Comments (2)
rwst
commented on July 18, 2024
there IS a check for connectivity in cleanup() before structure layout, but it only triggers after the hydrogen placer placed missing hydrogens. The question is, is it safe to make the hydrogen placer PART OF the connectivity checking to catch these cases, maybe use a dummy to avoid side effects on the checked molecule?
from jchempaint.
rwst
commented on July 18, 2024
Reason was all H atoms were deleted in cdk.layout.StructureDiagramGenerator:258 which makes this a CDK issue.-
The relevant tracker entry / pull request are
https://sourceforge.net/tracker/?func=detail&aid=3555353&group_id=20024&atid=320024
and
https://github.com/rwst/cdk/commit/1659dadc0f5050dd462cec73170944fded44665e
from jchempaint.
Related Issues (20)
- no viewer applet distributed, nor a jcp...viewer.jar in the zip
- option set fit to screen should be default ON
- add option 'surround charged molecules with brackets'
- Exported Inchi values from a mol structure doesn't give the same structure
- Viewer applet gives null error when only provide SMILES (instead of load)
- Viewer Applet does not Work
- How to load a mol file from another Directory? HOT 1
- Can't use applet because of security issues HOT 1
- Building the app is not working HOT 1
- Relayout button doesn't preserve cis-/trans- double bonds HOT 1
- Run JChemPaint from .Net how to handover a File? HOT 1
- Add more functions to handle selections
- Compilation fails with CDK 1.5.12 HOT 6
- Smile generated (by copy as smile) doesn't contain stereochemical information HOT 2
- Hydrogens on terminal hydroxyl groups are missing HOT 8
- Loading MDL mol file causes valences to be displayed for each atom HOT 2
- Switch to using SWT instead of Swing HOT 6
- update to CDK 2.2 HOT 6
- copy/paste not working on MacOS HOT 8
- Interest in packaging jchempaint as Flatpak for Linux?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from jchempaint.