im-rdkit-utilities 1.0.0

Informatics Matters RDKit Utilities

A Python package of RDKit-specific helpers shared by Squonk2 Data Manager Jobs: molecule readers/writers over SDF and delimited-SMILES text formats, fragment selection, and a handful of small molecule-inspection helpers.

This consolidates the rdkit_utils.py module that had been copy-pasted, and had begun to diverge, across several Job repositories (squonk2-desc-rdkit, squonk2-desc-mordred, squonk2-jaqpot and virtual-screening) into a single, tested, authoritative source.

Installation (Python)

The package is published on PyPI and can be installed from there:

pip install im-rdkit-utilities

Once installed, import it as rdkit_utils (matching the module name it replaces, so existing call sites need no changes beyond the import path):

>>> import rdkit_utils
>>> reader = rdkit_utils.create_reader('molecules.smi', delimiter='\t')

Public surface

• create_reader() / create_writer() — construct a reader/writer for a .sdf, .sdf.gz or delimited-SMILES file, based on its extension.

• SdfReader / SdfWriter / SmilesReader / SmilesWriter — the underlying reader/writer implementations.

• generate_headers() — build output headers for a tab/comma separated file, given the ID column configuration.

• fragment() — pick the largest fragment of a (typically salted) molecule, by heavy-atom count or molecular weight.

• fragmentAndFingerprint() — fragment a stream of molecules and fingerprint the result.

• get_num_chiral_centers() / get_num_sp3_centres() — small molecule-inspection helpers.

• check_molecules_are_3d() — check whether the molecules in a .sdf file have 3D conformers.

• rdk_read_single_mol() / rdk_read_mols() / rdk_read_molecule_files() / rdk_merge_mols() / rdk_mol_supplier() / sdf_record_gen() — molecule-file reading helpers.

• updateChargeFlagInAtomBlock() — adds the legacy charge-flag encoding to a full CTAB molblock (counts line included), for tools such as rDock that only understand the old syntax. This is not the same as dm_job_utilities.utils.update_charge_flag_in_atom_block(), which operates on just the atom-block portion of a molblock (one line further in) — the two take different input shapes and are not interchangeable. This RDKit-oriented variant lives here because it’s used directly alongside the readers/writers above; the job-utilities function remains the natural home for pure string manipulation with no RDKit dependency.

Get in touch

• Report bugs, suggest features or view the source code on GitHub.