mdsuite.graph_modules.molecular_graph module

MDSuite: A Zincwarecode package.

License

This program and the accompanying materials are made available under the terms of the Eclipse Public License v2.0 which accompanies this distribution, and is available at https://www.eclipse.org/legal/epl-v20.html

SPDX-License-Identifier: EPL-2.0

Copyright Contributors to the Zincwarecode Project.

Contact Information

email: zincwarecode@gmail.com github: https://github.com/zincware web: https://zincwarecode.com/

Citation

If you use this module please cite us with:

Summary

class mdsuite.graph_modules.molecular_graph.MolecularGraph(experiment: Experiment, molecule_input_data: Molecule)

Bases: object

Class for building and studying molecular graphs.

reference_property

MDSuite property to use for reference during the unwrapping.

Type:

str

build_configuration_graph() → Tensor

Build a graph for the configuration.

Returns:

adjacency_matrix – An adjacency matrix for the configuration describing which atoms are bonded to which others.

Return type:

tf.Tensor

molecular_groups: dict

molecular_mass: float

mdsuite.graph_modules.molecular_graph.build_smiles_graph(smiles_string: str) → tuple

Build molecular graphs from SMILES strings.

Parameters:

smiles_string (str) – SMILES string to use in the graph construction.

Returns:

• smiles_graph – Graph object returned by PySmiles

• species (dict) – A dict object containing species information about the molecule.

mdsuite.graph_modules.molecular_graph.get_neighbour_list(positions: Tensor, cell: Optional[list] = None) → Tensor

Generate the neighbour list.

Parameters:

• positions (tf.Tensor) – Tensor with shape (number_of_configurations, n_atoms, 3) representing the coordinates

• cell (list) – If periodic boundary conditions are used, please supply the cell dimensions, e.g. [13.97, 13.97, 13.97]. If the cell is provided minimum image convention will be applied!

Returns:

neighbour_list – Neighbour list for a single configuration.

Return type:

tf.Tensor