openforcefield.utils.toolkits.
AmberToolsToolkitWrapper
[source]¶AmberTools toolkit wrapper
Warning
This API is experimental and subject to change.
Attributes: |
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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 () |
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toolkit_is_available () |
Check whether the AmberTools toolkit is installed |
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 () |
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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. |
toolkit_is_available
()[source]¶Check whether the AmberTools toolkit is installed
Returns: |
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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: |
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compute_partial_charges
(molecule, charge_model=None)[source]¶Compute partial charges with AmberTools using antechamber/sqm
Warning
This API experimental and subject to change.
Todo
Parameters: |
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Raises: |
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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: |
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Raises: |
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from_file
(filename, file_format, allow_undefined_stereo=False)¶Return an openforcefield.topology.Molecule from a file using this toolkit.
Parameters: |
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from_file_obj
(file_obj, file_format, allow_undefined_stereo=False)¶Parameters: |
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Returns: |
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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.