Ejemplo n.º 1
0
	def testInverseDistanceMean(self):
		print "testing inverse_distance_mean"
		Ms1 = cluster.inverse_distance_mean(self.distance_list1)
		Ms2 = cluster.inverse_distance_mean(self.distance_list2)
		Ms3 = cluster.inverse_distance_mean(self.distance_list3)
		assert Ms1 > Ms3, "no-cluster sample has larger Ms value than two-clustered sample"

		assert Ms2 == 0.5, "Ms of clustered sample is not correct"
Ejemplo n.º 2
0
	def setUp(self):
		#kdrew: load pdb file
		pdb_filename = "data/1UBQ.pdb"
		pdb_handle = open(pdb_filename)
		pdb_string = pdb_handle.read()

		#kdrew: using list of residue ids that are near each other
		clustered_ids =  [2,3,15,16,64]
		self.dist_list = cluster.structure_distance_calc(pdb_string, clustered_ids)
		self.Ms = cluster.inverse_distance_mean(self.dist_list)
		self.random_Ms_list = cluster.random_structure_distance_calc(pdb_string, len(clustered_ids))
		print self.random_Ms_list