Utilities for Molecular Science
Project description
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
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