def __init__(self,
distCutoff=distCutoff,
distCutoff2=distCutoff2,
d2min=d2min,
d2max=d2max,
d3min=d3min,
d3max=d3max,
a2min=a2min,
a2max=a2max,
a3min=a3min,
a3max=a3max,
donorTypes=allDonors,
acceptorTypes=allAcceptors,
distOnly=False):
d = self.paramDict = {}
d['distCutoff'] = distCutoff
d['distCutoff2'] = distCutoff2
d['d2min'] = d2min
d['d2max'] = d2max
d['d3min'] = d3min
d['d3max'] = d3max
d['a2min'] = a2min
d['a2max'] = a2max
d['a3min'] = a3min
d['a3max'] = a3max
d['donorTypes'] = donorTypes
d['acceptorTypes'] = acceptorTypes
d['distOnly'] = distOnly
self.distSelector = DistanceSelector(return_dist=0)
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)
