"""
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
-------
Module for the MDSuite molecule dataclass
"""
from dataclasses import dataclass
[docs]@dataclass
class Molecule:
"""
Data class to define a molecule.
Attributes
----------
name : str
Name of the molecule. This name will be stored in the database.
smiles : str (optional)
SMILES string to use in the definition of the molecule internally.
e.g. CCN1C=C[N+](+C1)C
species_dict : dict (optional)
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}
amount : int
Number of molecules of this species in the trajectory.
reference_configuration_idx : int (default=0)
A specific configuration to use in the construction of the molecules.
cutoff : float
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.
mol_pbc : bool
If true, the simulation that was run was using molecule-based PBC, i.e.
molecules were not allowed to break in the simulation.
"""
name: str
amount: int
cutoff: float
smiles: str = None
species_dict: dict = None
reference_configuration_idx: int = 0
mol_pbc: bool = False