def __init__(self, receptor_file, percentCutoff=1., detect_pi=False, dist_cutoff=6, verbose=False,
distanceSelector=None, hydrogen_bond_builder=None, distanceSelectorWithCutoff=None,
aromatic_cycle_bond_selector=None):
self.receptor_file = receptor_file
receptor = Read(receptor_file)
assert(len(receptor)==1)
assert isinstance(receptor, MoleculeSet)
self.macro = receptor[0]
self.macro_atoms = self.macro.allAtoms
self.macro.buildBondsByDistance()
self.verbose = verbose
#??useful??
self.percentCutoff = percentCutoff
self.detect_pi = detect_pi
self.distanceSelector = distanceSelector
if self.distanceSelector is None:
self.distanceSelector = CloserThanVDWSelector(return_dist=0)
self.hydrogen_bond_builder = hydrogen_bond_builder
if self.hydrogen_bond_builder is None:
self.hydrogen_bond_builder = HydrogenBondBuilder()
self.distanceSelectorWithCutoff = distanceSelectorWithCutoff
if self.distanceSelectorWithCutoff is None:
self.distanceSelectorWithCutoff = DistanceSelector()
self.dist_cutoff=float(dist_cutoff)
self.results = d = {}
self.report_list =['lig_hb_atoms','lig_close_atoms']
self.aromatic_cycle_bond_selector = aromatic_cycle_bond_selector
if self.aromatic_cycle_bond_selector is None:
self.aromatic_cycle_bond_selector = AromaticCycleBondSelector()
if detect_pi:
self.report_list.extend(['pi_cation','pi_pi', 'cation_pi', 't_shaped'])
if self.verbose: print("self.report_list=", self.report_list)
def test_CloserThanVDWSelector_setupCutoff(self):
"""
CloserThanVDWSelector cutoff is expected shape
"""
cutoff = CloserThanVDWSelector().setupCutoff(self.rec.allAtoms, self.lig.allAtoms, 3.0)
self.assertEquals(cutoff.shape[0], len(self.lig.allAtoms))
self.assertEquals(cutoff.shape[1], len(self.rec.allAtoms))
def test_CloserThanVDWSelector_select(self):
"""
CloserThanVDWSelector.select returns expected number of atoms
"""
d_sel = CloserThanVDWSelector()
resultD, distD = d_sel.select(self.lig.allAtoms, self.rec.allAtoms)
#check that 14 atoms in the ligand are near 1 or more atoms in the receptor
self.assertEquals(len(resultD.keys()), 14)
d = {}
for k in resultD.values():
for item in k:
d[item] = 0
#check that 16 atoms in the receptor are near an atom in the ligand
self.assertEquals(len(d.keys()), 16)
def test_CloserThanVDWSelector(self):
"""
instantiate a CloserThanVDWSelector
"""
d_sel = CloserThanVDWSelector()
self.assertEquals(d_sel.__class__, CloserThanVDWSelector)
