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Inconsistent display of a separate phosphate in the sequence representation in the Sequence mode #4607

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ViktoriaTkacheva opened this issue May 10, 2024 · 1 comment · Fixed by #4766
Closed

Inconsistent display of a separate phosphate in the sequence representation in the Sequence mode #4607

ViktoriaTkacheva opened this issue May 10, 2024 · 1 comment · Fixed by #4766
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@DmitriiP-EPAM
Labels
bug Macromolecules Priority: Medium Sequence mode Bucket: Sequence mode related issues
Milestone
Ketcher 2.23.0-rc.1

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@ViktoriaTkacheva
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ViktoriaTkacheva commented May 10, 2024 •
edited by olganaz
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Steps to Reproduce

  1. Switch to the Macro mode

  2. Open this file Separate p in sequence.zip
    image

  3. Switch to the Sequence mode
    image

  4. Add one more nucleotide at the end of the sequence
    image

Actual behavior
The phosphate is displayed as “p”

Expected behavior

  1. Single phosphate that is not a part of nucleotide (in the middle of the chain) or nucleoside (at the end of the chain) should be displayed as 'p' in sequence mode.
  2. A group of multiple (more or equal than two) phosphates should be displayed as '@'.
    Images for better understanding:

Desktop (please complete the following information):

  • OS: Windows 10 Pro (version 22H2) x64
  • Browser: Сhrome
  • Version: (124.0.6367.92) x64

Ketcher version 2.21.0-rc.2, Build at 2024-05-10; 05:30:51

Issue found while testing #3734
@ViktoriaTkacheva ViktoriaTkacheva added this to the Ketcher 2.23.0-rc.1 milestone May 10, 2024
@DmitriiP-EPAM DmitriiP-EPAM self-assigned this Jun 5, 2024
DmitriiP-EPAM added a commit that referenced this issue Jun 6, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
c656774 
…dNucleotide(1)`
@DmitriiP-EPAM DmitriiP-EPAM linked a pull request Jun 6, 2024 that will close this issue
#4607 - Inconsistent display of a separate phosphate in the sequence representation in the Sequence mode #4766
Merged
9 tasks
DmitriiP-EPAM added a commit that referenced this issue Jun 6, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
cb7e4d6 
…hate and linker in `add(1)`
DmitriiP-EPAM added a commit that referenced this issue Jun 12, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
6e4430d 
…dNucleotide(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 12, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
67d8c3d 
…hate and linker in `add(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
e5a8053 
…dNucleotide(1)`
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
d2dacd7 
…hate and linker in `add(1)`
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
edbc94b 
…dNucleotide(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
7eaa04c 
…hate and linker in `add(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Test (Import-Saving-Files): Run `npm run docker:update Import…
53d20ab 
…-Saving-Files/saving-svg.spec.ts`
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Test (sequence-mode.spec.ts): Run `npm run docker:update sequ…
3683b28 
…ence-mode.spec.ts:393`
DmitriiP-EPAM added a commit that referenced this issue Jun 13, 2024
@DmitriiP-EPAM
#4607 - Test (Sequence-Mode): Run `npm run docker:update Sequence-Mod…
5b51afb 
…e/sequence-mode.spec.ts:671`
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
022dce8 
…dNucleotide(1)`
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
d050f10 
…hate and linker in `add(1)`
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Bugfix (monomers.ts): Correct isValidNucleoside(1), `isVali…
b03cbf3 
…dNucleotide(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Bugfix (Chain.ts): Correct the definition of individual phosp…
94ae1b0 
…hate and linker in `add(1)` (step 2)
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Test (Import-Saving-Files): Run `npm run docker:update Import…
2a45a3f 
…-Saving-Files/saving-svg.spec.ts`
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Test (sequence-mode.spec.ts): Run `npm run docker:update sequ…
353c817 
…ence-mode.spec.ts:393`
DmitriiP-EPAM added a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Test (Sequence-Mode): Run `npm run docker:update Sequence-Mod…
2b2e9fd 
…e/sequence-mode.spec.ts:671`
rrodionov91 pushed a commit that referenced this issue Jun 14, 2024
@DmitriiP-EPAM
#4607 - Inconsistent display of a separate phosphate in the sequence …
22ad484 
…representation in the Sequence mode (#4766)

- correct isValidNucleoside() and isValidNucleotide()
- correct the definition of individual phosphate and linker
@Zhirnoff
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Zhirnoff commented Jul 3, 2024

Tested. Bug fixed.

2024-07-03_14h43_16

Desktop:

  • OS: Windows 11
  • Browser Chrome
  • Version 124.0.6367.79 (Official Build) (64-bit)

Ketcher version
[Version 2.23.0-rc.1]
Indigo version
[Version 1.22.0-rc.1]

@ViktoriaTkacheva ViktoriaTkacheva mentioned this issue Jul 12, 2024
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Labels
bug Macromolecules Priority: Medium Sequence mode Bucket: Sequence mode related issues
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Milestone
Ketcher 2.23.0-rc.1
3 participants
@Zhirnoff @ViktoriaTkacheva @DmitriiP-EPAM