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 test_parsePDBQT():
"""
check that pdbqt format files can be read
"""
from MolKit.pdbParser import PdbqtParser
parser = PdbqtParser("Data/1ent_rec.pdbqt")
m = parser.parse()[0]
assert len(m.allAtoms)==2901
def test_parsePDBQT():
"""
check that pdbqt format files can be read
"""
from MolKit.pdbParser import PdbqtParser
parser = PdbqtParser("Data/1ent_rec.pdbqt")
m = parser.parse()[0]
assert len(m.allAtoms) == 2901
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"
def Read(filename=None, alllines=None, dataformat='pdb', modelsAs='molecules'):
if not alllines and not filename:
raise AssertionError("%s invalid molecule" % filename)
elif alllines and filename:
alllines = None
elif filename:
if not os.path.exists(filename):
raise AssertionError("%s does't exist" % filename)
if alllines:
ext = dataformat
args = [None, alllines]
else:
ext = filename.split('.')[1]
args = [filename, None]
if ext == 'pdb':
parser = PdbParser(*args, modelsAs=modelsAs)
elif ext == 'pdbq':
parser = PdbqParser(*args, modelsAs=modelsAs)
elif ext == 'pdbqt':
parser = PdbqtParser(*args, modelsAs=modelsAs)
elif ext == 'pdbqs':
parser = PdbqsParser(*args, modelsAs=modelsAs)
elif ext == 'pqr':
parser = PQRParser(*args, modelsAs=modelsAs)
# FIXME: pass all lines???
elif ext == 'mol2':
parser = Mol2Parser(
filename) # ??should modelsAs be available for mol2 format??
elif ext == 'cif':
parser = MMCIFParser(filename)
elif ext == 'f2d':
parser = F2DParser(filename)
else:
print("File Format unknown can't parse it")
return []
molecules = parser.parse()
return molecules
def Read(filename, modelsAs='molecules'):
if not os.path.exists(filename):
raise AssertionError, "%s does't exist" % filename
from MolKit.pdbParser import PdbParser, PdbqParser,PdbqsParser,\
PdbqtParser, PQRParser, F2DParser
from MolKit.mol2Parser import Mol2Parser
from MolKit.mmcifParser import MMCIFParser
ext = string.split(filename, '.')
if ext[-1] == 'pdb':
parser = PdbParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbq':
parser = PdbqParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbqt':
parser = PdbqtParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbqs':
parser = PdbqsParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pqr':
parser = PQRParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'mol2':
parser = Mol2Parser(
filename) #??should modelsAs be available for mol2 format??
elif ext[-1] == 'cif':
parser = MMCIFParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'f2d':
parser = F2DParser(filename)
else:
print "File Format unknown can't parse it"
return []
molecules = parser.parse()
return molecules
