Skip to content

HELM ver 1 scope: support multiple sequences and connection tables (import and export) #1188

@even1024

Description

@even1024

Background
Indigo macromolecules support

Solution
Import and export of multiple RNA, PEPRIDE, CHEM in one string. Support connection tables.
Tests should include corresponding KET<>HELM<>MOL conversions.

HELM notation could be found here: https://www.pistoiaalliance.org/helm-notation/
Reference: HELM Specification 2_04-1.pdf
Decided to support only features that implemented in Ketcher already
That is

  • 5.2 Simple Polymer section
    Implementation of two types of specific simple polymers: PEPTIDE, and RNA
    Implementation of non-specific simple polymer type: CHEM
    Implementation of unknown polymer type: BLOB
    Implementation of simple polymer notation (i.e. chains consists of polymers of supported types)
    Out of scope:
    Monomer Lists (pp. 5.2.4.1 should not be implemented)
    Monomer repeating units (pp. 5.2.4.2 should not be implemented)
    Monomer annotation (pp. 5.2.5 should not be implemented)
  • 5.3 Complex Polymer
    Implementation of list of connection between backbone chains
    Out of scope:
    Unknown positions
    Hydrogen pairings (pp. 5.2.5 should not be implemented)
  • 5.6 In-line HELM notation
    Implementation of SMILES and Extended SMILES formats support

Metadata

Metadata

Labels

HELMBucket: Bugs related to Export to HELM formatTest Cases WrittenTest cases has been written for that issueepic: macromolecules

Projects

Status

Done

Relationships

None yet

Development

No branches or pull requests

Issue actions