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(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 corresponding toolkit can be imported

__init__($self, /, *args, **kwargs)¶

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

Methods

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 corresponding toolkit can be imported

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.

toolkit_name¶

The name of the toolkit wrapped by this class.

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_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.

static toolkit_is_available()[source]¶

Check whether the corresponding toolkit can be imported

Note

This method call may be expensive.

Returns:	is_installed : bool True if corresponding toolkit 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 is available for use, False otherwise

from_file(filename, file_format, allow_undefined_stereo=False)[source]¶

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)[source]¶

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.