def get_bonds(self):
"""
A method for identifying all of the bonds in a conformer
"""
bond_list = []
for bond in self.rdkit_molecule.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for index, indices in enumerate(bond_list):
i, j = indices
length = self.ase_molecule.get_distance(i, j)
center = False
if ((self.rmg_molecule.atoms[i].label) and (
self.rmg_molecule.atoms[j].label)):
center = True
bond = Bond(index=index,
atom_indices=indices,
length=length,
reaction_center=center)
mask = self.get_mask(bond)
bond.mask = mask
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_ts_bonds(self):
rdmol_copy = self.create_pseudo_geometry()
bond_list = []
for bond in rdmol_copy.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for indices in bond_list:
i, j = indices
length = self.ase_ts.get_distance(i, j)
reaction_center = "No"
if (self.rmg_ts.atoms[i].label != ""
and self.rmg_ts.atoms[j].label != ""):
reaction_center = "Yes"
elif ((self.rmg_ts.atoms[i].label != ""
and self.rmg_ts.atoms[j].label == "")
or (self.rmg_ts.atoms[i].label == ""
and self.rmg_ts.atoms[j].label != "")):
reaction_center = "Close"
bond = Bond(indices=indices,
length=length,
reaction_center=reaction_center)
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_bonds(self,
rdkit_molecule=None,
ase_molecule=None,
rmg_molecule=None):
"""
A method for identifying all of the bonds in a conformer
"""
if not rdkit_molecule:
rdkit_molecule = self.rdkit_molecule
if not ase_molecule:
ase_molecule = self.ase_molecule
if not rmg_molecule:
rmg_molecule = self.rmg_molecule
rdmol_copy = rdkit_molecule
bond_list = []
for bond in rdmol_copy.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for index, indices in enumerate(bond_list):
i, j = indices
length = ase_molecule.get_distance(i, j)
center = False
if ((rmg_molecule.atoms[i].label)
and (rmg_molecule.atoms[j].label)):
center = True
bond = Bond(index=index,
atom_indices=indices,
length=length,
reaction_center=center)
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_bonds(self):
rdmol_copy = self.rdkit_molecule
bond_list = []
for bond in rdmol_copy.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for indices in bond_list:
i, j = indices
length = self.ase_molecule.get_distance(i, j)
reaction_center = "No"
bond = Bond(indices=indices,
length=length,
reaction_center=reaction_center)
bonds.append(bond)
self.bonds = bonds
return self.bonds
def setUp(self):
self.bond = Bond(index=1,
atom_indices=[1, 2],
length=1.8,
reaction_center=True,
mask=[True, True, True])