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Add ability to update monomers library API in SDF format #7674

Description

@ljubica-milovic

Background
Currently, the only format which can be used in monomers library update API is KET. In scope of this ticket, the library update API should be extended to have an ability to receive data in SDF format.

Requirements

  1. Monomers library update API function should be extended to work both with SDF and KET files. Additional parameter "format" should be added. In case of SDF format, ketcher should first send data to indigo to convert it from SDF to KET, and then update the library.

  2. replaceMonomersLibrary method should be added to ketcher API:

  • ketcher.updateMonomersLibrary(sdfString, { format: 'sdf' }) - will add/replace items in default Ketcher monomers library
  • ketcher.replaceMonomersLibrary(sdfString, { format: 'sdf' }) - will remove default Ketcher monomers library and use the provided one

Addition from @AlexeyGirin:
Here is the list of entities (most of them are monomers) that I wouldn't expect to be able to add to the Library:

  1. Ambiguous mixed peptide
  2. Unknown peptide
  3. Ambiguous alternative sugar
  4. Ambiguous mixed sugar
  5. Unknown sugar
  6. Ambiguous mixed DNA base
  7. Ambiguous mixed RNA base
  8. Ambiguous mixed base
  9. Unknown base
  10. Ambiguous alternative phosphate
  11. Ambiguous mixed phosphate
  12. Unknown phopsphate
  13. Unknown unsplit nucleotide
  14. Ambiguous alternative CHEM
  15. Ambiguous mixed CHEM
  16. Unknown CHEM
  17. Unknown monomer
  18. Molecule
  19. Micromolecule

Here is the list of monomers I would expect to be possible to add to the Library:

  1. Natural analog peptide
  2. Peptide with natural analog (E)
  3. Peptide without natural analog
  4. Ambiguous alternative peptide
  5. Natural sugar
  6. Sugar with natural analog
  7. Natural base
  8. Base with natural analog (C) and 3 connection points
  9. Base without natural analog
  10. Ambiguous alternative DNA base
  11. Ambiguous alternative RNA base
  12. Ambiguous alternative base
  13. Natural phosphate
  14. Phosphate with natural analog
  15. Unsplit monomer
  16. Unsplit monomer without natural analog
  17. CHEM

Activity

  1. changed the title [-]Add additional parameter (KET/SDF) to API functions that deal with macromolecules library[/-] [+]Add ability to update monomers library API in SDF format[/+] on Aug 26, 2025
  2. self-assigned this
    on Sep 22, 2025
  3. added a commit that references this issue on Sep 23, 2025
  4. added 3 commits that reference this issue on Sep 25, 2025
  5. added 2 commits that reference this issue on Oct 4, 2025
  6. Zhirnoff commented on Oct 10, 2025

    @Zhirnoff
    Collaborator

    Tested.

    Image Image Image Image Image Image Image Image Image Image Image

    Desktop:

    • OS: Windows 11
    • Browser Chrome
      Version 140.0.7339.128 (Official Build) (64-bit)

    Ketcher version
    [Version 3.9.0-rc.1]
    Indigo version
    [Version 1.37.0-rc.1]

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