im-standardize-molecule 0.1.0

Utilities for Molecular Science

The im-standardize_molecule module is a utility provided by Informatics Matters.

It contains a Python module to: 1. Take an original SMILES (Simple Molecule Input Line rESpresentation) and convert it to an Isomeric or Nonisomeric canonical SMILES representation in a consistent way. 2. Convert an rdkit.Chem.rdchem.Mol object to a standard format.

Preparation

Note that although this module is available on PyPI, it is not possible to simply install it and run it. The module is strongly dependent on RDKit. In most cases, one of the the Informatics Matters RDKit container images can be used. More details can be found here: IM-RDKit RDKit can also be installed with Conda.

Testing

To check installation is successful, from within an RDKit environment, run:

python -m unittest test.test

Usage

standardize_to_noniso_smiles (osmiles:str)

standardize_to_iso_smiles (osmiles:str)

Takes a smiles and returns the converted smiles and standardized molecule as an rdkit.Chem.rdchem.Mol

Example:

from standardize_molecule import standardize_to_noniso_smiles
noniso = standardize_to_noniso_smiles('N[C@@H](C[C@@H]1CCNC1O)[C@@H](O)CO')
[17:30:44] Initializing MetalDisconnector
[17:30:44] Running MetalDisconnector
[17:30:44] Initializing Normalizer
[17:30:44] Running Normalizer
[17:30:44] Running Uncharger
print(noniso[0])
NC(CC1CCNC1O)C(O)CO

standardize_molecule (molecule: object, osmiles:str = ‘NotProvided’)

Takes an rdkit.Chem.rdchem.Mol object and (optionally) a smiles string for logging and returns a standardized molecule.

Example:

from rdkit import Chem
from standardize_molecule import standardize_molecule
mol = Chem.MolFromSmiles('C1=CC=CC=C1')
std = standardize_molecule(mol, 'C1=CC=CC=C1')
[17:37:40] Initializing MetalDisconnector
[17:37:40] Running MetalDisconnector
[17:37:40] Initializing Normalizer
[17:37:40] Running Normalizer
[17:37:40] Running Uncharger
print(std)
<rdkit.Chem.rdchem.Mol object at 0x7f18ca2a93f0>
print(noniso[1].GetNumHeavyAtoms())
13