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

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AlexeyGirin opened this issue Dec 23, 2024 · 0 comments
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bug Priority: High Severity: High High level visibility to the user

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@AlexeyGirin
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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
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