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Add simple atom query primitives to the query specific properties #3298

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AlexanderSavelyev opened this issue Sep 12, 2023 · 4 comments · Fixed by #3322
Closed

Add simple atom query primitives to the query specific properties #3298

AlexanderSavelyev opened this issue Sep 12, 2023 · 4 comments · Fixed by #3322
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@AKZhuk
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epic: smarts feature request
Milestone
Ketcher 2.16.0-rc.1

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@AlexanderSavelyev
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AlexanderSavelyev commented Sep 12, 2023 •
edited by vanoprenko
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Background
Current set of atom query features lacks certain attributes supported by SMARTS standard. Missing features should be supported in Ketcher per below specification

Solution

1. Add following properties into the "Atom Properties/Query Specific" list of atom attributes.

  • Aromaticity (drop-down)
    • empty (default)
    • aromatic
    • aliphatic
  • Degree (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
    • 5
    • 6
  • Implicit H count (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
  • Ring membership (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
    • 5
  • Ring size (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
    • 5
  • Connectivity (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
    • 5
  • Ring connectivity (drop-down)
    • empty (default)
    • 0
    • 1
    • 2
    • 3
    • 4
    • 5
  • Chirality (drop-down)
    • empty (default)
    • anticlockwise
    • clockwise
  • Atomic mass (input field)
    • empty (default)
    • any number (> 0, < 1000)

2. Add following properties into the right click menu for the atoms/Query Properties (take values from the table above)

  • Aromaticity
  • Degree
  • Implicit H count
  • Ring membership
  • Ring size
  • Connectivity
  • Ring connectivity

3. Replace comma with semicolon between Atom properties:

image

Atom query properties should be stored in and loaded from KET format per specification provided in #3323
@AlexanderSavelyev AlexanderSavelyev added this to the Refined Backlog milestone Sep 12, 2023
AKZhuk added a commit that referenced this issue Sep 14, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
57e9d60 
…ties
@AKZhuk AKZhuk linked a pull request Sep 14, 2023 that will close this issue
#3298 - Add simple atom query primitives to the query specific properties #3322
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AKZhuk added a commit that referenced this issue Sep 14, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
e63d634 
…ties
AKZhuk added a commit that referenced this issue Sep 15, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
846e212 
…ties
AKZhuk added a commit that referenced this issue Sep 15, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
0d9b954 
…ties

- merge master into branch
AKZhuk added a commit that referenced this issue Sep 15, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
a9b6f32 
…ties

- update e2e tests
AKZhuk added a commit that referenced this issue Sep 18, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
7449140 
…ties

- update e2e tests
@MartaWilliams
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Test cases written

AKZhuk added a commit that referenced this issue Sep 18, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
4efee93 
…ties

- update e2e snapshots for save-file.spec.ts
AKZhuk added a commit that referenced this issue Sep 19, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
77fbb01 
…ties

- hide implicitHCount if atom in aromatized ring
Nitvex pushed a commit that referenced this issue Sep 19, 2023
@AKZhuk
#3298 - Add simple atom query primitives to the query specific proper…
0bd2756 
…ties (#3322)

* #3298 - Add simple atom query primitives to the query specific properties

* #3298 - Add simple atom query primitives to the query specific properties
- update e2e tests

* #3298 - Add simple atom query primitives to the query specific properties
- update e2e tests

* #3298 - Add simple atom query primitives to the query specific properties
- update e2e snapshots for save-file.spec.ts

* #3298 - Add simple atom query primitives to the query specific properties
- hide implicitHCount if atom in aromatized ring
@urszula-gawlowska urszula-gawlowska self-assigned this Oct 4, 2023
@ViktoriaTkacheva
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  1. When saving a structure with Atom Properties in .Ket format, in Preview the "hCount" indicator in different cases is constantly greater by 1 than it is displayed on the canvas
image
  1. If add Atom Properties to the structure (see the screenshot below) and click "Save as", an error is displayed, but this error can be closed, and save the file. The file opens correctly in .Ket format, but distorted in .mol format (not all Atom Properties are displayed)
image
  1. If add slightly different Atom Properties to the structure (see the screenshot below) and save it in .Ket format, then when opening this file, an error appears and the file does not open
image

@AKZhuk
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AKZhuk commented Oct 5, 2023

  1. When saving a structure with Atom Properties in .Ket format, in Preview the "hCount" indicator in different cases is constantly greater by 1 than it is displayed on the canvas
image 2. If add Atom Properties to the structure (see the screenshot below) and click "Save as", an error is displayed, but this error can be closed, and save the file. The file opens correctly in .Ket format, but distorted in .mol format (not all Atom Properties are displayed) image 3. If add slightly different Atom Properties to the structure (see the screenshot below) and save it in .Ket format, then when opening this file, an error appears and the file does not open image

1 - not a bug, the same behaviour in version 2.13.0
2,3 - - fixed in #3398

@urszula-gawlowska urszula-gawlowska removed their assignment Oct 9, 2023
@urszula-gawlowska urszula-gawlowska mentioned this issue Oct 9, 2023
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@ViktoriaTkacheva
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  1. The bug has been moved to a separate ticket An error appears when saving a structure with Atom Properties from the "Query specific" section Indigo#1311
  2. The bug is fixed

@AKZhuk AKZhuk removed this from the Ketcher 2.16.0-rc.1 milestone Oct 18, 2023
@AKZhuk AKZhuk added this to the SMART-Enhancement milestone Oct 18, 2023
@Nitvex Nitvex modified the milestones: SMART Enhancement, Ketcher 2.16.0-rc.1 Oct 23, 2023
@github-project-automation github-project-automation bot moved this to Done in Ketcher Aug 27, 2024
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@AKZhuk AKZhuk

Labels
epic: smarts feature request
Projects
Ketcher
Status: Done
Milestone
Ketcher 2.16.0-rc.1
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#3298 - Add simple atom query primitives to the query specific properties epam/ketcher
6 participants
@AlexanderSavelyev @AKZhuk @Nitvex @MartaWilliams @ViktoriaTkacheva @urszula-gawlowska