epam / ketcher

Web-based molecule sketcher
https://lifescience.opensource.epam.com/ketcher/demo.html
Apache License 2.0
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After add/remove explicit hydrogens 3D structure become a 2D #5884

Open wiscgazf opened 1 month ago

wiscgazf commented 1 month ago

Steps to Reproduce

  1. Add in Micro mode from Structure Library 3D structure C20H20
  2. Press add/remove explicit hydrogens 2 times
  3. Press 3D Viewer button and look on structure

Actual behavior After add/remove explicit hydrogens 3D structure become a 2D

Expected behavior After add/remove explicit hydrogens 3D structure not become a 2D

Screenshots

https://github.com/user-attachments/assets/65399367-27a9-432f-8ee2-042bfec8aa4f

Desktop:

Ketcher version [Version 2.26.0-rc.6] Indigo version [Version 1.25.0-rc.4]

Description provided by the user:

Remove explicit hydrogens Structure error after switching

if the original structure is 3D structure, I now switch more than 3 times, the original structure has changed, the 3D structure should have become 2D

MOL Struct It's in 3D struct


  Ketcher 10302411 12D 1   1.00000     0.00000     0

 40 50  0  0  0  0  0  0  0  0999 V2000
   13.1532   -7.7757   -2.7155 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6565   -6.2596   -2.7886 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6090   -6.7985   -1.6168 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0744   -4.6859   -1.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7458   -7.2543   -1.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3600   -5.3293   -0.5122 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8458   -7.3637   -0.7224 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6323   -7.1512   -2.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6841   -7.3076   -1.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2892   -9.2211   -1.7447 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.6897   -9.6193    0.3837 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6816   -8.6938    0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1878   -6.2858   -0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2042   -7.8533    1.1684 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.0874   -8.6860    2.7771 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6615  -10.1692    1.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.5916   -9.0478    0.7882 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1105  -10.2641   -0.1449 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3462   -7.8837    2.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7750   -8.8886    0.3668 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8377   -8.2264    0.1912 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1768   -7.6569    1.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6797   -4.7406    0.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0235   -6.7554   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2615   -5.9270   -0.7658 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2641   -8.1721    1.6401 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0201   -7.6183    0.7433 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6962   -7.1587    2.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1839   -6.2715   -0.2167 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7054   -5.5937    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.5922   -6.2301    1.2227 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7179   -5.3154    2.0918 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1298   -7.2887    1.6098 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3796   -6.4589    1.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1472   -5.8952    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2617   -8.7454   -1.1975 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7131   -9.0816   -0.0953 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4798   -8.5079   -0.9871 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1480   -9.5883   -2.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7296   -7.6781   -1.5827 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 40  1  0  0  0  0
  2  3  1  0  0  0  0
  3  9  1  0  0  0  0
  3 25  1  0  0  0  0
  3 40  1  0  0  0  0
  4 25  1  0  0  0  0
  5  7  1  0  0  0  0
  6 29  1  0  0  0  0
  7 21  1  0  0  0  0
  7 29  1  0  0  0  0
  7 40  1  0  0  0  0
  8  9  1  0  0  0  0
  9 24  1  0  0  0  0
  9 38  1  0  0  0  0
 10 38  1  0  0  0  0
 11 12  1  0  0  0  0
 12 17  1  0  0  0  0
 12 27  1  0  0  0  0
 12 38  1  0  0  0  0
 13 24  1  0  0  0  0
 14 27  1  0  0  0  0
 15 26  1  0  0  0  0
 16 17  1  0  0  0  0
 17 26  1  0  0  0  0
 17 37  1  0  0  0  0
 18 37  1  0  0  0  0
 19 22  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 37  1  0  0  0  0
 22 26  1  0  0  0  0
 22 34  1  0  0  0  0
 23 35  1  0  0  0  0
 24 27  1  0  0  0  0
 24 35  1  0  0  0  0
 25 29  1  0  0  0  0
 25 35  1  0  0  0  0
 26 33  1  0  0  0  0
 27 33  1  0  0  0  0
 28 33  1  0  0  0  0
 29 34  1  0  0  0  0
 30 34  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 31 35  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 36 39  1  0  0  0  0
 36 40  1  0  0  0  0
 31 34  1  0  0  0  0
M  END

This is initial

ketcher (1)

Click the button three times

ketcher (2)

At this point the 3D structure also disappeared and the preview 3D became 2D