opls_typing

class biochar.opls_typing.AtomTyper

Bases: object

Assign OPLS-AA atom types based on chemical environment.

assign_atom_types(mol)

Assign OPLS-AA atom types to all atoms.

Parameters:

mol – RDKit molecule

Return type:

Dict[int, str]

Returns:

Dictionary of {atom_idx – opls_type}

Parameters:

mol (Mol)

class biochar.opls_typing.ChargeAssigner

Bases: object

Assign partial charges to atoms using OPLS-AA parameters.

Strategy: Use predefined OPLS charges, with adjustments for unusual groups.

assign_charges(mol, atom_types)

Assign partial charges to all atoms.

Parameters:

• mol – RDKit molecule

• atom_types – Dictionary of {atom_idx: opls_type}

Return type:

Dict[int, float]

Returns:

Dictionary of {atom_idx – charge}

Parameters:

• mol (Mol)

• atom_types (Dict[int, str])