Hello all,
I am trying to create a molecule from geometry (a numpy array n_atoms x 3),
symbols (list of atom symbols) and a connectivity map (list of list where
each list is [atom_1_idx, atom_2_idx, bond_type]). The information also has
all hydrogens. The following code works most of the time:
from rdkit import Chem
from rdkit.Geometry.rdGeometry import Point3D
_BO_DISPATCH_TABLE = {1: Chem.BondType.SINGLE, 2: Chem.BondType.DOUBLE, 3:
Chem.BondType.TRIPLE}
conformer = Chem.Conformer(len(symbols))
molecule = Chem.Mol()
em = Chem.RWMol(molecule)
for i, s in enumerate(symbols):
atom = em.AddAtom(Chem.Atom(cmiles.utils._symbols[s]))
atom_position = Point3D(geometry[i][0], geometry[i][1], geometry[i][2])
conformer.SetAtomPosition(atom, atom_position)
# Add connectivity
for bond in connectivity:
bond_type = _BO_DISPATCH_TABLE[bond[-1]]
em.AddBond(bond[0], bond[1], bond_type)
molecule = em.GetMol()
Chem.SanitizeMol(molecule)
However, if a molecule has a tetravalent nitrogen, the data that I have
does not have the explicit formal charge for each atom so I get the
following error:
ValueError: Sanitization error: Explicit valence for atom # 0 N, 4, is
greater than permitted
Given that I have all the hydrogen and the total charge of the
molecules, I can go in and add the charge to the problematic nitrogen
and check that the total charge is still the same. But I am not sure
how to capture the offending atom instance. I can get the information
from parsing the error message (which is the hack I use now) but I was
wondering if there is a better way to do it.
Thank you,
Chaya
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