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Display molecules in macro mode: basic structures with atoms and bonds #5359

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rrodionov91 opened this issue Aug 26, 2024 · 1 comment · Fixed by #5617 or #5636
Closed

Display molecules in macro mode: basic structures with atoms and bonds #5359

rrodionov91 opened this issue Aug 26, 2024 · 1 comment · Fixed by #5617 or #5636
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feature request Test Cases Written Test cases has been written for that issue

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@rrodionov91
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rrodionov91 commented Aug 26, 2024

Background
Currently molecules are displayed same as chems in macromolecules mode. Structure of molecule is not clear until user hover it to see preview.

Solution
It needs to display molecules in macro mode in similar view as in molecules mode. Task covers basic structures only to simplify the first iteration. It includes next list of features:

  • Bonds. Single, Double, Single Up and Single Down types of bonds should be implemented. Lines of double bonds should not overlap each other on any angle (same as implemented for double bond in molecules mode now).
  • Atoms. Only single atoms are in scope. Carbon atom should not be displayed. Hydrogen label should be placed after/before atom label with number subscript which in case if atom has valence more than connections. Valence validation errors are out of scope. Charge is out of scope.
  • Connections. It should be possible to establish connection between monomer and molecule in macromolecules mode by drawing the bond between monomer and molecule's attachment point, created in molecules mode.
  • User settings. Applying user settings are out of scope.
  • All other entities( sgroups, rgroups, rgroup attachment points, e.t.c) are out of scope.
@rrodionov91 rrodionov91 added this to the Ketcher 2.26.0-rc.1 milestone Aug 26, 2024
@rrodionov91 rrodionov91 self-assigned this Sep 17, 2024
@Zhirnoff Zhirnoff added the Test Cases Written Test cases has been written for that issue label Sep 27, 2024
rrodionov91 added a commit that referenced this issue Oct 2, 2024
…and bonds (#5617)

- added initial atoms and several types of bonds displaying in macromolecules mode
rrodionov91 added a commit that referenced this issue Oct 3, 2024
…and bonds

- fixed monomer to atom bonds repositioning issue after switching between modes if there are more than one molecule
rrodionov91 added a commit that referenced this issue Oct 3, 2024
…and bonds (#5636)

- fixed monomer to atom bonds repositioning issue after switching between modes if there are more than one molecule
This was referenced Oct 7, 2024
@AlexeyGirin
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Verified with issues.

  • Ketcher Version 2.26.0-rc.1 Build at 2024-10-04; 18:45:04
  • Indigo Toolkit Version 1.25.0-rc.1.0-g704673fcb-wasm32-wasm-clang-19.0.0
  • Chrome Version 129.0.6668.90 (Official Build) (64-bit)
  • Win10

Guch1g0v pushed a commit that referenced this issue Oct 17, 2024
…and bonds (#5636)

- fixed monomer to atom bonds repositioning issue after switching between modes if there are more than one molecule
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