def atoms_positions_parser(input):
"""
:param input: The input string
:type input: str
:rtype: Molecule
"""
lines = input.split('\n')
element_table = OBElementTable()
mol = OBMol()
for line in lines:
matches = search(atoms_positions_pattern, line)
# Create the atom
atom = mol.NewAtom()
# Set the proper atomic number with respect of the atomic symbol
atomic_number = element_table.GetAtomicNum(matches.group(2))
atom.SetAtomicNum(atomic_number)
# Set the atom vector
x = float(matches.group(3)) * 0.529177
y = float(matches.group(4)) * 0.529177
z = float(matches.group(5)) * 0.529177
atom.SetVector(x, y, z)
return Molecule(mol)
def ToCannonicalSmiles(self):
atomCache={}
mol=OBMol()
for sourceAtom in self.atoms:
atom=mol.NewAtom()
atom.SetAtomicNum(sourceAtom.GetAtomicNum())
if sourceAtom.IsAromatic():
atom.SetAromatic()
atom.SetSpinMultiplicity(2)
atomCache[sourceAtom]=atom
for sourceBond in self.bonds:
mol.AddBond(atomCache[sourceBond.atom1].GetIdx(), atomCache[sourceBond.atom2].GetIdx(), sourceBond.GetBondOrder())
writer=OBConversion()
writer.SetInAndOutFormats("smi", "can")
return writer.WriteString(mol).strip()
def ToOBMol(self):
atomCache={}
mol=OBMol()
mol.BeginModify()
for sourceAtom in self.atoms:
atom=mol.NewAtom()
atom.SetAtomicNum(sourceAtom.GetAtomicNum())
if sourceAtom.IsAromatic():
atom.SetAromatic()
## atom.SetSpinMultiplicity(2)
atomCache[sourceAtom]=atom
for sourceBond in self.bonds:
mol.AddBond(atomCache[sourceBond.atom1].GetIdx(), atomCache[sourceBond.atom2].GetIdx(), sourceBond.GetBondOrder())
## mol.SetAromaticPerceived()
mol.AssignSpinMultiplicity()
## mol.UnsetAromaticPerceived()
mol.EndModify()
return mol
