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

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even1024 opened this issue Jul 19, 2023 · 3 comments · Fixed by #2040
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epic: macromolecules Test Cases Written Test cases has been written for that issue

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@even1024
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even1024 commented Jul 19, 2023

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
@even1024 even1024 added this to the Indigo-1.14.0-rc.1 milestone Jul 19, 2023
@AlexanderSavelyev AlexanderSavelyev changed the title HELM 1.0 finalization: add multiple sequences and connection tables HELM 1.0 support multiple sequences and connection tables (import and export) Jul 19, 2023
@even1024 even1024 modified the milestones: Indigo-1.18.0-rc.1, Indigo-1.19.0-rc.1 Dec 28, 2023
@AlexeyGirin
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@AlexeyGirin
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Test Set V1_0.xlsx

@AlexeyGirin AlexeyGirin changed the title HELM 1.0 support multiple sequences and connection tables (import and export) HELM ver 2.04 support multiple sequences and connection tables (import and export) Jun 11, 2024
@AlexeyGirin AlexeyGirin added the Test Cases Written Test cases has been written for that issue label Jun 13, 2024
@AlexeyGirin
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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)

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Labels
epic: macromolecules Test Cases Written Test cases has been written for that issue
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Status: Done
5 participants