def normalizeWaterScore(self): #pose,entropyPenalty=False):
# keep track of the original energy values
if self.debug:
old_e = self.pose['energy']
old_leff = self.pose['leff']
# rec_displaced waters
rec_displaced = 0
for p in self.pose['water_over_rec_penalty']:
rec_displaced += p
# print p # XXX
#print "RECDISP", rec_displaced # XXX
# lig_displaced waters
lig_displaced = 0
for p in self.pose['water_over_lig_penalty']:
lig_displaced += p
# clustering-displaced
clust_displaced = 0
for p in self.pose['water_cluster_penalty']:
clust_displaced += p
# count heavy at for lig.efficiency
heavy_atoms = 0
for a in self.pose['text']:
if hf.isAtom(a) and (not hf.getAtype(a) in ['HD', 'W']):
heavy_atoms += 1
# energy correction
if self.conservedwaterentropy:
# XXX read the penalty from a variable!
entropy = (0.2) * len(self.pose['water_bridge'])
#print " ENTROPY PENALTY = ", entropy
else:
entropy = 0
self.pose[
'energy'] += lig_displaced + rec_displaced + clust_displaced + entropy
# lig.efficiency correction
self.pose['leff'] = self.pose['energy'] / float(heavy_atoms)
if self.debug:
#print "\n# PENALTY:\t +%2.3f [rec: %2.3f, lig: %2.3f, clust: %2.3f ]" % (rec_displaced+lig_displaced+clust_displaced,
# rec_displaced, lig_displaced, clust_displaced)
print " Penalties:"
print " - lig overlap : %2.3f" % lig_displaced
print " - rec overlap : %2.3f" % rec_displaced
print " - cluster penalty : %2.3f" % clust_displaced
print " - extra entropy : %2.3f" % entropy
print " ENERGY:\t %2.3f [ old: %2.3f ]" % (self.pose['energy'],
old_e)
print " L.EFF.:\t %2.3f [ old: %2.3f ]\n" % (self.pose['leff'],
old_leff)
def normalizeWaterScore(self): #pose,entropyPenalty=False):
# keep track of the original energy values
if self.debug:
old_e = self.pose['energy']
old_leff = self.pose['leff']
# rec_displaced waters
rec_displaced = 0
for p in self.pose['water_over_rec_penalty']:
rec_displaced += p
# print p # XXX
#print "RECDISP", rec_displaced # XXX
# lig_displaced waters
lig_displaced = 0
for p in self.pose['water_over_lig_penalty']:
lig_displaced += p
# clustering-displaced
clust_displaced = 0
for p in self.pose['water_cluster_penalty']:
clust_displaced += p
# count heavy at for lig.efficiency
heavy_atoms = 0
for a in self.pose['text']:
if hf.isAtom(a) and ( not hf.getAtype(a) in ['HD', 'W'] ):
heavy_atoms += 1
# energy correction
if self.conservedwaterentropy:
# XXX read the penalty from a variable!
entropy = (0.2)*len(self.pose['water_bridge'])
#print " ENTROPY PENALTY = ", entropy
else:
entropy = 0
self.pose['energy'] += lig_displaced + rec_displaced + clust_displaced + entropy
# lig.efficiency correction
self.pose['leff'] = self.pose['energy'] / float( heavy_atoms )
if self.debug:
#print "\n# PENALTY:\t +%2.3f [rec: %2.3f, lig: %2.3f, clust: %2.3f ]" % (rec_displaced+lig_displaced+clust_displaced,
# rec_displaced, lig_displaced, clust_displaced)
print " Penalties:"
print " - lig overlap : %2.3f" % lig_displaced
print " - rec overlap : %2.3f" % rec_displaced
print " - cluster penalty : %2.3f" % clust_displaced
print " - extra entropy : %2.3f" % entropy
print " ENERGY:\t %2.3f [ old: %2.3f ]" % (self.pose['energy'], old_e)
print " L.EFF.:\t %2.3f [ old: %2.3f ]\n" % (self.pose['leff'], old_leff)
