rdkit.Chem.rdMIF module

Module containing functions for calculating molecular interaction fields (MIFs) NOTE: This functionality is experimental and the API and/or results may change in future releases.

class rdkit.Chem.rdMIF.Coulomb(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeCharge: float = 1.0, absVal: bool = False, chargeKey: str = '_GasteigerCharge', softcoreParam: float = 0.0, cutoff: float = 1.0)
class rdkit.Chem.rdMIF.Coulomb(self, charges: object, positions: object, probeCharge: float = 1.0, absVal: bool = False, softcoreParam: float = 0.0, cutoff: float = 1.0)

Bases: object

Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric).

Overloaded function.

  1. __init__(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeCharge: float = 1.0, absVal: bool = False, chargeKey: str = '_GasteigerCharge', softcoreParam: float = 0.0, cutoff: float = 1.0) -> None

Constructor for Coulomb class.

ARGUMENTS: - mol: the molecule of interest - confId: the ID of the conformer to be used (defaults to -1) - probeCharge charge of probe [e] (defaults to 1.0 e) - absVal: if True, absolute values of interactions are calculated (defaults to False) - chargeKey property key for retrieving partial charges of atoms from molecule (defaults to ‘_GasteigerCharge’) - softcoreParam softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (defaults to 0.0) - cutoff minimum cutoff distance [A] (defaults to 1.0)

  1. __init__(self, charges: object, positions: object, probeCharge: float = 1.0, absVal: bool = False, softcoreParam: float = 0.0, cutoff: float = 1.0) -> None

Alternative constructor for Coulomb class.

ARGUMENTS: - charges: array of partial charges of a molecule’s atoms - positions: array of positions of a molecule’s atoms - probeCharge charge of probe [e] (defaults to 1.0 e) - absVal: if True, absolute values of interactions are calculated (defaults to False) - softcoreParam softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (defaults to 0.0) - cutoff minimum cutoff distance [A] (defaults to 1.0)

class rdkit.Chem.rdMIF.CoulombDielectric(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeCharge: float = 1.0, absVal: bool = False, chargeKey: str = '_GasteigerCharge', softcoreParam: float = 0.0, cutoff: float = 1.0, epsilon: float = 80.0, xi: float = 4.0)
class rdkit.Chem.rdMIF.CoulombDielectric(self, charges: object, positions: object, probeCharge: float = 1.0, absVal: bool = False, softcoreParam: float = 0.0, cutoff: float = 1.0, epsilon: float = 80.0, xi: float = 4.0)

Bases: object

Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in by taking a distance-dependent dielectric into account. Same energy term as used in GRID MIFs. References: - J. Med. Chem. 1985, 28, 849. - J. Comp. Chem. 1983, 4, 187.

Overloaded function.

  1. __init__(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeCharge: float = 1.0, absVal: bool = False, chargeKey: str = '_GasteigerCharge', softcoreParam: float = 0.0, cutoff: float = 1.0, epsilon: float = 80.0, xi: float = 4.0) -> None

Constructor for CoulombDielectric class.

ARGUMENTS: - mol: the molecule of interest - confId: the ID of the conformer to be used (defaults to -1) - probeCharge charge of probe [e] (defaults to 1.0 e) - absVal: if True, absolute values of interactions are calculated (defaults to False) - chargeKey property key for retrieving partial charges of atoms from molecule (defaults to ‘_GasteigerCharge’) - softcoreParam softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (defaults to 0.0) - cutoff minimum cutoff distance [A] (defaults to 1.0) - epsilon relative permittivity of solvent (defaults to 80.0) - xi relative permittivity of solute (defaults to 4.0)

  1. __init__(self, charges: object, positions: object, probeCharge: float = 1.0, absVal: bool = False, softcoreParam: float = 0.0, cutoff: float = 1.0, epsilon: float = 80.0, xi: float = 4.0) -> None

Alternative constructor for CoulombDielectric class.

  • charges: array of partial charges of a molecule’s atoms

  • positions: array of positions of a molecule’s atoms

  • probeCharge charge of probe [e] (defaults to 1.0 e)

  • absVal: if True, absolute values of interactions are calculated (defaults to False)

  • softcoreParam softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (defaults to 0.0)

  • cutoff minimum cutoff distance [A] (defaults to 1.0)

  • epsilon relative permittivity of solvent (defaults to 80.0)

  • xi relative permittivity of solute (defaults to 4.0)

class rdkit.Chem.rdMIF.HBond(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeAtomType: str = 'OH', fixed: bool = True, cutoff: float = 1.0)

Bases: object

Class for calculation of hydrogen bonding energy between a probe and a molecule.

Similar to GRID hydrogen bonding descriptors. References: - J.Med.Chem. 1989, 32, 1083. - J.Med.Chem. 1993, 36, 140. - J.Med.Chem. 1993, 36, 148.

Constructor for HBond class.

ARGUMENTS: - mol: the molecule of interest - confId: the ID of the conformer to be used (defaults to -1) - probeAtomType: atom type for the probe atom (either ‘OH’, ‘O’, ‘NH’ or ‘N’) (defaults to ‘OH’) - fixed: for some groups, two different angle dependencies are defined:

one which takes some flexibility of groups (rotation/swapping of lone pairs and hydrogen) into account and one for strictly fixed conformations if True, strictly fixed conformations (defaults to True)

  • cutoff minimum cutoff distance [A] (defaults to 1.0)

class rdkit.Chem.rdMIF.Hydrophilic(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, fixed: bool = True, cutoff: float = 1.0)

Bases: object

Class for calculation of a hydrophilic potential of a molecule at a point.

The interaction energy of hydrogen and oxygen of water is calculated at each point as a hydrogen bond interaction (either OH or O probe). The favored interaction is returned.

Constructor for Hydrophilic class.

ARGUMENTS: - mol: the molecule of interest - confId: the ID of the conformer to be used (defaults to -1) - fixed: for some groups, two different angle dependencies are defined:

one which takes some flexibility of groups (rotation/swapping of lone pairs and hydrogen) into account and one for strictly fixed conformations if True, strictly fixed conformations (defaults to True)

  • cutoff minimum cutoff distance [A] (default:1.0)

exception rdkit.Chem.rdMIF.MIFIndexError

Bases: IndexError

exception rdkit.Chem.rdMIF.MIFValueError

Bases: ValueError

class rdkit.Chem.rdMIF.MMFFVdWaals(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeAtomType: int = 6, scaling: bool = False, cutoff: float = 1.0)

Bases: object

Class for calculating van der Waals interactions between molecule and a probe at a gridpoint based on the MMFF forcefield.

Parameters:

  • object (- mol molecule)

  • atoms (- confId conformation id which is used to get positions of)

  • atom (- probeAtomType MMFF94 atom type for the probe)

  • (default (- cutoff minimum cutoff distance [A]) – 1.0)

  • account (- scaling scaling of VdW parameters to take hydrogen bonds into)

class rdkit.Chem.rdMIF.UFFVdWaals(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1, probeAtomType: str = 'O_3', cutoff: float = 1.0)

Bases: object

Class for calculating van der Waals interactions between molecule and a probe at a gridpoint based on the UFF forcefield.

Parameters:

  • object (- mol molecule)

  • atoms (- confId conformation id which is used to get positions of)

  • atom (- probeAtomType UFF atom type for the probe)

  • (default (- cutoff minimum cutoff distance [A]) – 1.0)