BuiltInToolkitWrapper

class openff.toolkit.utils.toolkits.BuiltInToolkitWrapper[source]

Built-in ToolkitWrapper for very basic functionality. Intended for testing and not much more.

Warning

This API is experimental and subject to change.

__init__()[source]

Methods

__init__()

assign_partial_charges(molecule[, ...])

Compute partial charges with the built-in toolkit using simple arithmetic operations, and assign the new values to the partial_charges attribute.

from_file(file_path, file_format[, ...])

Return an openff.toolkit.topology.Molecule from a file using this toolkit.

from_file_obj(file_obj, file_format[, ...])

Return an openff.toolkit.topology.Molecule from a file-like object (an object with a ".read()" method using this toolkit.

is_available()

Check whether the corresponding toolkit can be imported

requires_toolkit()

Attributes

toolkit_file_read_formats

List of file formats that this toolkit can read.

toolkit_file_write_formats

List of file formats that this toolkit can write.

toolkit_installation_instructions

Instructions on how to install the wrapped toolkit.

toolkit_name

Return the name of the toolkit wrapped by this class as a str

toolkit_version

Return the version of the wrapped toolkit as a str

assign_partial_charges(molecule, partial_charge_method=None, use_conformers=None, strict_n_conformers=False, normalize_partial_charges=True, _cls=None)[source]

Compute partial charges with the built-in toolkit using simple arithmetic operations, and assign the new values to the partial_charges attribute.

Warning

This API is experimental and subject to change.

Parameters
  • molecule (Molecule) – Molecule for which partial charges are to be computed

  • partial_charge_method (str, optional, default=None) – The charge model to use. One of [‘zeros’, ‘formal_charge’]. If None, ‘formal_charge’ will be used.

  • use_conformers (iterable of unit-wrapped numpy arrays, each with shape) – (n_atoms, 3) and dimension of distance. Optional, default = None Coordinates to use for partial charge calculation. If None, an appropriate number of conformers will be generated.

  • strict_n_conformers (bool, default=False) – Whether to raise an exception if an invalid number of conformers is provided for the given charge method. If this is False and an invalid number of conformers is found, a warning will be raised instead of an Exception.

  • normalize_partial_charges (bool, default=True) – Whether to offset partial charges so that they sum to the total formal charge of the molecule. This is used to prevent accumulation of rounding errors when the partial charge generation method has low precision.

  • _cls (class) – Molecule constructor

Raises
  • ChargeMethodUnavailableError if this toolkit cannot handle the requested charge method

  • IncorrectNumConformersError if strict_n_conformers is True and use_conformers is provided

  • and specifies an invalid number of conformers for the requested method

  • ChargeCalculationError if the charge calculation is supported by this toolkit, but fails

from_file(file_path, file_format, allow_undefined_stereo=False)

Return an openff.toolkit.topology.Molecule from a file using this toolkit.

Parameters
  • file_path (str) – The file to read the molecule from

  • file_format (str) – Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.

  • allow_undefined_stereo (bool, default=False) – If false, raises an exception if any molecules contain undefined stereochemistry.

  • _cls (class) – Molecule constructor

Returns

molecules (Molecule or list of Molecules) – a list of Molecule objects is returned.

from_file_obj(file_obj, file_format, allow_undefined_stereo=False, _cls=None)

Return an openff.toolkit.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.

Parameters
  • file_obj (file-like object) – The file-like object to read the molecule from

  • file_format (str) – Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.

  • allow_undefined_stereo (bool, default=False) – If false, raises an exception if any molecules contain undefined stereochemistry. If false, the function skips loading the molecule.

  • _cls (class) – Molecule constructor

Returns

molecules (Molecule or list of Molecules) – a list of Molecule objects is returned.

classmethod is_available()

Check whether the corresponding toolkit can be imported

Returns

is_installed (bool) – True if corresponding toolkit is installed, False otherwise.

property toolkit_file_read_formats

List of file formats that this toolkit can read.

property toolkit_file_write_formats

List of file formats that this toolkit can write.

property toolkit_installation_instructions

Instructions on how to install the wrapped toolkit.

property toolkit_name

Return the name of the toolkit wrapped by this class as a str

Warning

This API is experimental and subject to change.

Returns

toolkit_name (str) – The name of the wrapped toolkit

property toolkit_version

Return the version of the wrapped toolkit as a str

Warning

This API is experimental and subject to change.

Returns

toolkit_version (str) – The version of the wrapped toolkit