mdsuite.transformations.map_molecules 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.transformations.map_molecules.MolecularMap

Bases: Transformations

Class for mapping atoms in a database to molecules.

scale_function

A dictionary referencing the memory/time scaling function of the transformation.

Type:

dict

molecules

Molecule dictionary to use as reference. e.g.

{'emim': {'smiles': 'CCN1C=C[N+](+C1)C', 'amount': 20}, 'PF6':
{'smiles': 'F[P-](F)(F)(F)(F)F', 'amount': 20}}

would be the input for the emim-PF6 ionic liquid.

Type:

dict

run_transformation(molecules: List[Molecule])

Perform the transformation.

Parameters:

molecules (List[Molecule]) – A list of MDSuite Molecule objects. For each, a molecule will be mapped.

Return type:

Update the experiment database.