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Macro: Migrate Monomer library from MOL V2K to KET format #4307

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rrodionov91 opened this issue Mar 21, 2024 · 2 comments · Fixed by #4515 or #4542
Closed

Macro: Migrate Monomer library from MOL V2K to KET format #4307

rrodionov91 opened this issue Mar 21, 2024 · 2 comments · Fixed by #4515 or #4542
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feature request Monomer Library Test Cases Written Test cases has been written for that issue

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@rrodionov91
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rrodionov91 commented Mar 21, 2024

Background
Currently monomer library stored as sdf file based on MolV2000. This format does not support features which are planned to be implemented in Ketcher in nearest future (variant monomers, umbiguos connections, storing rna presets, etc ).
It was decided to migrate library to ket format to have ability to support all necessary features in future.

Solution
The list of monomers from current library should be converted to list of templates with its definitions. For example:

{
  "root": {
    "templates": [
       {
          "$ref": "monomerTemplate-A___Alanine"
       },
       ...
    ]
  },
  "monomerTemplate-A___Alanine": {
    // monomer template content
  },
  ...
}

Library should be loaded into ketcher during the build process (as it is done now for current library).
Library internal object model in ketcher should not be changed.

Additional context
Current library stored in packages/ketcher-macromolecules/src/data/monomers.sdf file of ketcher repository

@rrodionov91 rrodionov91 added this to the Ketcher 2.22.0-rc.1 milestone Mar 21, 2024
rrodionov91 added a commit that referenced this issue Apr 22, 2024
- also added rna presets to ket library and removed hardcoded rna presets
@rrodionov91 rrodionov91 self-assigned this Apr 23, 2024
rrodionov91 added a commit that referenced this issue Apr 24, 2024
)

- migrated monomers library from sdf to ket
- added rna presets to ket library and removed hardcoded rna presets
- moved library import and storage to core package
- fixed chems displaying in sequence view and favorites tab of library
rrodionov91 added a commit that referenced this issue Apr 26, 2024
- fixed performance issue with monomer library conversion
- removed connections from monomer group templates
- fixed keys of monomer group templates
@rrodionov91 rrodionov91 linked a pull request Apr 26, 2024 that will close this issue
9 tasks
rrodionov91 added a commit that referenced this issue Apr 26, 2024
)

- fixed performance issue with monomer library conversion
- removed connections from monomer group templates
- fixed keys of monomer group templates

Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
@AlexeyGirin
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No test cases needed for that particular issue

@AlexeyGirin AlexeyGirin added the Test Cases Written Test cases has been written for that issue label May 8, 2024
@AlexeyGirin
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Verified.

  • Indigo Toolkit Version 1.20.0-dev.1.32-gf28bad61-wasm32-wasm-clang-12.0.0
  • Ketcher Version 2.21.0-rc.2 Build at 2024-05-13; 05:32:02
  • Chrome Version 124.0.6367.201 (Official Build) (64-bit)
  • Windows 10

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