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)
