openforcefield.utils.toolkits.
AmberToolsToolkitWrapper
[source]¶AmberTools toolkit wrapper
Warning
This API is experimental and subject to change.
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
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Compute partial charges with AmberTools using antechamber/sqm |
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Compute partial charges with AmberTools using antechamber/sqm. |
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Return an openforcefield.topology.Molecule from a file using this toolkit. |
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Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this |
Check whether the AmberTools toolkit is installed |
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Methods
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Initialize self. |
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Compute partial charges with AmberTools using antechamber/sqm |
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Compute partial charges with AmberTools using antechamber/sqm. |
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Return an openforcefield.topology.Molecule from a file using this toolkit. |
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Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this |
Check whether the AmberTools toolkit is installed |
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Attributes
List of file formats that this toolkit can read. |
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List of file formats that this toolkit can write. |
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classmethod(function) -> method |
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The name of the toolkit wrapped by this class. |
is_available
()[source]¶Check whether the AmberTools toolkit is installed
True if AmberTools is installed, False otherwise.
compute_partial_charges
(self, molecule, charge_model=None)[source]¶Compute partial charges with AmberTools using antechamber/sqm
Warning
This API experimental and subject to change.
Molecule for which partial charges are to be computed
The charge model to use. One of [‘gas’, ‘mul’, ‘bcc’]. If None, ‘bcc’ will be used.
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
(self, 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.
Molecule for which partial charges are to be computed
from_file
(self, file_path, file_format, allow_undefined_stereo=False)¶Return an openforcefield.topology.Molecule from a file using this toolkit.
The file to read the molecule from
Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.
If false, raises an exception if any molecules contain undefined stereochemistry.
a list of Molecule objects is returned.
from_file_obj
(self, file_obj, file_format, allow_undefined_stereo=False)¶toolkit.
The file-like object to read the molecule from
Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.
If false, raises an exception if any molecules contain undefined stereochemistry. If false, the function skips loading the molecule.
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.