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

[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

[AlexeyGirin]

http://webeditor.openhelm.org/hwe/examples/App.htm

[AlexeyGirin]

Test Set V1_0.xlsx

[AlexeyGirin]

Verified.

Ketcher Version 2.23.0-rc.1 Build at 2024-07-02; 08:57:41 Indigo Version 1.22.0-rc.1.0-g2bef0ce6c-wasm32-wasm-clang-19.0.0 Win 10 Chrome Version 126.0.6478.127 (Official Build) (64-bit)