def parse_MOL2_Bonds(self, bondlines):
""" Function to build the bonds object using the bond record of
the mol2 file."""
bondlines = map(string.split, bondlines)
for bd in bondlines:
at1 = self.mol.atmNum[int(bd[1])]
at2 = self.mol.atmNum[int(bd[2])]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.type = bd[3]
try:
bond.bondOrder = int(bd[3])
except:
if bd[3] == 'ar':
bond.bondOrder = 'aromatic'
elif bd[3] == 'am':
bond.bondOrder = 'amide'
else:
bond.bondOrder = bd[3]
self.mol.bondsflag = 1
self.mol.hasBonds = 1
def parse_MOL2_Bonds(self, bondlines):
""" Function to build the bonds object using the bond record of
the mol2 file."""
bondlines = map(string.split, bondlines)
for bd in bondlines:
at1 = self.mol.atmNum[int(bd[1])]
at2 = self.mol.atmNum[int(bd[2])]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.type = bd[3]
try:
bond.bondOrder = int(bd[3])
except:
if bd[3]=='ar':
bond.bondOrder = 'aromatic'
elif bd[3]=='am':
bond.bondOrder = 'amide'
else:
bond.bondOrder = bd[3]
self.mol.bondsflag = 1
self.mol.hasBonds = 1
def getMolecule(self, molInd):
molecules = []
if molInd == len(self.molIndex) - 1:
lastLine = -1
else:
lastLine = self.molIndex[molInd + 1]
# lines fotr that molecule
lines = self.allLines[self.molIndex[molInd]:lastLine]
lineIndex = 0
atomsSeen = {} # dict of atom types and number of atoms seen
# parser header
molName = lines[lineIndex].strip()
lineIndex += 3
# create molecule
mol = Protein(name=molName)
mol.info = lines[lineIndex + 1]
mol.comment = lines[lineIndex + 1]
#self.mol.parser = self
chain = Chain(id='1', parent=mol, top=mol)
res = Residue(type='UNK', number='1', parent=chain, top=mol)
mol.levels = [Protein, Chain, Residue, Atom]
# parse count line
line = lines[lineIndex]
assert line[
33:
39] == " V2000", "Format error: only V2000 is suported, got %s" % line[
33:39]
nba = int(line[0:3]) # number of atoms
nbb = int(line[3:6]) # number of bonds
nbal = int(line[6:9]) # number of atom lists
ccc = int(line[12:15]) # chiral flag: 0=not chiral, 1=chiral
sss = int(line[15:18]) # number of stext entries
lineIndex += 1
# parse atoms
for anum in range(nba):
line = lines[lineIndex]
element = line[31:34].strip()
if element in atomsSeen:
atomsSeen[element] += 1
else:
atomsSeen[element] = 1
atom = Atom(name='%s_%s' % (element, atomsSeen[element]),
parent=res,
chemicalElement=element,
top=mol)
atom._coords = [[
float(line[0:10]),
float(line[10:20]),
float(line[20:30])
]]
atom._charges['sdf'] = int(line[35:38])
atom.chargeSet = 'sdf'
mol.allAtoms.append(atom)
atom.massDiff = int(line[34:36])
atom.stereo = int(line[38:41])
atom.hcount = line[41:44]
atom.valence = int(line[47:50])
atom.hetatm = 1
atom.occupancy = 0.0
atom.temperatureFactor = 0.0
lineIndex += 1
# parse bonds
for bnum in range(nba):
line = lines[lineIndex]
at1 = mol.allAtoms[int(line[0:3]) - 1]
at2 = mol.allAtoms[int(line[3:6]) - 1]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.bondOrder = int(line[6:9])
#1 = Single, 2 = Double,
#3 = Triple, 4 = Aromatic,
#5 = Single or Double,
#6 = Single or Aromatic,
#7 = Double or Aromatic, 8 = Any
bond.stereo = int(line[9:12])
#Single bonds: 0 = not stereo,
#1 = Up, 4 = Either,
#6 = Down, Double bonds: 0 = Use x-, y-, z-coords
#from atom block to determine cis or trans,
#3 = Cis or trans (either) double bond
bond.topo = int(line[15:18])
# 0 = Either, 1 = Ring, 2 = Chain
try:
bond.ReactionCenter = int(line[18:21])
except ValueError:
bond.ReactionCenter = 0
#0 = unmarked, 1 = a center, -1 = not a center,
#Additional: 2 = no change,
#4 = bond made/broken,
#8 = bond order changes
#12 = 4+8 (both made/broken and changes);
#5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1)
# "M END" and properties are not parsed at this point
self.mol = mol
mname = mol.name
strRpr = mname + ':::'
mol.allAtoms.setStringRepr(strRpr)
strRpr = mname + ':'
mol.chains.setStringRepr(strRpr)
for c in mol.chains:
cname = c.id
strRpr = mname + ':' + cname + ':'
c.residues.setStringRepr(strRpr)
for r in c.residues:
rname = r.name
strRpr = mname + ':' + cname + ':' + rname + ':'
r.atoms.setStringRepr(strRpr)
molList = mol.setClass()
molList.append(mol)
mol.parser = self
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr(name)
strRpr = name + ':::'
molList.allAtoms.setStringRepr(strRpr)
return molList