rdkit_utilities.rdForceFieldHelpers

rdkit_utilities.rdForceFieldHelpers.FFOptimizeMolecule(mol, forcefield='MMFF94', maxIters=200, vdwThresh=10.0, nonBondedThresh=100.0, confId=-1, ignoreInterfragInteractions=True)[source]

Optimize molecule

Parameters

  • mol (rdkit.Chem.Mol) – Molecule of interest

  • forcefield (Literal[“UFF”, “MMFF”, “MMFF94”, “MMFF94S”] or RDKit force field) – Force field name or RDKit force field. If an MMFF force field is used, you can choose the MMFF94 or MMFF94s variant. “MMFF” defaults to MMFF94.

  • maxIters (int) – the maximum number of iterations

  • ignoreInterfragInteractions (bool) – If True, nonbonded terms between fragments will not be added to the forcefield.

  • vdwThresh (float) – Used to exclude long-range van der Waals interactions. Only used for the UFF force field.

  • nonBondedThresh (float) – Used to exclude long-range non-bonded interactions. Only used for the MMFF force field.

  • confId (int) – Which conformer to optimize

Returns

success – 0 if the optimization converged, 1 if more iterations are required.

Return type

int

Parameters

  • mol (Mol) –

  • forcefield (Union[ForceField, Literal['UFF', 'MMFF', 'MMFF94', 'MMFF94S']]) –

  • maxIters (int) –

  • vdwThresh (float) –

  • nonBondedThresh (float) –

  • confId (int) –

  • ignoreInterfragInteractions (bool) –

rdkit_utilities.rdForceFieldHelpers.FFOptimizeMoleculeConfs(mol, forcefield='MMFF94', maxIters=200, numThreads=1, vdwThresh=10.0, nonBondedThresh=100.0, confId=-1, ignoreInterfragInteractions=True)[source]

Optimize molecule conformers

Parameters

  • mol (rdkit.Chem.Mol) – Molecule of interest

  • forcefield (Literal[“UFF”, “MMFF”, “MMFF94”, “MMFF94S”] or RDKit force field) – Force field name or RDKit force field. If an MMFF force field is used, you can choose the MMFF94 or MMFF94s variant. “MMFF” defaults to MMFF94.

  • maxIters (int) – the maximum number of iterations

  • numThreads (int) – the number of threads to use, only has an effect if the RDKit was built with thread support (defaults to 1). If set to zero, the max supported by the system will be used.

  • ignoreInterfragInteractions (bool) – If True, nonbonded terms between fragments will not be added to the forcefield.

  • vdwThresh (float) – Used to exclude long-range van der Waals interactions. Only used for the UFF force field.

  • nonBondedThresh (float) – Used to exclude long-range non-bonded interactions. Only used for the MMFF force field.

  • confId (int) – Which conformer to optimize

Returns

success_energies – List of tuples of (success, energy) for each conformer. The success is 0 if the optimization converged, 1 if more iterations are required.

Return type

List[Tuple[int, float]]

Parameters

  • mol (Mol) –

  • forcefield (Union[ForceField, Literal['UFF', 'MMFF', 'MMFF94', 'MMFF94S']]) –

  • maxIters (int) –

  • numThreads (int) –

  • vdwThresh (float) –

  • nonBondedThresh (float) –

  • confId (int) –

  • ignoreInterfragInteractions (bool) –

rdkit_utilities.rdForceFieldHelpers.GetMoleculeForceField(mol, forcefield='MMFF94', ignoreInterfragInteractions=True, vdwThresh=10.0, nonBondedThresh=100.0, confId=-1)[source]

Get molecule force field with string

Parameters

  • mol (rdkit.Chem.Mol) – Molecule of interest

  • forcefield (Literal[“UFF”, “MMFF”, “MMFF94”, “MMFF94S”]) – Force field name. If an MMFF force field is used, you can choose the MMFF94 or MMFF94s variant. “MMFF” defaults to MMFF94.

  • ignoreInterfragInteractions (bool) – If True, nonbonded terms between fragments will not be added to the forcefield.

  • vdwThresh (float) – Used to exclude long-range van der Waals interactions. Only used for the UFF force field.

  • nonBondedThresh (float) – Used to exclude long-range non-bonded interactions. Only used for the MMFF force field.

  • confId (int) – Which conformer to optimize

Return type

rdkit.Chem.rdForceFieldHelpers.ForceField

Parameters

  • mol (Mol) –

  • forcefield (Literal['UFF', 'MMFF', 'MMFF94', 'MMFF94S']) –

  • ignoreInterfragInteractions (bool) –

  • vdwThresh (float) –

  • nonBondedThresh (float) –

  • confId (int) –