def process_flex_res_lines(self, lines):
# processremove BEGIN_RES, REMARK lines
# change ROOT/ENDROOT to BRANCH/ENDBRANCH LigROOTATOM# first resAtom#
#print "in pfrl: len(lines)=", len(lines)
parser = PdbqtParser()
pl = []
flex_res = ResidueSet()
for i in range(len(lines)):
l = lines[i]
#print l
if l.find('BEGIN_RES')>-1:
#print "found BEGIN_RES", len(pl)
pl = [l]
elif l.find('END_RES')>-1:
#print "found END_RES", len(pl)
if len(pl):
#pl.append(l)
parser.allLines = pl[1:-1]
mol = parser.parse()[0]
mol.chains.residues[-1].torTree = mol.torTree
#for res in mol.chains.residues:
flex_res += mol.chains.residues
#flex_res.extend(mol.chains.residues)
#print '2:', len(flex_res)
if i!=len(lines)-1:
pl = []
else:
pl.append(l)
#print "returning ", flex_res
return flex_res
def _buildInputLig(self, lines, filename):
if self.parser.version>=4.0:
parser = PdbqtParser()
#pdbqParser.allLines = self._hackLigLineFormat(lines)
else:
parser = PdbqParser()
if hasattr(self.parser, 'hasFlexRes') and self.parser.hasFlexRes:
lines.extend(self.parser.flex_res_lines)
self.flex_res = self.process_flex_res_lines(self.parser.flex_res_lines)
#print "flex_res=", self.flex_res
parser.allLines = lines
parser.filename = filename
#filename = pdbqParser.filename = self.dpo['move']['value']
#the parser does this
#nameStr = os.path.splitext(filename)[0]
try:
mol = parser.parse()[0]
return mol
except:
print "exception in _buildInputLig"
