Requirements

• Python >=3.5

• ATB Outputs python module: `https://github.com/ATB-UQ/atb_outputs.git

• Nauty: This modules relies on the dreadnaut executable which is part of the nauty package. Nauty can very easily be installed from source or using a package manager such as homebrew for Mac OS X users.

Configuration

• The code assumes that dreadnaut will be installed in /usr/local/bin. If installing in a different location, you can change the NAUTY_EXECUTABLE path in config.py.

Usage

A simple example is included in examples/test.py

For more comprehensive examples see the src/chemical_equivalence/test.py script which contains code to run the chemical equivalence prediction algorithm on a series of test cases found in the testing/ directory.

• First, a MolData (Molecule Data) object has to be initialised. It describes the topology and coordinate of the molecule. Please see the documentation of the atb_outputs module for further description of the MolData object.

>>> from chemical_equivalence.helpers.types_helpers import MolData
>>> mol_data = MolData(open('testing/chlorocyclohexane.pdb').read())

• The chemical equivalence can be run in a single line of code:

>>> from chemical_equivalence.calcChemEquivalency import getChemEquivGroups
>>> equivalence_dict, n_iterations = getChemEquivGroups(mol_data)

• It returns a dictionary mapping each atom index (atom['id']) to a unique int for each equivalence class:

>>> equivalence_dict
{1: 0, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 6, 8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, 17: 16, 18: 17}

• It can easily be mapped back to each atom by iterating over the atoms of the MolData object:

>>> list((atom['symbol'], equivalence_dict[atom['id']]) for atom in mol_data.atoms.values())
[('H8', 0), ('C2', 1), ('Cl1', 2), ('C7', 3), ('H17', 4), ('H18', 5), ('C3', 6), ('H9', 7), ('H10', 8), ('C4', 9), ('H11', 10), ('H12', 11), ('C5', 12), ('H13', 13), ('H14', 14), ('C6', 15), ('H15', 16), ('H16', 17)]

Citation / Attribution

To cite this work, please use the following Zenodo DOI.