Macs in Chemistry

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HELM notation in Jupyter Notebook

I was recently asked for a way to visualise HELM notation

HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules such as proteins, nucleotides, antibody drug conjugates etc. whose size and complexity render existing small-molecule and sequence-based informatics methodologies impractical or unusable.

The RDKit provides limited support for HELM notation (currently peptide).

rdkit.Chem.rdmolfiles.MolFromHELM((AtomPairsParameters)text[, (bool)sanitize=True]) → Mol :
Construct a molecule from a HELM string (currently only supports peptides).


text: string containing the HELM sanitize: (optional) toggles sanitization of the molecule. Defaults to true

a Mol object, None on failure.

A simple Jupyter Notebook provides an easy interface as shown below. Simply replace the helm string with the one you want to visualise, you can also convert the Mol object to other formats e.g. SMILES, and of curse you can convert it to HELM notation.


You can download the notebook here

Last Updated 1 May 2019.