assess_atoms#

assess_atoms(mol, add_atom=None, use_formal_charge=False)[source]#

Assess an RDKit molecule’s atoms to determine which are charged or not fully satisfied.

Parameters:

  • mol (rdkit.Chem.Mol) – RDKit molecule.

  • add_atom (str, optional) – If provided, the number of hanging bonds will be the number of this atom type present.

  • use_formal_charge (bool, optional) – Whether to use the atomic formal charge in get_atom_charge().

Returns:

  • charge (float) – Total charge of the molecule.

  • hanging_bonds (int) – Number of hanging bonds to contribute toward the oxidation state of the metal.

  • charged_atoms (dict) – Detailed information on atoms showing a charge or not satisfied with full bonding.

    Each entry contains:
    symbolstr

    Atomic symbol.

    chargeint

    Formal charge of the atom as defined by get_atom_charge().

    bond_orderslist of tuple
    List of bonds to this atom. Each bond is represented by a tuple:
    bond_typestr

    rdkit.Chem.BondType.name

    bond_orderint

    Custom integer value representing the bond type (DATIVE=0).

    BeginAtom_Symbolstr

    Atomic symbol of the “BeginAtom”.

    BeginAtomIdxint

    Molecule index of the “BeginAtom”.

    EndAtom_Symbolstr

    Atomic symbol of the “EndAtom”.

    EndAtomIdxint

    Molecule index of the “EndAtom”.

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