def getMolecularWeight(self):
"""
Return the molecular weight of the molecule in kg/mol.
"""
mass = 0
H = elements.getElement('H')
for atom in self.vertices:
mass += atom.element.mass
return mass
def fromOBMol(self, obmol, implicitH=False):
"""
Convert an OpenBabel OBMol object `obmol` to a molecular structure. Uses
`OpenBabel <http://openbabel.org/>`_ to perform the conversion.
"""
self.vertices = []
self.edges = {}
# Add hydrogen atoms to complete molecule if needed
obmol.AddHydrogens()
# Iterate through atoms in obmol
for i in range(0, obmol.NumAtoms()):
obatom = obmol.GetAtom(i + 1)
# Use atomic number as key for element
number = obatom.GetAtomicNum()
element = elements.getElement(number=number)
# Process spin multiplicity
radicalElectrons = 0
spinMultiplicity = obatom.GetSpinMultiplicity()
if spinMultiplicity == 0:
radicalElectrons = 0; spinMultiplicity = 1
elif spinMultiplicity == 1:
radicalElectrons = 2; spinMultiplicity = 1
elif spinMultiplicity == 2:
radicalElectrons = 1; spinMultiplicity = 2
elif spinMultiplicity == 3:
radicalElectrons = 2; spinMultiplicity = 3
# Process charge
charge = obatom.GetFormalCharge()
coord = np.array([obatom.x(), obatom.y(), obatom.z()])
label = obatom.GetIdx()
atom = Atom(element, coord, radicalElectrons, spinMultiplicity, 0, charge, str(label))
self.vertices.append(atom)
self.edges[atom] = {}
# Add bonds by iterating again through atoms
for j in range(0, i):
obatom2 = obmol.GetAtom(j + 1)
obbond = obatom.GetBond(obatom2)
if obbond is not None:
order = 0
# Process bond type
if obbond.IsSingle(): order = 'S'
elif obbond.IsDouble(): order = 'D'
elif obbond.IsTriple(): order = 'T'
elif obbond.IsAromatic(): order = 'B'
bond = Bond(order)
atom1 = self.vertices[i]
atom2 = self.vertices[j]
self.edges[atom1][atom2] = bond
self.edges[atom2][atom1] = bond
# Make hydrogens implicit to conserve memory
if implicitH: self.makeHydrogensImplicit()
return self
def fromOBMol(self, obmol):
"""
Convert an OpenBabel OBMol object `obmol` to a molecular structure. Uses
`OpenBabel <http://openbabel.org/>`_ to perform the conversion.
"""
cython.declare(i=cython.int)
cython.declare(radicalElectrons=cython.int, spinMultiplicity=cython.int, charge=cython.int)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, bond=Bond)
self.vertices = []
# Add hydrogen atoms to complete molecule if needed
obmol.AddHydrogens()
# Iterate through atoms in obmol
for i in range(0, obmol.NumAtoms()):
obatom = obmol.GetAtom(i + 1)
# Use atomic number as key for element
number = obatom.GetAtomicNum()
element = elements.getElement(number)
# Process spin multiplicity
radicalElectrons = 0
spinMultiplicity = obatom.GetSpinMultiplicity()
if spinMultiplicity == 0:
radicalElectrons = 0; spinMultiplicity = 1
elif spinMultiplicity == 1:
radicalElectrons = 2; spinMultiplicity = 1
elif spinMultiplicity == 2:
radicalElectrons = 1; spinMultiplicity = 2
elif spinMultiplicity == 3:
radicalElectrons = 2; spinMultiplicity = 3
elif spinMultiplicity == 4:
radicalElectrons = 3; spinMultiplicity = 4
elif spinMultiplicity == 5:
radicalElectrons = 4; spinMultiplicity = 5
# Process charge
charge = obatom.GetFormalCharge()
atom = Atom(element, radicalElectrons, spinMultiplicity, charge)
self.vertices.append(atom)
# Add bonds by iterating again through atoms
for j in range(0, i):
obatom2 = obmol.GetAtom(j + 1)
obbond = obatom.GetBond(obatom2)
if obbond is not None:
order = 0
# Process bond type
if obbond.IsSingle(): order = 'S'
elif obbond.IsDouble(): order = 'D'
elif obbond.IsTriple(): order = 'T'
elif obbond.IsAromatic(): order = 'B'
bond = Bond(self.vertices[i], self.vertices[j], order)
self.addBond(bond)
# Set atom types and connectivity values
self.updateConnectivityValues()
self.updateAtomTypes()
return self
def fromOBMol(self, obmol, implicitH=False):
"""
Convert an OpenBabel OBMol object `obmol` to a molecular structure. Uses
`OpenBabel <http://openbabel.org/>`_ to perform the conversion.
"""
self.vertices = []
self.edges = {}
# Add hydrogen atoms to complete molecule if needed
obmol.AddHydrogens()
# Iterate through atoms in obmol
for i in range(0, obmol.NumAtoms()):
obatom = obmol.GetAtom(i + 1)
# Use atomic number as key for element
number = obatom.GetAtomicNum()
element = elements.getElement(number=number)
# Process spin multiplicity
radicalElectrons = 0
spinMultiplicity = obatom.GetSpinMultiplicity()
if spinMultiplicity == 0:
radicalElectrons = 0
spinMultiplicity = 1
elif spinMultiplicity == 1:
radicalElectrons = 2
spinMultiplicity = 1
elif spinMultiplicity == 2:
radicalElectrons = 1
spinMultiplicity = 2
elif spinMultiplicity == 3:
radicalElectrons = 2
spinMultiplicity = 3
# Process charge
charge = obatom.GetFormalCharge()
coord = np.array([obatom.x(), obatom.y(), obatom.z()])
label = obatom.GetIdx()
atom = Atom(element, coord, radicalElectrons, spinMultiplicity, 0,
charge, str(label))
self.vertices.append(atom)
self.edges[atom] = {}
# Add bonds by iterating again through atoms
for j in range(0, i):
obatom2 = obmol.GetAtom(j + 1)
obbond = obatom.GetBond(obatom2)
if obbond is not None:
order = 0
# Process bond type
if obbond.IsSingle(): order = 'S'
elif obbond.IsDouble(): order = 'D'
elif obbond.IsTriple(): order = 'T'
elif obbond.IsAromatic(): order = 'B'
bond = Bond(order)
atom1 = self.vertices[i]
atom2 = self.vertices[j]
self.edges[atom1][atom2] = bond
self.edges[atom2][atom1] = bond
# Make hydrogens implicit to conserve memory
if implicitH: self.makeHydrogensImplicit()
return self