rdkit_utilities.rdDistGeom

rdkit_utilities.rdDistGeom.CalculateElectrostaticEnergy(mol, forcefield='MMFF94')

Calculate electrostatic energy of all conformers using force field

Returns

energies – Array of energies, one for each conformer

Return type

numpy.ndarray

Parameters

• mol (Mol) –

• forcefield (Literal['MMFF94', 'MMFF94s']) –

rdkit_utilities.rdDistGeom.CalculateMMFFCharges(mol, forcefield='MMFF94', normalize_partial_charges=True)

Calculate MMFF charges for molecule

Parameters

• mol (Mol) –

• forcefield (Literal['MMFF94', 'MMFF94s']) –

• normalize_partial_charges (bool) –

Return type

ndarray

rdkit_utilities.rdDistGeom.GenerateConformers(mol, numConfs=10, numConfPool=None, maximizeDiversity=False, selectELFConfs=False, ELFPercentage=2.0, pruneRmsThresh=-1.0, diverseRmsThresh=0.05, energyWindow=-1.0, maxAttempts=0, randomSeed=-1, clearConfs=True, useRandomCoords=False, boxSizeMult=2.0, randNegEig=True, numZeroFail=1, coordMap={}, forceTol=0.001, ignoreSmoothingFailures=False, enforceChirality=True, numThreads=1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, printExpTorsionAngles=False, useSmallRingTorsions=False, useMacrocycleTorsions=False, ETversion=1, optimizeConfs=False, forcefield='MMFF94', optMaxIters=200, ffVdwThresh=10.0, ffNonBondedThresh=100, ffIgnoreInterfragInteractions=True, removeTransAcidConformers=True)

Generate conformers on molecule in-place.

Parameters

• numConfs (int) – Max number of conformers to end up with

• numConfPool (Optional[int]) – Max number of conformers to initially generate, for ELF or RMS selection.

• maximizeDiversity (bool) – Whether to maximize diversity via heavy-atom RMS

• selectELFConfs (bool) – Whether to select conformers using the electrostatically least-interacting functional group (ELF) technique

• ELFPercentage (float) – % (out of 100) of conformers to keep from numConfPool when selecting ELF conformers

• pruneRmsThresh (float) – RMS threshold to keep conformers initially generated from numConfPool

• diverseRmsThresh (float) – Minimum RMS threshold for distinguishing conformers when selecting maximally diverse conformers

• energyWindow (float) – If positive, only conformers within this energy window as determined by forcefield will be kept.

• optimizeConfs (bool) – Whether to optimize conformers generated initially, prior to selecting ELF and RMS diverse conformers.

• forcefield (Literal[“UFF”, “MMFF94”, “MMFF94S”]) – Which force field to use for optimizing conformers and calculating energies for energyWindow.

• optMaxIters (int) – Maximum iterations for optimization

• ffVdwThresh (float) – VdW threshold for optimization and calculating energies using force field

• ffNonBondedThresh (float) – Non-bonded threshold for optimization and calculating energies using force field

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

• **kwargs – See the RDKit documentation for rdkit.Chem.rdDistGeom.EmbedMultipleConfs for more.

Parameters

• mol (Mol) –

• numConfs (int) –

• numConfPool (Optional[int]) –

• maximizeDiversity (bool) –

• selectELFConfs (bool) –

• ELFPercentage (float) –

• pruneRmsThresh (float) –

• diverseRmsThresh (float) –

• energyWindow (float) –

• maxAttempts (int) –

• randomSeed (int) –

• clearConfs (bool) –

• useRandomCoords (bool) –

• boxSizeMult (float) –

• randNegEig (bool) –

• numZeroFail (int) –

• coordMap (Dict[int, Union[ndarray, List[float]]]) –

• forceTol (float) –

• ignoreSmoothingFailures (bool) –

• enforceChirality (bool) –

• numThreads (int) –

• useExpTorsionAnglePrefs (bool) –

• useBasicKnowledge (bool) –

• printExpTorsionAngles (bool) –

• useSmallRingTorsions (bool) –

• useMacrocycleTorsions (bool) –

• ETversion (int) –

• optimizeConfs (bool) –

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

• optMaxIters (int) –

• ffVdwThresh (float) –

• ffNonBondedThresh (float) –

• ffIgnoreInterfragInteractions (bool) –

• removeTransAcidConformers (bool) –

Return type

List[int]

rdkit_utilities.rdDistGeom.GetExclusions(mol)

Get exclusions with a molecule between atoms 2- and 3- sites away

Parameters

mol (Mol) –

Return type

Set[Tuple[int, int]]

rdkit_utilities.rdDistGeom.RemoveConformersOutsideEnergyWindow(mol, energyWindow=30.0, forcefield='MMFF94', numThreads=1, ffVdwThresh=10.0, ffNonBondedThresh=100, ffIgnoreInterfragInteractions=True)

Remove conformers outside energy window using force field, in-place

The window covers an energy range from the conformer with the lowest energy. The molecule also has its conformers sorted by force field energy.

Returns

numConfs – The number of remaining conformers

Return type

int

Parameters

• mol (Mol) –

• energyWindow (float) –

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

• numThreads (int) –

• ffVdwThresh (float) –

• ffNonBondedThresh (float) –

• ffIgnoreInterfragInteractions (bool) –

rdkit_utilities.rdDistGeom.RemoveTransAcidConformers(mol)

Remove conformers from molecule if they contain a trans carboxylic acid

Parameters

mol (Mol) –

rdkit_utilities.rdDistGeom.SelectDiverseConformers(mol, numConfs=10, diverseRmsThresh=0.05)

Select conformers for max diversity by RMS, in-place.

This uses a greedy algorithm. Unselected conformers are deleted.

Parameters

• mol (Mol) –

• numConfs (int) –

• diverseRmsThresh (float) –

rdkit_utilities.rdDistGeom.SelectDiverseELFConformers(mol, numConfs=10, ELFPercentage=2.0, diverseRmsThresh=0.05, removeTransAcidConformers=True)

Select diverse conformers using the ELF technique, in-place.

Other conformers are deleted from the molecule.

Parameters

• mol (Mol) –

• numConfs (int) –

• ELFPercentage (float) –

• diverseRmsThresh (float) –

• removeTransAcidConformers (bool) –

rdkit_utilities.rdDistGeom.SelectELFConformers(mol, ELFPercentage=2.0, removeTransAcidConformers=True)

Keep percentage of conformers, ranked by electrostatic energy, in-place.

The other conformers are deleted.

Parameters

• mol (Mol) –

• ELFPercentage (float) –

• removeTransAcidConformers (bool) –

rdkit_utilities.rdDistGeom.SortConformersByElectrostaticInteraction(mol, forcefield='MMFF94')

Sort conformers in-place by electrostatic energy using MMFF

Parameters

• mol (Mol) –

• forcefield (Literal['MMFF94', 'MMFF94s']) –

rdkit_utilities.rdDistGeom.SortConformersByEnergy(mol, forcefield='MMFF94', numThreads=1, ffVdwThresh=10.0, ffNonBondedThresh=100, ffIgnoreInterfragInteractions=True, reverse=False)

Sort conformers in-place on molecule by force field energy.

Returns

energies

Return type

List[float]

Raises

ValueError – If the force field cannot calculate energies

Parameters

• mol (Mol) –

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

• numThreads (int) –

• ffVdwThresh (float) –

• ffNonBondedThresh (float) –

• ffIgnoreInterfragInteractions (bool) –

• reverse (bool) –