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Add ability to update monomers library API in SDF format #7674
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
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.
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:
Ambiguous mixed peptide
Unknown peptide
Ambiguous alternative sugar
Ambiguous mixed sugar
Unknown sugar
Ambiguous mixed DNA base
Ambiguous mixed RNA base
Ambiguous mixed base
Unknown base
Ambiguous alternative phosphate
Ambiguous mixed phosphate
Unknown phopsphate
Unknown unsplit nucleotide
Ambiguous alternative CHEM
Ambiguous mixed CHEM
Unknown CHEM
Unknown monomer
Molecule
Micromolecule
Here is the list of monomers I would expect to be possible to add to the Library:
Natural analog peptide
Peptide with natural analog (E)
Peptide without natural analog
Ambiguous alternative peptide
Natural sugar
Sugar with natural analog
Natural base
Base with natural analog (C) and 3 connection points
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
Activity
[-]Add additional parameter (KET/SDF) to API functions that deal with macromolecules library[/-][+]Add ability to update monomers library API in SDF format[/+]#7674 - Add ability to update monomers library API in SDF format
#7674 - Add ability to update monomers library API in SDF format
#7674 - Add ability to update monomers library API in SDF format
#7674 - Add ability to update monomers library API in SDF format (#7916)
#7674 - Add ability to update monomers library API in SDF format (#7916)
Autotests: 7948 autotests allow for modification of the attachment po…
Zhirnoff commentedon Oct 10, 2025
Tested.
Desktop:
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]
#8185 - Only enforce groupClass on records with group metadata