equilibrator-cheminfo 0.5.0

Light adapter classes around Open Babel, RDKit, and ChemAxon for the functionality needed in eQulibrator.

Light adapter classes around Open Babel, RDKit, and ChemAxon for the functionality needed in eQulibrator.

Install

Please note that while equilibrator-cheminfo as a pure Python package is operating system independent, the same is not true for the cheminformatics backends Open Babel, RDkit, or ChemAxon. While both Open Babel and RDKit nowadays provide Python wheels, we do not test them on all platforms.

RDKit

pip install equilibrator-cheminfo[rdkit]

or

Open Babel

pip install equilibrator-cheminfo[openbabel]

ChemAxon

If you wish to use ChemAxon, you need to install the software, acquire a license, and set the environment variable CHEMAXON_HOME.

pip install equilibrator-cheminfo[chemaxon]

Usage

The main feature in this package is a uniform class interface to molecules from Open Babel, RDKit, or ChemAxon. The interface is defined by the equilibrator_cheminfo.AbstractMolecule abstract class that the three concrete classes adhere to.

from equilibrator_cheminfo.chemaxon import ChemAxonMolecule
from equilibrator_cheminfo.rdkit import RDKitMolecule
from equilibrator_cheminfo.openbabel import OpenBabelMolecule

Some of the supported methods are:

mol = OpenBabelMolecule.from_smiles("CC=O")
mol.get_charge()  # 0
mol.get_molecular_formula()  # 'C2H4O'
mol.get_molecular_mass()  # 44.05
mol.get_inchi_key()  # 'IKHGUXGNUITLKF-UHFFFAOYSA-N'

You can also always access the cheminformatics backend object directly and pass it as an argument to functions directly imported from there.

mol.native  # <openbabel.pybel.Molecule at 0x7f2a14b36c70>
mol.native.calcfp().bits  # [330, 624, 671]

If there are general methods that you think are missing from the abstract interface, please say so in an issue.

Copyright

• Copyright © 2021, Moritz E. Beber.

• Free software distributed under the Apache Software License 2.0.