Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ambiguous DNA bases (N, D, H, W) wrongly converted to DNA bases on antisense creation #6196

Closed
Tracked by #6600
AlexeyGirin opened this issue Dec 23, 2024 · 1 comment · Fixed by #6372 or #6389
Closed
Tracked by #6600
Assignees
Labels
Antisense Bucket: Antisense related issues Priority: High Severity: High High level visibility to the user

Comments

@AlexeyGirin
Copy link
Collaborator

AlexeyGirin commented Dec 23, 2024

Steps to Reproduce

  1. Go to Macro mode - Snake mode
  2. Load from HELM: RNA1{R(A,C,G,T)P.R(A,G,T)P.R(A,C,T)P.R(A,T)P}$$$$V2.0
    image
  3. Create antisense for that chain

Actual behavior
System creates all DNA bases instead of RNA ones in antisense chain.
HELM export result: RNA1{R(A,C,G,T)P.R(A,G,T)P.R(A,C,T)P.R(A,T)P}|RNA2{R(A,C,G,T)P.R(A,C,T)P.R(A,G,T)P.R(A,T)P}$RNA1,RNA2,2:pair-2:pair|RNA1,RNA2,5:pair-5:pair|RNA1,RNA2,8:pair-8:pair|RNA1,RNA2,11:pair-11:pair$$$V2.0
image

Expected behavior
System creates all RNA bases
HELM export result: RNA1{R(A,C,G,T)P.R(A,G,T)P.R(A,C,T)P.R(A,T)P}|RNA2{R(A,C,G,U)P.R(A,C,U)P.R(A,G,U)P.R(A,U)P}$RNA1,RNA2,2:pair-2:pair|RNA1,RNA2,5:pair-5:pair|RNA1,RNA2,8:pair-8:pair|RNA1,RNA2,11:pair-11:pair$$$V2.0
image

As per requirement:

Complementary bases

Sense base Antisense base
N (ambiguous DNA base) and N (ambiguous RNA base) N (ambiguous RNA base)
D (ambiguous DNA base) and D (ambiguous RNA base) H (ambiguous RNA base)
H (ambiguous DNA base) and H (ambiguous RNA base) D (ambiguous RNA base)
W (ambiguous DNA base) and W (ambiguous RNA base) W (ambiguous RNA base)

Versions

  • Ketcher Version 2.28.0-rc.3 Build at 2024-12-11; 14:32:57
  • Indigo Version 1.27.0-rc.1.0-g8d656a341-wasm32-wasm-clang-19.0.0
  • Chrome Version 131.0.6778.109 (Official Build) (64-bit)
  • Win10

Issue found while testing - #5678

@AlexeyGirin AlexeyGirin added bug Priority: High Severity: High High level visibility to the user labels Dec 23, 2024
@AlexeyGirin AlexeyGirin added this to the Ketcher 2.28.0-rc.4 milestone Dec 23, 2024
@AlexeyGirin AlexeyGirin changed the title N, D, H, W, Y ambiguous DNA bases wrongly converted to DNA bases on antisense creation N, D, H, W ambiguous DNA bases wrongly converted to DNA bases on antisense creation Dec 23, 2024
@AlexeyGirin AlexeyGirin changed the title N, D, H, W ambiguous DNA bases wrongly converted to DNA bases on antisense creation Ambiguous DNA bases (N, D, H, W) wrongly converted to DNA bases on antisense creation Dec 23, 2024
@svvald svvald modified the milestones: Ketcher 2.28.0-rc.4, Ketcher 2.28.0-rc.5 Dec 25, 2024
@AlexeyGirin AlexeyGirin modified the milestones: Ketcher 2.28.0-rc.5, Ketcher 3.0.0-rc.2 Jan 9, 2025
@AlexeyGirin AlexeyGirin removed the bug label Jan 16, 2025
@KristinaKasyanovskaya KristinaKasyanovskaya self-assigned this Jan 22, 2025
@AlexeyGirin AlexeyGirin added the Antisense Bucket: Antisense related issues label Jan 24, 2025
rrodionov91 pushed a commit that referenced this issue Jan 29, 2025
@AlexeyGirin
Copy link
Collaborator Author

Verified.
Image

  • Ketcher Version 3.0.0-rc.7 Build at 2025-02-05; 16:27:42
  • Indigo Version 1.28.0-rc.3.0-gd5bcc27cb-wasm32-wasm-clang-19.0.0
  • Chrome Version 133.0.6943.54 (Official Build) (64-bit)
  • Win10

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment