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.

Sign up for GitHub

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

Jump to bottom

Save to CDX converts aromatic benzene ring to dashed ring #1774

Closed
AlexeyGirin opened this issue Mar 4, 2024 · 3 comments · Fixed by #1785, #1846, #1847, #1889 or #1890
Closed

Save to CDX converts aromatic benzene ring to dashed ring #1774

AlexeyGirin opened this issue Mar 4, 2024 · 3 comments · Fixed by #1785, #1846, #1847, #1889 or #1890
Assignees
@AliaksandrDziarkach
Labels
Bug Priority: High
Milestone
Indigo-1.19.0-rc.3

Comments

@AlexeyGirin
Copy link
Collaborator

AlexeyGirin commented Mar 4, 2024 •
edited
Loading

Describe the bug
Save to CDX converts plus into lone pair

Steps to Reproduce

  1. Put on the canvas following SMILE: c1ccccc1
  2. Save to CDX format file
  3. Open it in ChemDraw (ver 15 in my case)
    image

Actual behavior
Save to CDX converts aromatic benzene ring to dashed ring
image

Expected behavior
System opens ordinary aromatic benzene ring
image

Environment details (please complete the following information):

  • Indigo Toolkit Version 1.18.0-rc.9.0-gc7efb4e71-wasm32-wasm-clang-12.0.0
  • Ketcher Version 2.18.0-rc9 Build at 2024-02-27; 16:16:47
  • Chrome Version 122.0.6261.70 (Official Build) (64-bit)
  • Win10
@AlexeyGirin AlexeyGirin added this to the Indigo-1.19.0-rc.1 milestone Mar 4, 2024
AliaksandrDziarkach added a commit that referenced this issue Mar 7, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring
aacc0db 
Fix bond save in CDX. Add UT. Fix UTs.
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Mar 7, 2024 that will close this issue
#1774 Save to CDX converts aromatic benzene ring to dashed ring #1785
Merged
7 tasks
AlexanderSavelyev pushed a commit that referenced this issue Mar 11, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring (#1785)
9077966
@AlexeyGirin
Copy link
Collaborator Author

Not fixed.

  • Indigo Toolkit Version 1.19.0-rc.1.0-g8cd9f1e27-x86_64-linux-gnu-11.2.1
  • Ketcher Version 2.20.0-rc1 Build at 2024-03-15; 15:42:19
  • Chrome Version 122.0.6261.129 (Official Build) (64-bit)
  • Win10

image

@AlexeyGirin AlexeyGirin reopened this Mar 18, 2024
AliaksandrDziarkach added a commit that referenced this issue Mar 19, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring
a957452 
Add	kCDXProp_Bond_Display2 property saving. Fix UT
AliaksandrDziarkach added a commit that referenced this issue Mar 19, 2024
@AliaksandrDziarkach
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashed…
b5d9b4f 
… ring

Add	kCDXProp_Bond_Display2 property saving. Fix UT
This was linked to pull requests Mar 19, 2024
#1774 Save to CDX converts aromatic benzene ring to dashed ring #1846
Merged
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashed ring #1847
Merged
AliaksandrDziarkach added a commit that referenced this issue Mar 19, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring (#1846)
05de89c
AliaksandrDziarkach added a commit that referenced this issue Mar 19, 2024
@AliaksandrDziarkach
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashed…
793cceb 
… ring (#1847)
@AlexeyGirin
Copy link
Collaborator Author

AlexeyGirin commented Mar 28, 2024 •
edited
Loading

Not fully fixed.
Now indigo saves aromatic benzine ring as Double-Aromatic bond ring.
image
and if we open CDX created by indigo back in Ketcher - it opens corrupted molecule:
image

At the same time - CDX created by Chem Draw - has better consistency - CDX_From_ChemDraw.zip
it is opened in Ketcher well:
image

As well as in Chem Draw itself:
image

@AlexeyGirin AlexeyGirin reopened this Mar 28, 2024
AliaksandrDziarkach added a commit that referenced this issue Mar 31, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring
457bf0a 
Fix cdx bond load to set direction only for single bond. Fix UT
AliaksandrDziarkach added a commit that referenced this issue Mar 31, 2024
@AliaksandrDziarkach
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashed…
214b5f6 
… ring

Fix cdx bond load to set direction only for single bond. Fix UT
This was linked to pull requests Mar 31, 2024
#1774 Save to CDX converts aromatic benzene ring to dashed ring #1889
Merged
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashedring #1890
Merged
AlexanderSavelyev pushed a commit that referenced this issue Apr 1, 2024
@AliaksandrDziarkach
#1774 Save to CDX converts aromatic benzene ring to dashed ring (#1889)
f0c977e
AlexanderSavelyev pushed a commit that referenced this issue Apr 1, 2024
@AliaksandrDziarkach
Backmerge: #1774 Save to CDX converts aromatic benzene ring to dashed…
a15408f 
…ring (#1890)
@AlexeyGirin
Copy link
Collaborator Author

Fixed.
image
Ketcher Version 2.21.0-rc.1 Build at 2024-04-15; 20:00:15
Indigo Version 1.20.0-rc.1.0-g8e8ffc3c3-wasm32-wasm-clang-12.0.0

@Zhirnoff Zhirnoff mentioned this issue Jun 12, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@AliaksandrDziarkach AliaksandrDziarkach

Labels
Bug Priority: High
Projects
None yet
Milestone
Indigo-1.19.0-rc.3
2 participants
@AliaksandrDziarkach @AlexeyGirin