https://github.com/informaticsmatters/standardize-molecule

Utilities for SMILES analysis
https://github.com/informaticsmatters/standardize-molecule

Last synced: 10 months ago
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Utilities for SMILES analysis

• Host: GitHub
• URL: https://github.com/informaticsmatters/standardize-molecule
• Owner: InformaticsMatters
• License: gpl-3.0
• Created: 2021-03-18T14:02:41.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2021-03-18T17:32:59.000Z (about 5 years ago)
• Last Synced: 2025-04-11T09:59:49.502Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 46.9 KB
• Stars: 5
• Watchers: 2
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Informatics Matters Standardize Molecule Utility

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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.

For installation and testing, see the associated README.rst file.

## 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)

    

    print(noniso[1].GetNumHeavyAtoms())

    13