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Warnings appear while saving any structure as Daylight SMARTS #3431

Closed
urszula-gawlowska opened this issue Oct 12, 2023 · 0 comments · Fixed by #3439
Closed

Warnings appear while saving any structure as Daylight SMARTS #3431

urszula-gawlowska opened this issue Oct 12, 2023 · 0 comments · Fixed by #3439
Assignees
@AKZhuk
Labels
bug epic: smarts
Milestone
Ketcher 2.16.0-rc.1

Comments

@urszula-gawlowska
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urszula-gawlowska commented Oct 12, 2023 •
edited by AKZhuk
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Steps to Reproduce

  1. Launch "Ketcher"
  2. Draw any structure
  3. Click 'Save as' button
  4. Change file format to 'Daylight SMARTS'

Actual behavior
Warnings tab appears with text "Structure contains query properties of atoms and bonds that are not supported in the SMARTS. Query properties will not be reflected in the file saved."

Expected behaviour

  1. Warning "Structure contains query properties of atoms and bonds that are not supported in the SMARTS. Query properties will not be reflected in the file saved," should not appear.

  2. The following Indigo warnings should appear for ALL formats except SMARTS and KET if the structure contains the following query functions

  • Warning "Structure contains query features" should be appear for:

    • Atom/Query specific
    • Atom/custom query
    • Atom list
    • Bond/Topology

  • Warning "Structure contains query features for atoms" should be appear for:

    • Atom/reaction flags

  • Warning "Structure contains generic atoms. They will be saved as any atom” should be appear for:

    • Atom type special

  • Warning "Structure contains query features for bonds” should be appear for:

    • Bond/reacting center
  1. Need to create a ticket for Indigo for the following properties:
    • Bond/custom query
    • Bond/any type except (single, single up/down, double, triple, aromatic)
  • Warning "Structure contains query properties of atoms and bonds that are not supported in the SMARTS. Query properties will not be reflected in the file saved." should appear for SMARTS only if structure contains query properties of atoms and bonds that are not supported in the SMARTS.
    • Atom/radical
    • Atom unsaturated
    • Atom/reaction flags
    • Bond/reacting center
    • Bond/hydrogen
    • Bond/dative

Screenshots
ketcher_smarts_warnings

Desktop

  • OS: Windows 11 Pro
  • Browser: Chrome Version 117.0.5938.150

Ketcher version
2.15.0-rc.1 and 2.15.0-rc.2

Additional context
Related to #712
@urszula-gawlowska urszula-gawlowska assigned AKZhuk and unassigned Nitvex Oct 12, 2023
@AKZhuk AKZhuk added this to the Ketcher 2.16.0-rc.1 milestone Oct 12, 2023
AKZhuk added a commit that referenced this issue Oct 12, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
29f8612
AKZhuk added a commit that referenced this issue Oct 12, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
7601d51 
- Update fields max length for isotope and charge
@AKZhuk AKZhuk linked a pull request Oct 12, 2023 that will close this issue
#3431 – warnings appear while saving any structure as daylight smarts #3439
Merged
9 tasks
AKZhuk added a commit that referenced this issue Oct 13, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
a32d2b4 
- Update e2e snapshots
AKZhuk added a commit that referenced this issue Oct 13, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
86fc5d5 
- Fix pr comments
AKZhuk added a commit that referenced this issue Oct 16, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
c63579d
AKZhuk added a commit that referenced this issue Oct 16, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
3bd3bd8 
- Update fields max length for isotope and charge
AKZhuk added a commit that referenced this issue Oct 16, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
8ba24e8 
- Update e2e snapshots
AKZhuk added a commit that referenced this issue Oct 16, 2023
@AKZhuk
#3431 - Warnings appear while saving any structure as Daylight SMARTS
8384708 
- Fix pr comments
@AliaksandrDziarkach AliaksandrDziarkach mentioned this issue Oct 18, 2023
Closed
@AKZhuk AKZhuk modified the milestones: Ketcher 2.16.0-rc.1, SMART-Enhancement Oct 18, 2023
Nitvex pushed a commit that referenced this issue Oct 18, 2023
@AKZhuk @Zhirnoff
#3431 – warnings appear while saving any structure as daylight smarts (…
97ebc29 
…#3439)

* #3431 - Warnings appear while saving any structure as Daylight SMARTS

* #3431 - Warnings appear while saving any structure as Daylight SMARTS
- Update fields max length for isotope and charge

* #3431 - Warnings appear while saving any structure as Daylight SMARTS
- Update e2e snapshots

* #3431 - Warnings appear while saving any structure as Daylight SMARTS
- Fix pr comments

* - updated 1 snapshot for 'reagents-SMILES'

---------

Co-authored-by: Mikhail Zhirnov <[email protected]>
@Nitvex Nitvex modified the milestones: SMART Enhancement, Ketcher 2.16.0-rc.1 Oct 23, 2023
@urszula-gawlowska urszula-gawlowska mentioned this issue Nov 16, 2023
Closed
@github-project-automation github-project-automation bot moved this to Done in Ketcher Aug 27, 2024
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Assignees

@AKZhuk AKZhuk

Labels
bug epic: smarts
Projects
Ketcher
Status: Done
Milestone
Ketcher 2.16.0-rc.1
Development

Successfully merging a pull request may close this issue.

#3431 – warnings appear while saving any structure as daylight smarts epam/ketcher
3 participants
@AKZhuk @Nitvex @urszula-gawlowska