openforcefield.utils.toolkits.AmberToolsToolkitWrapper

class openforcefield.utils.toolkits.AmberToolsToolkitWrapper[source]

AmberTools toolkit wrapper

Warning

This API is experimental and subject to change.

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

classmethod(function) -> method

toolkit_name

The name of the toolkit wrapped by this class.

Methods

compute_partial_charges(molecule[, charge_model]) Compute partial charges with AmberTools using antechamber/sqm
compute_partial_charges_am1bcc(molecule) Compute partial charges with AmberTools using antechamber/sqm.
from_file(filename, file_format[, …]) Return an openforcefield.topology.Molecule from a file using this toolkit.
from_file_obj(file_obj, file_format[, …]) Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this
is_available() Check whether this toolkit wrapper is available for use because the underlying toolkit can be found.
requires_toolkit()
toolkit_is_available() Check whether the AmberTools toolkit is installed
__init__()[source]

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__() Initialize self.
compute_partial_charges(molecule[, charge_model]) Compute partial charges with AmberTools using antechamber/sqm
compute_partial_charges_am1bcc(molecule) Compute partial charges with AmberTools using antechamber/sqm.
from_file(filename, file_format[, …]) Return an openforcefield.topology.Molecule from a file using this toolkit.
from_file_obj(file_obj, file_format[, …]) Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this
is_available() Check whether this toolkit wrapper is available for use because the underlying toolkit can be found.
requires_toolkit()
toolkit_is_available() Check whether the AmberTools toolkit is installed

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 classmethod(function) -> method
toolkit_name The name of the toolkit wrapped by this class.
static toolkit_is_available()[source]

Check whether the AmberTools toolkit is installed

Returns:
is_installed : bool

True if AmberTools is installed, False otherwise.

classmethod is_available()[source]

Check whether this toolkit wrapper is available for use because the underlying toolkit can be found.

Note

This method caches the result of any costly checks for file paths or module imports.

Parameters:
is_available : bool

True if toolkit wrapper is available for use, False otherwise

compute_partial_charges(molecule, charge_model=None)[source]

Compute partial charges with AmberTools using antechamber/sqm

Warning

This API experimental and subject to change.

Parameters:
molecule : Molecule

Molecule for which partial charges are to be computed

charge_model : str, optional, default=None

The charge model to use. One of [‘gas’, ‘mul’, ‘bcc’]. If None, ‘bcc’ will be used.

Raises:
ValueError if the requested charge method could not be handled

Notes

Currently only sdf file supported as input and mol2 as output https://github.com/choderalab/openmoltools/blob/master/openmoltools/packmol.py

compute_partial_charges_am1bcc(molecule)[source]

Compute partial charges with AmberTools using antechamber/sqm. This will calculate AM1-BCC charges on the first conformer only.

Warning

This API experimental and subject to change.

Parameters:
molecule : Molecule

Molecule for which partial charges are to be computed

Raises:
ValueError if the requested charge method could not be handled
from_file(filename, file_format, allow_undefined_stereo=False)

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

Parameters:
filename : 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.

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)
Return an openforcefield.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.

Returns:
molecules : Molecule or list of Molecules

a list of Molecule objects is returned.

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

classmethod(function) -> method

Convert a function to be a class method.

A class method receives the class as implicit first argument, just like an instance method receives the instance. To declare a class method, use this idiom:

class C:

@classmethod def f(cls, arg1, arg2, …):

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class. If a class method is called for a derived class, the derived class object is passed as the implied first argument.

Class methods are different than C++ or Java static methods. If you want those, see the staticmethod builtin.

toolkit_name

The name of the toolkit wrapped by this class.