Hello,
I am trying to load a dataset using a vector of atoms (e.g [6,6,7,6,6,8])
and the corresponding adjacency matrix. I am using the following script to
transform these into a mol object:
def MolFromGraphs(node_list, adjacency_matrix):
# create empty editable mol object
mol = Chem.RWMol()
# add atoms to mol and keep track of index
node_to_idx = {}
for i in range(len(node_list)):
a = Chem.Atom(node_list[i].item())
molIdx = mol.AddAtom(a)
node_to_idx[i] = molIdx
# add bonds between adjacent atoms
for ix, row in enumerate(adjacency_matrix):
for iy, bond in enumerate(row):
# only traverse half the matrix
if iy <= ix:
continue
# add relevant bond type (there are many more of these)
if bond == 0:
continue
elif bond == 1:
bond_type = Chem.rdchem.BondType.SINGLE
mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)
elif bond == 2:
bond_type = Chem.rdchem.BondType.DOUBLE
mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)
elif bond == 3:
bond_type = Chem.rdchem.BondType.TRIPLE
mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)
elif bond == 1.5:
bond_type = Chem.rdchem.BondType.AROMATIC
mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)
# Convert RWMol to Mol object
mol = mol.GetMol()
return mol
When I try to get the hybridization of atoms using the mol object generated
from the function above, I get *UNSPECIFIED.*
To make sure that this function works, I used *MolToSmiles *to generate a
SMILES string from the generated mol object and it matched the actual
SMILES from the dataset. Interestingly, when I regenerate the mol object
from the SMILES that I already generated from the above function, I can get
the hybridization from the new mol object with no problem. I was wondering
if there is a flag or variable that I should set in the above function to
be able to get hybridization from the generated mol object.
Thanks!
Navid
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