def weakWaterCleanup(self): #
#pose, cutoff_weak = -0.35, cutoff_strong=-0.5, interact_dist=3.5 ):
""" clean-up extra_weak waters (increment ['water_rec_over_penalty'], if necessary"""
org_waters = len(self.pose['water_bridge'])
#ignore_types = ['HD']
lone_water = []
interact_dist = self.interact_dist**2
hb_types = ['OA', 'NA', 'SA', 'N', 'O', 'OA', 'NA', 'SA']
hb_types += hf.METALS
for idx in range(len(self.pose['water_bridge'])):
water = self.pose['water_bridge'][idx]
score = self.pose['water_bridge_scores'][idx]
# analyze only waters that are not ranked strong
if score >= self.cutoff_strong:
atom_pool = [ a for a in self.pose['water_bridge_contacts'][idx] if hf.getAtype(a) in hb_types]
if self.debug:
hf.writeList('ATOM_POOL_%d_HB_%d.pdb' % (idx, sess), atom_pool, addNewLine=True)
lone_water.append(water)
try:
for a in atom_pool:
if (dist(water, a, sq=0)<= interact_dist):
#print "FOUND MATE",
#print dist(water, a, sq=True)
#print a.strip()
#print "------------------"
raise self.qs
#print "NO MATE FOR THIS", score
#print water.strip()
except:
lone_water.remove(water)
for w in lone_water:
idx = self.pose['water_bridge'].index(w)
del self.pose['water_bridge'][idx]
del self.pose['water_bridge_contacts'][idx]
# EXPERIMENTAL
#w_score = self.pose['water_bridge_scores'][idx]
#if w_score >
# XXX THIS shouldn't happen:
# a weakly bound water could be hanging in the bulk, but it should be accounted for
# ...?
# how to describe the bulk solvent?
# combine desolv map + discrete waters?
#
self.pose['water_over_rec_penalty'].append( -self.pose['water_bridge_scores'].pop(idx) )
# update PDBQT text
#print pose['water_over_rec_penalty'] # XXX
text_idx = self.pose['text'].index(w)
del self.pose['text'][text_idx]
if self.debug:
print "LONE WATERS # REMOVED: ", (org_waters- len(self.pose['water_bridge']) )
def weakWaterCleanup(self): #
#pose, cutoff_weak = -0.35, cutoff_strong=-0.5, interact_dist=3.5 ):
""" clean-up extra_weak waters (increment ['water_rec_over_penalty'], if necessary"""
org_waters = len(self.pose['water_bridge'])
#ignore_types = ['HD']
lone_water = []
interact_dist = self.interact_dist**2
hb_types = ['OA', 'NA', 'SA', 'N', 'O', 'OA', 'NA', 'SA']
hb_types += hf.METALS
for idx in range(len(self.pose['water_bridge'])):
water = self.pose['water_bridge'][idx]
score = self.pose['water_bridge_scores'][idx]
# analyze only waters that are not ranked strong
if score >= self.cutoff_strong:
atom_pool = [ a for a in self.pose['water_bridge_contacts'][idx] if hf.getAtype(a) in hb_types]
if self.debug:
hf.writeList('ATOM_POOL_%d_HB_%d.pdb' % (idx, sess), atom_pool, addNewLine=True)
lone_water.append(water)
try:
for a in atom_pool:
if (dist(water, a, sq=0)<= interact_dist):
#print "FOUND MATE",
#print dist(water, a, sq=True)
#print a.strip()
#print "------------------"
raise self.qs
#print "NO MATE FOR THIS", score
#print water.strip()
except:
lone_water.remove(water)
for w in lone_water:
idx = self.pose['water_bridge'].index(w)
del self.pose['water_bridge'][idx]
del self.pose['water_bridge_contacts'][idx]
# EXPERIMENTAL
#w_score = self.pose['water_bridge_scores'][idx]
#if w_score >
# XXX THIS shouldn't happen:
# a weakly bound water could be hanging in the bulk, but it should be accounted for
# ...?
# how to describe the bulk solvent?
# combine desolv map + discrete waters?
#
self.pose['water_over_rec_penalty'].append( -self.pose['water_bridge_scores'].pop(idx) )
# update PDBQT text
#print pose['water_over_rec_penalty'] # XXX
text_idx = self.pose['text'].index(w)
del self.pose['text'][text_idx]
if self.debug:
print "LONE WATERS # REMOVED: ", (org_waters- len(self.pose['water_bridge']) )
