def reader(file, stripHydrogens=1):
lines = collector(file)
while 1:
try:
fields = {}
name = lines.next().strip()
userLine = lines.next().strip()
comment = lines.next().strip()
molinfo = lines.next()
numAtoms, numBonds = int(molinfo[0:3]), int(molinfo[3:6])
atoms = [] # this is the full list of atoms
_atoms = [] # this is the (potentially stripped list
# of atoms. I.e. no hydrogens.)
i = 0
for index in range(numAtoms):
line = lines.next()
x,y,z,symbol,mass,charge,stereo,hcount,hcount_fixed = parse_atom(line)
if symbol == "H" and stripHydrogens:
atoms.append(None)
else:
atom = Atom()
atoms.append(atom)
_atoms.append(atom)
atom.set_symbol(symbol)# = symbol
atom.explicit_hcount = hcount
atom.charge = charge
atom._line = line
atom.x = x
atom.y = y
atom.z = z
if hcount_fixed:
print "hcount fixed"
atom.fixed_hcount = 1 # oops, we shouldn't use this
atom.has_explicit_hcount = True
if mass:
atom.weight = atom.mass + mass
atom.index = i
i = i + 1
bonds = []
for index in range(numBonds):
line = lines.next()
a1, a2, bondtype, stereo, remainder = parse_bond(line)
symbol, bondorder, bondtype, fixed = BOND_SYMBOL[bondtype]
atom1, atom2 = atoms[a1], atoms[a2]
if atom1 is not None and atom2 is not None:
h1, h2 = atom1.handle, atom2.handle
bond = Bond(symbol, bondorder, bondtype, fixed)
bonds.append(bond)
bond._line = remainder
bond.index = index
bond.atoms = [atom1, atom2]
try:
bond.stereo = BOND_LOOKUP_STEREO[bondtype-1][stereo]
except KeyError:
raise MolReaderError("An SD record cannot have a bondtype of %s and a stereo value of %s"%(bondtype, stereo))
except IndexError:
print "*"*44
print line
print "bondtype, stereo", bondtype, stero
raise
atom1.bonds.append(bond)
atom2.bonds.append(bond)
atom1.oatoms.append(atom2)
atom2.oatoms.append(atom1)
if atom1.symbol == "H": atom2.explicit_hcount += 1
if atom2.symbol == "H": atom1.explicit_hcount += 1
else:
if atom1 is None and atom2 is not None:
atom2.explicit_hcount += 1
elif atom2 is None and atom1 is not None:
atom1.explicit_hcount += 1
##############################################################
# read the mprops if necessary
line = lines.next().strip()
while 1:
if line and line[0:6] == "M END":
line = lines.next().strip()
break
elif line == "M CHG":
groups = line[6:].split()[1:]
index = 0
while index < len(groups):
atomIndex = int(groups[index]) - 1
atom = self.atoms[atomIndex]
charge = int(groups[index+1])
self.atoms[atomIndex].charge = charge
index += 2
line = lines.next().strip()
elif line and line[0] == ">":
break
elif line[0:4] == "$$$$":
break
line = lines.next().strip()
# What about end of mol?
#############################################################
# read the fields if necessary
while line != "$$$$":
if line and line[0] == ">":
res = FIELDPATTERN.match(line)
if res: field, potentialID = res.groups()
else:
res = ALTFIELDPATTERN.match(line)
if res:
field = res.groups()[0]
potentialID = None
else:
field, potentialID = None, None
if name is None: name = potentialID
if field:
data = []
line = lines.next().strip()
while line and line != "$$$$":
data.append(line)
line = lines.next().strip()
fields[field] = os.linesep.join(data)
line = lines.next().strip()
mol = Molecule(_atoms, bonds)
mol.name = name
mol.fields = fields
mol.name = name
yield mol, lines.dump(), None
except StopIteration:
break
except Exception:
line = lines.current.strip()
while line[0:4] != "$$$$":
line = lines.next().strip()
stdout, stderr = sys.stdout, sys.stderr
sys.stdout = sys.stderr = io = StringIO()
traceback.print_exc()
sys.stdout = stdout
sys.stderr = stderr
yield None, lines.dump(), io.getvalue()
