schrodinger.protein.helm package

A module to parse convert biomolecules to and from HELM strings.

The Hierarchical Editing Language for Macromolecules(HELM) was designed to create a single notation that can encode the structure of all biomolecules.

HELM encodes different types of biomolecules, including XNA, peptides, and Chem polymers, but also allows users to defined custom polymer types.

The HELM specification can be found at

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schrodinger.protein.helm.is_coarse_grain_mol(mol: rdkit.Chem.rdchem.Mol) bool

whether the mol contains monomers generated through HelmModel

schrodinger.protein.helm.to_coarse_grain(helm_model: schrodinger.protein.helm._helm_parser.HelmModel) rdkit.Chem.rdchem.Mol
schrodinger.protein.helm.parse_helm(input_helm: str) schrodinger.protein.helm._helm_parser.HelmModel

A helper function that processes a helm string into it’s individual components i.e. a HelmModel object