openff.recharge.esp.storage.MoleculeESPRecord

model openff.recharge.esp.storage.MoleculeESPRecord[source]

Bases: BaseModel

A record which contains information about the molecule that the ESP was measured for (including the exact conformer coordinates), provenance about how the ESP was calculated, and the values of the ESP at each of the grid points.

Fields

  • conformer (openff.recharge.utilities.pydantic.Array)

  • electric_field (Optional[openff.recharge.utilities.pydantic.Array])

  • esp (openff.recharge.utilities.pydantic.Array)

  • esp_settings (openff.recharge.esp._esp.ESPSettings)

  • grid_coordinates (openff.recharge.utilities.pydantic.Array)

  • tagged_smiles (str)

field tagged_smiles: str [Required]

The tagged SMILES patterns (SMARTS) which encodes both the molecule stored in this record, a map between the atoms and the molecule and their coordinates.

field conformer: openff.recharge.utilities.pydantic.Array [Required]

The coordinates [Angstrom] of this conformer with shape=(n_atoms, 3).

field grid_coordinates: openff.recharge.utilities.pydantic.Array [Required]

The grid coordinates [Angstrom] which the ESP was calculated on with shape=(n_grid_points, 3).

field esp: openff.recharge.utilities.pydantic.Array [Required]

The value of the ESP [Hartree / e] at each of the grid coordinates with shape=(n_grid_points, 1).

field electric_field: Optional[openff.recharge.utilities.pydantic.Array] [Required]

The value of the electric field [Hartree / (e . a0)] at each of the grid coordinates with shape=(n_grid_points, 3).

field esp_settings: openff.recharge.esp._esp.ESPSettings [Required]

The settings used to generate the ESP stored in this record.

property conformer_quantity: pint.util.Quantity
property grid_coordinates_quantity: pint.util.Quantity
property esp_quantity: pint.util.Quantity
property electric_field_quantity: pint.util.Quantity
classmethod from_molecule(molecule: Molecule, conformer: Quantity, grid_coordinates: Quantity, esp: Quantity, electric_field: Optional[Quantity], esp_settings: ESPSettings) → MoleculeESPRecord[source]

Creates a new MoleculeESPRecord from an existing molecule object, taking care of creating the InChI and SMARTS representations.

Parameters

  • molecule – The molecule to store in the record.

  • conformer – The coordinates [Angstrom] of this conformer with shape=(n_atoms, 3).

  • grid_coordinates – The grid coordinates [Angstrom] which the ESP was calculated on with shape=(n_grid_points, 3).

  • esp – The value of the ESP [Hartree / e] at each of the grid coordinates with shape=(n_grid_points, 1).

  • electric_field – The value of the electric field [Hartree / (e . a0)] at each of the grid coordinates with shape=(n_grid_points, 3).

  • esp_settings – The settings used to generate the ESP stored in this record.

Return type

The created record.