def testPDB_contactmap(self):
# preparation
pdb_native = atomset.PDB()
pdb_native.initialise("tests/data/pdb_test_contact.pdb")
symmetryEvaluator = sym.SymmetryContactMapEvaluator([])
# function to test
contact_map, contacts = symmetryEvaluator.createContactMap(
pdb_native, "AIN", 8)
golden_contact_map = np.array([[1, 0, 0, 0], [0, 1, 1, 1]])
golden_contacts = pdb_native.countContacts("AIN", 8)
np.testing.assert_array_equal(contact_map, golden_contact_map)
self.assertEqual(golden_contacts, contacts)
PDBobj.initialise(snapshot, resname=resname, topology=topology_contents)
yield PDBobj
else:
for cluster in clAcc.clusters.clusters:
yield cluster.pdb
if __name__ == "__main__":
traj_name, clustering, nRes, lig_resname, contactThreshold, top = parseArguments()
if clustering is None:
clusterAcc = None
else:
clusetrAcc = utilities.readClusteringObject(clustering)
totalAcc = []
symEval = SymmetryContactMapEvaluator.SymmetryContactMapEvaluator()
refPDB = None
for pdb in generateConformations(lig_resname, clusetrAcc, traj_name, top):
if refPDB is None:
refPDB = pdb
contactMap, foo = symEval.createContactMap(pdb, lig_resname, contactThreshold)
if len(totalAcc):
totalAcc += contactMap.sum(axis=0, dtype=bool).astype(int)
else:
totalAcc = contactMap.sum(axis=0, dtype=bool).astype(int)
proteinList = symEval.proteinList
residueCounts = {}
totCounts = 0
for atomID, counts in zip(proteinList, totalAcc):