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HELM ver 1 scope: support multiple sequences and connection tables (import and export) #1188
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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
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
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Test Cases Written
Test cases has been written for that issue
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Jun 13, 2024
This was referenced Jul 2, 2024
System doesn't show side chain bonds if chain loaded directly to Snake-mode canvas
epam/ketcher#4977
Closed
Verified. Ketcher Version 2.23.0-rc.1 Build at 2024-07-02; 08:57:41 |
rrodionov91
changed the title
HELM ver 2.04 support multiple sequences and connection tables (import and export)
HELM ver 1 scope: support multiple sequences and connection tables (import and export)
Jul 9, 2024
This was referenced Aug 5, 2024
This was referenced Sep 11, 2024
This was referenced Sep 23, 2024
This was referenced Oct 9, 2024
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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
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)
Implementation of list of connection between backbone chains
Out of scope:
Unknown positions
Hydrogen pairings (pp. 5.2.5 should not be implemented)
Implementation of SMILES and Extended SMILES formats support
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