def __init__(self): WeightedMultiTerm.__init__(self) self.add_term(Electrostatics(), 0.1146) self.add_term(NewHydrogenBonding(), 0.1852) #.0656*2.82292 = 0.1851836 self.add_term(NewVanDerWaalsHybridWeights(), 1.0) #varying weights in scorer self.add_term(NewDesolvation(), 1.0) #.1711*0.10188 = 0.0174317
def __init__(self,atomset1,atomset2,scorer_ad_type='305'): EnergyScorer.__init__(self,atomset1,atomset2) self.r = self.ms.add_entities(self.atomset1) self.l = self.ms.add_entities(self.atomset2) self.scorer = WeightedMultiTerm() self.scorer.set_molecular_system(self.ms) self.scorer_ad_type = scorer_ad_type if self.scorer_ad_type == '305': self.ESTAT_WEIGHT_AUTODOCK = 0.1146 # electrostatics self.HBOND_WEIGHT_AUTODOCK = 0.0656 # hydrogen bonding self.VDW_WEIGHT_AUTODOCK = 0.1485 # van der waals self.DESOLV_WEIGHT_AUTODOCK= 0.1711 # desolvation # different terms to be use for score self.estat= Electrostatics(self.ms) self.scorer.add_term(self.estat, self.ESTAT_WEIGHT_AUTODOCK) self.hbond=HydrogenBonding(self.ms) self.scorer.add_term(self.hBond, self.HBOND_WEIGHT_AUTODOCK) self.vdw = VanDerWaals(self.ms) self.scorer.add_term(self.vdw, self.VDW_WEIGHT_AUTODOCK) self.ds= Desolvation(self.ms) self.scorer.add_term(self.ds,self.DESOLV_WEIGHT_AUTODOCK)
def __init__(self): self.prop = 'ad4_energy' WeightedMultiTerm.__init__(self) AutoDockTermWeights4.__init__(self) self.add_term(Electrostatics(), self.estat_weight) self.add_term(NewHydrogenBonding(), self.hbond_weight) self.add_term(NewVanDerWaals(), self.vdw_weight) #.1485*1.002 self.add_term(NewDesolvation(), self.dsolv_weight)
def __init__(self): self.prop = 'ad305_energy' WeightedMultiTerm.__init__(self) AutoDockTermWeights305.__init__(self) self.add_term(Electrostatics(), self.estat_weight) self.add_term(HydrogenBonding(), self.hbond_weight) self.add_term(VanDerWaals(), self.vdw_weight) self.add_term(Desolvation(), self.dsolv_weight)
def __init__(self, exclude_torsFreeEnergy=False, verbose=False): self.verbose = verbose if verbose: print "initialized exclude_torsFreeEnergy=", exclude_torsFreeEnergy self.prop = 'ad41_energy' self.exclude_torsFreeEnergy=exclude_torsFreeEnergy WeightedMultiTerm.__init__(self) AutoDockTermWeights41.__init__(self) self.add_term(Electrostatics(), self.estat_weight) self.add_term(NewHydrogenBonding(), self.hbond_weight) self.add_term(NewVanDerWaals(), self.vdw_weight) self.add_term(NewDesolvation(), self.dsolv_weight) self.supported_types = self.get_supported_types()
def __init__(self, exclude_torsFreeEnergy=False, verbose=False): self.verbose = verbose if verbose: print "initialized exclude_torsFreeEnergy=", exclude_torsFreeEnergy self.prop = 'ad41_energy' self.exclude_torsFreeEnergy = exclude_torsFreeEnergy WeightedMultiTerm.__init__(self) AutoDockTermWeights41.__init__(self) self.add_term(Electrostatics(), self.estat_weight) self.add_term(NewHydrogenBonding(), self.hbond_weight) self.add_term(NewVanDerWaals(), self.vdw_weight) self.add_term(NewDesolvation(), self.dsolv_weight) self.supported_types = self.get_supported_types()
def __init__(self, weights=AutoDockVinaTermWeights(), cutoff=8.0, exclude_one_four=False, weed_bonds=False, verbose=False): self.prop = 'vina_energy' self.cutoff = cutoff WeightedMultiTerm.__init__(self) self.add_term(Gauss(0, 0.5, cutoff), weights.gauss1) self.add_term(Gauss(3.0, 2.0, cutoff), weights.gauss2) self.add_term(Repulsion(0., cutoff), weights.repulsion) self.add_term(Non_dir_h_bond(-0.7, 0., cutoff), weights.hydrogen) self.add_term(Hydrophobic(0.5, 1.5, cutoff), weights.hydrophobic) self.num_tors_div_wt = weights.rot #weight_rot=0.05846;((5*weight_rot/ 0.1) - 1)line618 main.cpp v.1.1.2 self.verbose = verbose
def __init__(self): WeightedMultiTerm.__init__(self) self.add_term(Electrostatics(), self.estat_weight) self.add_term(NewHydrogenBonding(), self.hbond_weight) self.add_term(NewVanDerWaals(), self.vdw_weight) #.1485*1.002 self.add_term(NewDesolvationLigOnly(), self.dsolv_weight)
def __init__(self): WeightedMultiTerm.__init__(self) AutoDockTermWeights4.__init__(self) self.add_term(NewHydrogenBonding(), self.hbond_weight) self.add_term(NewVanDerWaals(), self.vdw_weight) self.add_term(NewDesolvationAtomMap(), self.dsolv_weight)
def __init__(self): WeightedMultiTerm.__init__(self) AutoDockTermWeights305.__init__(self) self.add_term(HydrogenBonding(), self.hbond_weight) self.add_term(VanDerWaals(), self.vdw_weight) self.add_term(Desolvation(), self.dsolv_weight)
class PyPairWiseEnergyScorer(EnergyScorer): """For each atom in one AtomSet, determine the electrostatics energy vs all the atoms in a second AtomSet """ def __init__(self,atomset1,atomset2,scorer_ad_type='305'): EnergyScorer.__init__(self,atomset1,atomset2) self.r = self.ms.add_entities(self.atomset1) self.l = self.ms.add_entities(self.atomset2) self.scorer = WeightedMultiTerm() self.scorer.set_molecular_system(self.ms) self.scorer_ad_type = scorer_ad_type if self.scorer_ad_type == '305': self.ESTAT_WEIGHT_AUTODOCK = 0.1146 # electrostatics self.HBOND_WEIGHT_AUTODOCK = 0.0656 # hydrogen bonding self.VDW_WEIGHT_AUTODOCK = 0.1485 # van der waals self.DESOLV_WEIGHT_AUTODOCK= 0.1711 # desolvation # different terms to be use for score self.estat= Electrostatics(self.ms) self.scorer.add_term(self.estat, self.ESTAT_WEIGHT_AUTODOCK) self.hbond=HydrogenBonding(self.ms) self.scorer.add_term(self.hBond, self.HBOND_WEIGHT_AUTODOCK) self.vdw = VanDerWaals(self.ms) self.scorer.add_term(self.vdw, self.VDW_WEIGHT_AUTODOCK) self.ds= Desolvation(self.ms) self.scorer.add_term(self.ds,self.DESOLV_WEIGHT_AUTODOCK) def update_coords(self, index='arconformationIndex'): """ update the coords """ if hasattr(self.mol1, index): num = self.mol1.__dict__.get('index') self.atomset1.setConformation(num) if hasattr(self.mol2, index): num = self.mol1.__dict__.get('index') self.atomset2.setConformation(num) for ind in (self.r, self.l): # clear distance matrix self.ms.clear_dist_mat(ind) def get_score(self): score = self.scorer.get_score() estat = min(round(self.estat.get_score() * self.ESTAT_WEIGHT_AUTODOCK,2),1000.) hbond = min(round(self.hbond.get_score() * self.HBOND_WEIGHT_AUTODOCK,2),1000.) vdw = min(round(self.vdw.get_score() * self.VDW_WEIGHT_AUTODOCK,2),1000.) ds = min(round(self.ds.get_score() * self.DESOLV_WEIGHT_AUTODOCK,2),1000.) return (score,estat,hbond,vdw,ds)
def __init__(self, exclude_one_four=False, weed_bonds=False): WeightedMultiTerm.__init__(self) self.exclude_one_four = exclude_one_four self.weed_bonds = weed_bonds