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Normally, file formats such as SMILES, SLN or MDL's SDF format, specify
the formal on each atom of a connection table. However, when reading
from lesser file formats or when repairing "broken" molecules, it may
be convenient to assign formal charges to each atom such that the atomic
valence is consistent. OEChem provides this functionality via the
OEAssignFormalCharges function. This function requires that bond
orders and implicit hydrogen counts have been set on a molecule. It then
adjusts the formal charge on each uncharged atom to correct common valence
model mismatches. For example, quaternary nitrogens are assigned a +1
formal charge, and terminal oxygen connected only by a single bond (with
no implicit hydrogens) is assigned a -1 formal charge.
A more technical discussion of the formal charges that are assigned by this function are described in the "OpenEye Charge Model" section of the "Valence Models" chapter of this document.
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