def recOverlapWaters(self): # pose, cutoff = CLASH,
#ignore_types = ['HD', 'H', 'W'] ):
""" INPUT : pdb lig (multi)model and pdb target model
OUTPUT: cleaned pdb lig model
"""
#print "WARNING! missing interactions! Line B1"
overlapping = []
atom_pool = []
cutoff = self.clash**2
#cutoff += 0.5
#cutoff = 0
#for a in self.pose['vdw_contacts']: # PDBQT, no-HD # XXX TODO BUG Line B1
for aset in self.pose[
'water_bridge_contacts']: # PDBQT, no-HD # XXX TODO BUG Line B1
for a in aset:
if not hf.getAtype(a) in self.ignore_types:
atom_pool.append(a)
if self.debug:
fp = open('DEBUG_rec_overlap.pdb', 'w')
fp.write("REMARK WATERS REMOVED BY RECEPTOR CLASHES")
for w in self.pose['water_bridge']:
try: # try/except is faster
for a in atom_pool:
#if hf.dist(w, a, sq=False) < self.clash:
if hf.dist(w, a, sq=False) < cutoff:
overlapping.append(w)
self.pose['text'].remove(w)
#print "\n\n\n #### REMOVED", w
if self.debug:
fp.write(w + "\n")
fp.write(a + "\n")
raise self.qs
except:
pass
if self.debug:
fp.close()
print "Processed: %d | Rec-overlap %d" % (len(
self.pose['water_bridge']), len(overlapping))
for w in overlapping:
idx = self.pose['water_bridge'].index(w)
del self.pose['water_bridge_contacts'][idx]
self.pose['water_bridge'].remove(w)
self.pose['water_over_rec'] = overlapping
def recOverlapWaters(self): # pose, cutoff = CLASH,
#ignore_types = ['HD', 'H', 'W'] ):
""" INPUT : pdb lig (multi)model and pdb target model
OUTPUT: cleaned pdb lig model
"""
#print "WARNING! missing interactions! Line B1"
overlapping = []
atom_pool = []
cutoff = self.clash**2
#cutoff += 0.5
#cutoff = 0
#for a in self.pose['vdw_contacts']: # PDBQT, no-HD # XXX TODO BUG Line B1
for aset in self.pose['water_bridge_contacts']: # PDBQT, no-HD # XXX TODO BUG Line B1
for a in aset:
if not hf.getAtype(a) in self.ignore_types:
atom_pool.append(a)
if self.debug:
fp = open('DEBUG_rec_overlap.pdb','w')
fp.write("REMARK WATERS REMOVED BY RECEPTOR CLASHES")
for w in self.pose['water_bridge']:
try: # try/except is faster
for a in atom_pool:
#if hf.dist(w, a, sq=False) < self.clash:
if hf.dist(w, a, sq=False) < cutoff:
overlapping.append(w)
self.pose['text'].remove(w)
#print "\n\n\n #### REMOVED", w
if self.debug:
fp.write(w+"\n")
fp.write(a+"\n")
raise self.qs
except:
pass
if self.debug:
fp.close()
print "Processed: %d | Rec-overlap %d" % (len(self.pose['water_bridge']), len(overlapping) )
for w in overlapping:
idx = self.pose['water_bridge'].index(w)
del self.pose['water_bridge_contacts'][idx]
self.pose['water_bridge'].remove(w)
self.pose['water_over_rec'] = overlapping
