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Preview for ambiguous monomers #4555

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olganaz opened this issue Apr 30, 2024 · 1 comment · Fixed by #5411
Closed

Preview for ambiguous monomers #4555

olganaz opened this issue Apr 30, 2024 · 1 comment · Fixed by #5411
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@svvald
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feature request Macromolecules Requirements Done Test Cases Written Test cases has been written for that issue variant_monomers
Milestone
Ketcher 2.25.0-rc.1

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@olganaz
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olganaz commented Apr 30, 2024 •
edited by ljubica-milovic
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Background
Ambiguous monomers are used to describe ambiguity in the structure of a macromolecule.
Ambiguous monomers could be classified in two types:

  • Alternatives (XOR) - this type of ambiguous monomer is used to describe that at a specific position in the macromolecule, any monomer from a list of options can be present.
  • Mixed (AND) - this type of ambiguous monomer is used to specify not only the list of possible monomers that can be used, but also the probabilities (weights) with which these ambiguous may occur at that position.

The scope of this task includes preview for ambiguous monomers (chem structures, ratios, AND/XOR)

Requirements

  1. For the ambiguous monomer preview, it should contain the list of monomers (full names) that make up the ambiguous monomer.
  2. If the ambiguous monomer is "alternatives" (without probabilities) the list should be ordered alphabetically.
  3. If the ambiguous monomer is "mixed" (with probabilities) the list should be ordered by probabilities.
    3.1. If there are multiple monomers with same probability, they should be ordered alphabetically.
  4. The list should be limited to 5 monomers.
  5. For mixtures, the weights of each monomer should also be displayed in the preview (see mockups).
  6. In the case of X, "Any Amino Acid" should be displayed in the preview.
  7. In the case of N (both RNA and DNA versions), "Any Base" should be displayed in the preview.
  8. All the previews (micro mode, flex/snake mode, library) are as described, while the preview in sequence mode for nucleotides/nucleosides with a ambiguous base should have the name written as: sugar(base)phosphate (see mockups).

UX
image
@olganaz olganaz added the draft label Jun 29, 2024
@olganaz olganaz changed the title Macro: Preview for variant monomers Preview for variant monomers Jun 29, 2024
@rrodionov91 rrodionov91 added this to the Ketcher 2.25.0-rc.1 milestone Jul 22, 2024
This was referenced Jul 30, 2024
Closed
Closed
@ljubica-milovic ljubica-milovic mentioned this issue Aug 6, 2024
Closed
@Zhirnoff Zhirnoff added the Test Cases Written Test cases has been written for that issue label Aug 12, 2024
@svvald svvald assigned svvald and unassigned Andrey-Antonov and olganaz Aug 21, 2024
@ljubica-milovic ljubica-milovic changed the title Preview for variant monomers Preview for ambiguous monomers Aug 26, 2024
@github-project-automation github-project-automation bot moved this to In progress in Ketcher Aug 27, 2024
svvald added a commit that referenced this issue Aug 29, 2024
@svvald
#4555 – Add preview for ambiguous monomers in the library and on canvas
c0bd456
svvald added a commit that referenced this issue Aug 29, 2024
@svvald
#4555 – Add preview for ambiguous monomers in sequence mode
6f5c701
@svvald svvald linked a pull request Aug 29, 2024 that will close this issue
#4555 – Preview for ambiguous monomers #5390
Closed
9 tasks
@svvald svvald moved this from In progress to Code review in Ketcher Aug 29, 2024
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in the library and on canvas
01c94be
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in sequence mode
ac3df37
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in the library and on canvas
a1feea2
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in sequence mode
ac0348e
@rrodionov91 rrodionov91 linked a pull request Sep 1, 2024 that will close this issue
#4555 – Preview for ambiguous monomers #5410
Closed
9 tasks
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in the library and on canvas
8d5bd18
rrodionov91 pushed a commit that referenced this issue Sep 1, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in sequence mode
a56e43a
@rrodionov91 rrodionov91 linked a pull request Sep 2, 2024 that will close this issue
#4555 – Preview for ambiguous monomers #5411
Merged
9 tasks
rrodionov91 pushed a commit that referenced this issue Sep 3, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in the library and on canvas
a81912a
rrodionov91 pushed a commit that referenced this issue Sep 3, 2024
@svvald @rrodionov91
#4555 – Add preview for ambiguous monomers in sequence mode
92caba6
rrodionov91 added a commit that referenced this issue Sep 3, 2024
@rrodionov91 @svvald
#4555 – Preview for ambiguous monomers (#5411)
f86f358 
- added preview for ambiguous monomers in sequence mode
- fixed preview position

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
@github-project-automation github-project-automation bot moved this from Code review to Ready for testing in Ketcher Sep 3, 2024
@AlexeyGirin AlexeyGirin mentioned this issue Sep 4, 2024
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@AlexeyGirin
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Verified.
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Versions

  • Ketcher Version 2.25.0-rc.1 Build at 2024-09-03; 15:31:03
  • Indigo Toolkit Version 1.24.0-rc.1.0-gb8f099851-wasm32-wasm-clang-19.0.0
  • Chrome Version 128.0.6613.114 (Official Build) (64-bit)
  • Win10

This was referenced Sep 17, 2024
Closed
Open
Guch1g0v pushed a commit that referenced this issue Oct 17, 2024
@rrodionov91 @svvald @Guch1g0v
#4555 – Preview for ambiguous monomers (#5411)
9f8c15f 
- added preview for ambiguous monomers in sequence mode
- fixed preview position

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
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@svvald svvald

Labels
feature request Macromolecules Requirements Done Test Cases Written Test cases has been written for that issue variant_monomers
Projects
Ketcher
Status: Ready for testing
Milestone
Ketcher 2.25.0-rc.1
7 participants
@svvald @rrodionov91 @AlexeyGirin @Zhirnoff @Andrey-Antonov @olganaz @ljubica-milovic