openforcefield.utils.toolkits.ToolkitWrapper

class openforcefield.utils.toolkits.ToolkitWrapper[source]

Toolkit wrapper base class.

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

from_file(self, file_path, file_format[, …])

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

from_file_obj(self, 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 the corresponding toolkit can be imported

requires_toolkit()

__init__(self, /, *args, **kwargs)

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

Methods

__init__(self, /, \*args, \*\*kwargs)

Initialize self.

from_file(self, file_path, file_format[, …])

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

from_file_obj(self, 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 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

classmethod(function) -> method

toolkit_name

The name of the toolkit wrapped by this class.

property toolkit_name

The name of the toolkit wrapped by this class.

property 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.

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.

static is_available()[source]

Check whether the corresponding toolkit can be imported

Returns
is_installedbool

True if corresponding toolkit is installed, False otherwise.

from_file(self, file_path, file_format, allow_undefined_stereo=False)[source]

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

Parameters
file_pathstr

The file to read the molecule from

file_formatstr

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_stereobool, default=False

If false, raises an exception if any molecules contain undefined stereochemistry.

Returns
——-
moleculesMolecule or list of Molecules

a list of Molecule objects is returned.

from_file_obj(self, file_obj, file_format, allow_undefined_stereo=False)[source]
Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this

toolkit.

Parameters
file_objfile-like object

The file-like object to read the molecule from

file_formatstr

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_stereobool, default=False

If false, raises an exception if any molecules contain undefined stereochemistry. If false, the function skips loading the molecule.

Returns
moleculesMolecule or list of Molecules

a list of Molecule objects is returned.