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Analyzed about 23 hours ago. based on code collected 1 day ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Aug 15, 2025 — Sep 14, 2025 Showing page 1 of 2 Search / Filter on:
Move the CDK AtomType Repos File test and fix the PDB one and the PubChem ASN reader.	John Mayfield	More...				3 days ago
Replace import of CMLReader with direct molecule creation. Bug 1014344 (https://sourceforge.net/p/cdk/bugs/231/) is testing CML round tripping so I've moved it there and switch it so CML depends on SMILES (test) rather than the other way around.	John Mayfield	More...				3 days ago
Avoid depending on the HinReader and create the molecule directly.	John Mayfield	More...				3 days ago
Merge pull request #1225 from JonasSchaub/sugar-detection-utility	John Mayfield	More...				4 days ago
adds the Sugar Detection Utility and fixes a few things in the Sugar Removal Utility	Jonas Schaub	More...				5 days ago
Do not sett rootAttachmentPoints if null.	John Mayfield	More...				6 days ago
Do not explicitly store the attachment atoms, instead we infer this from the explicit attachment points (wiggly crossed line).	John Mayfield	More...				6 days ago
When reading/writing RGroup queries we add on/trim explicit attachment points (wavy line across bond).	John Mayfield	More...				6 days ago
Add a utility method to AtomPlace which allows us to place a single atom which is sprouted off the structure.	John Mayfield	More...				6 days ago
Add a new utility to get the median bond length and fallback to a provided default if needed.	John Mayfield	More...				6 days ago
Move the AtomPlace to cdk-standard, we are going to need this. This does split the "layout" package but in future (CDK v3) they will all be collapsed together.	John Mayfield	More...				6 days ago
In CXSMILES we use an SGroup to store the attachment order. Rather than store a map in the 'RGroup' we can reuse this SGroup and get nicer rendering.	John Mayfield	More...				6 days ago
Improved stereochemistry invalidation when modifying molecules (Fixes #1221).	John Mayfield	More...				11 days ago
Grr DebugBong issues.	John Mayfield	More...				13 days ago
A constructor argument is also useful for refactoring code.	John Mayfield	More...				13 days ago
More replacements of IBond.Stereo with IBond.Display	John Mayfield	More...				14 days ago
A new addBond which accepts a display property as well so we can cleanup more usages of IBond.Stereo	John Mayfield	More...				14 days ago
Don't store crossed bonds as wavy.	John Mayfield	More...				14 days ago
Replace calls to IBond.getStereo() with IBond.getDisplay().	John Mayfield	More...				14 days ago
Merge pull request #1218 from JonasSchaub/LargestPiSystemDescriptor-visited-fix	John Mayfield	More...				15 days ago
makes LargestPiSystemDescriptor use an internal visited array instead of IChemObject flag VISITED for safe parallelisation	Jonas Schaub	More...				15 days ago
Replace usages of setStereo with setDisplay. We also add some alias names Up/Down for convenience.	John Mayfield	More...				15 days ago
Step 1 in cleaning up IBond.Stereo vs IBond.Display conflation. We deprecate IBond.Stereo get/set and implement them in terms of Display. The IBond.Stereo is mainly based on MDL/CML model of bonds but then also mixes in an explicit E/Z setting. We now have correct ways of storing this (IDoubleBondStereochemistry). There is a slight behaviour change in that by default double bonds now return E_Z_BY_COORDS by default which mirrors the MDL semantics.	John Mayfield	More...				15 days ago
Fix a corner case with titles for reactions not being set if no CXSMILES layers were present.	John Mayfield	More...				15 days ago
Allow hollowwedge display style.	John Mayfield	More...				15 days ago
Improver generated SVG when we have an alpha colour or NULL background.	John Mayfield	More...				21 days ago
Some additional documentation.	John Mayfield	More...				22 days ago
Correct reaction background box dimensions. I had used the wrong Dimensions here, we want to paint the box to be the size of the whole canvas.	John Mayfield	More...				22 days ago
Remove stray print to stderr.	John Mayfield	More...				23 days ago
Now the DepictionGenerator is the normal way of rendering, align the default values of these parameters.	John Mayfield	More...				24 days ago

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