mdsuite.utils.molecule 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¶

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Summary¶

Module for the MDSuite molecule dataclass

class mdsuite.utils.molecule.Molecule(name: str, amount: int, cutoff: float, smiles: Optional[str] = None, species_dict: Optional[dict] = None, reference_configuration_idx: int = 0, mol_pbc: bool = False)[source]¶

Bases: object

Data class to define a molecule.

name¶

Name of the molecule. This name will be stored in the database.

Type:: str

smiles¶

SMILES string to use in the definition of the molecule internally. e.g. CCN1C=C[N+](+C1)C

Type:: str (optional)

species_dict¶

A species dict for a custom molecule in the case where a SMILES string cannot be written. e.g. {‘C’: 6, ‘N’: 2, ‘H’: 12}

Type:: dict (optional)

amount¶

Number of molecules of this species in the trajectory.

Type:: int

reference_configuration_idx¶

A specific configuration to use in the construction of the molecules.

Type:: int (default=0)

cutoff¶

A cutoff value to use when identifying bonded pairs. Should be the largest bond distance in the system, perhaps with some buffer depending on the flexibility of bonds in the molecule and their distribution in the reference configuration.

Type:: float

mol_pbc¶

If true, the simulation that was run was using molecule-based PBC, i.e. molecules were not allowed to break in the simulation.

Type:: bool

amount: int¶

cutoff: float¶

mol_pbc: bool = False¶

name: str¶

reference_configuration_idx: int = 0¶

smiles: str = None¶

species_dict: dict = None¶