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
assign_fractional_bond_orders
(molecule[, …])Update and store list of bond orders this molecule.
assign_partial_charges
(molecule[, …])Compute partial charges with AmberTools using antechamber/sqm, and assign the new values to the partial_charges attribute.
compute_partial_charges_am1bcc
(molecule[, …])Compute partial charges with AmberTools using antechamber/sqm.
from_file
(file_path, 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 the AmberTools toolkit is installed
requires_toolkit
()Methods
__init__
()Initialize self.
assign_fractional_bond_orders
(molecule[, …])Update and store list of bond orders this molecule.
assign_partial_charges
(molecule[, …])Compute partial charges with AmberTools using antechamber/sqm, and assign the new values to the partial_charges attribute.
compute_partial_charges_am1bcc
(molecule[, …])Compute partial charges with AmberTools using antechamber/sqm.
from_file
(file_path, 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 the AmberTools toolkit is installed
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.