Python divisiveClustering Examples

Example #1

File: pdb.py Project: ryancoleman/tdt2014-part2

 def divisiveClusteringPdb_justC(self, maxClusters=30):
   '''gets all the models in this pdb file, does divisive clustering.
   since proteins are large, just use the carbon in the backbone to represent
   each residue. other options later maybe.'''
   eachModelXyz = self.getEachModelJustXyz_restrictAtomNames("C  ")
   import divisive_clustering
   clusters = divisive_clustering.divisiveClustering(eachModelXyz, maxClusters)
   return clusters

Example #2

File: mol2.py Project: ryancoleman/mol2db2

 def divisiveClustering(self):
   '''takes all conformations. bisects them along the longest dimension 
   (in N*atoms*3 space). Repeat on the biggest remaining cluster until there 
   are numClusters left, return the clusters as lists.'''
   numClusters = min(20, int(self.origXyzCount/3.))
   #print numClusters #debugging, find out target # of clusters
   clusters = divisive_clustering.divisiveClustering(self.atomXyz, numClusters)
   return clusters

Example #3

File: pdb.py Project: ryancoleman/tdt2014-part2

 def divisiveClusteringPdb(self, maxClusters=30):
   '''gets all the models in this pdb file, does divisive clustering'''
   eachModelXyz = self.getEachModelJustXyz()
   import divisive_clustering
   clusters = divisive_clustering.divisiveClustering(eachModelXyz, maxClusters)
   return clusters