schrodinger.protein.helm module¶

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 https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/13795362/HELM+Notation

class schrodinger.protein.helm.Monomer(position_in_polymer: int, position_in_token: int, name: str, is_branch: bool)[source]¶

Bases: object

position_in_polymer: int¶

position_in_token: int¶

name: str¶

is_branch: bool¶

__init__(position_in_polymer: int, position_in_token: int, name: str, is_branch: bool) → None¶

schrodinger.protein.helm.to_rdkit(helm: str) → rdkit.Chem.rdchem.Mol[source]¶: Converts a helm string to a residue-level ROMol

schrodinger.protein.helm.to_helm(cg_mol: rdkit.Chem.rdchem.Mol) → str[source]¶: Converts a coarse-grain residue-level ROMol to a helm string

schrodinger.protein.helm.convert_helm1_to_helm2(helm1: str) → str[source]¶

Helper function to convert helm1 to helm2

The helm specifications changed from: simple polymers$connections$H-bonds$annotations$
to: simple polymers$connections(including H-bonds)$polymer groups$annotations$V2.0