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Incorrect bond length and angle for non-natural monomers in the library #6573

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ljubica-milovic opened this issue Feb 26, 2025 · 1 comment · Fixed by #6618
Closed

Incorrect bond length and angle for non-natural monomers in the library #6573

ljubica-milovic opened this issue Feb 26, 2025 · 1 comment · Fixed by #6618
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@rrodionov91
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Ketcher 3.3.0-rc....

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@ljubica-milovic
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Steps to Reproduce

  1. Go to macromolecules library
  2. Add peptide monomer 1Nal to the canvas
  3. Go to small molecules mode
  4. Expand the monomer
  5. Draw cyclohexane
  6. Compare the bond lengths

Actual behavior
The bonds of the monomer are longer than the standard bond lenght:
Image

Expected behavior
All monomers should have standard bond lengths and angles.

Notes
Structures covered in tickets #6563, #4787, and #5111 do not need fixing.
@ljubica-milovic ljubica-milovic added this to the Ketcher 3.3.0-rc.1 milestone Feb 26, 2025
@rrodionov91 rrodionov91 self-assigned this Mar 5, 2025
rrodionov91 added a commit that referenced this issue Mar 6, 2025
@rrodionov91
#6573 - Incorrect bond length and angle for non-natural monomers in t…
2f7fb69 
…he library

- normalized bond length to the median one for each monomer structure
@rrodionov91 rrodionov91 linked a pull request Mar 6, 2025 that will close this issue
#6573 - Incorrect bond length and angle for non-natural monomers in the library #6618
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@rrodionov91
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List of monomers need to be redrawn manually:
monomer_need_manual_corrections.json

rrodionov91 added a commit that referenced this issue Mar 6, 2025
@rrodionov91
#6573 - Incorrect bond length and angle for non-natural monomers in t…
ed9cb5b 
…he library (#6618)

- normalized bond length to the median one for each monomer structure
- updated screenshots
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Ketcher 3.3.0-rc.1 (Current)
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#6573 - Incorrect bond length and angle for non-natural monomers in the library epam/ketcher
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@rrodionov91 @ljubica-milovic