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)