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):
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(), 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):
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)
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)
AutoDockTermWeights305.__init__(self)
self.add_term(HydrogenBonding(), self.hbond_weight)
self.add_term(VanDerWaals(), self.vdw_weight)
self.add_term(Desolvation(), 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)
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):
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)
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
