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Macro: Allow Nucleoside of sequence edit in RNA builder #4388

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ilya-asiyuk-epam opened this issue Apr 2, 2024 · 2 comments · Fixed by #4477
Closed

Macro: Allow Nucleoside of sequence edit in RNA builder #4388

ilya-asiyuk-epam opened this issue Apr 2, 2024 · 2 comments · Fixed by #4477
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@ilya-asiyuk-epam
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ilya-asiyuk-epam commented Apr 2, 2024

Background
Nucleotide = RNA preset added on canvas (sugar+phosphate+base)
Nucleoside = sugar+base, connected by the bond between R3 AP of sugar and R1 AP of base.

Requirements
In addition to the requirements from #3824

  1. Nucleoside should be editable in RNA builder.

  2. If a single nucleoside is loaded into RNA builder, then the "Phosphate" field in the RNA builder should be empty.

  3. If user adds phosphate to the RNA builder, then a nucleoside should become a nucleotide with corresponding phosphate.

  4. Bulk modifications of nucleotides and nucleosides simultaneously:

    • Instead of field 'name your structure', 'N nucleotides selected' should be displayed (N- the number of nucleotides and nucleosides)
    • In the 'phosphate' field - [multiple] should be displayed
    • Phosphate modifications should be applied to both nucleotides and nucleosides.
  5. If nucleoside is selected together with following it phosphate, then this combination should be considered as nucleotide AND phosphate modifications made in RNA builder should be applied to the selected phosphate.
    Image for better understanding (don't look at color scheme)
    image

  6. If among the selected elements on the canvas there is a single phosphate (selected without an adjacent nucleoside to the left), then in this case, editing in the builder should be prohibited.
    image

@ilya-asiyuk-epam ilya-asiyuk-epam self-assigned this Apr 2, 2024
@olganaz olganaz removed the draft label Apr 3, 2024
@ilya-asiyuk-epam ilya-asiyuk-epam added this to the Ketcher 2.22.0-rc.1 milestone Apr 8, 2024
@olganaz olganaz self-assigned this Apr 11, 2024
@ilya-asiyuk-epam ilya-asiyuk-epam linked a pull request Apr 17, 2024 that will close this issue
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@Zhirnoff
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Tests added to automation table.

ilya-asiyuk-epam added a commit that referenced this issue Apr 24, 2024
…uence-edit-in-rna-builder

#4388 - Macro: Allow Nucleoside of sequence edit in RNA builder
@AlexeyGirin AlexeyGirin added the Test Cases Written Test cases has been written for that issue label May 8, 2024
@AlexeyGirin AlexeyGirin self-assigned this May 14, 2024
@AlexeyGirin
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Verified.

Versions

  • 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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5 participants