7de draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:32:50 -0400
parents 70b071de9bee
children 198b1e30c739
comparison
equal deleted inserted replaced
6:e3a7d6cc87af 7:0d88631bb7de
67 targets = chemfp.open( args.input_path, format='fps' ) 67 targets = chemfp.open( args.input_path, format='fps' )
68 arena = chemfp.load_fingerprints( targets ) 68 arena = chemfp.load_fingerprints( targets )
69 distances = distance_matrix( arena, args.tanimoto_threshold ) 69 distances = distance_matrix( arena, args.tanimoto_threshold )
70 70
71 if args.similarity_matrix: 71 if args.similarity_matrix:
72 distances.tofile( args.similarity_matrix ) 72 numpy.savetxt(args.similarity_matrix, distances)
73 73
74 if args.cluster_image: 74 if args.cluster_image:
75 linkage = hcluster.linkage( distances, method="single", metric="euclidean" ) 75 linkage = hcluster.linkage(distances, method="single", metric="euclidean")
76 hcluster.dendrogram(linkage, labels=arena.ids, leaf_rotation=90.)
77 pylab.savefig(args.cluster_image, format=args.oformat)
76 78
77 hcluster.dendrogram(linkage, labels=arena.ids)
78
79 pylab.savefig( args.cluster_image, format=args.oformat )
80