John Mayfield
John Mayfield
Check lists of nice to haves for CDK 3.0 some of these are large sweeping API changes hence v3.0. - [x] Switch IElement.H etc to int rather than byte (pre-v3.0...
Fixes an issue with Hose Code nesting via #588. We can actually see from another test that the output was wrong since it didn't make sense. example:   ...
Models built on the existing HOSE Codes either need to be deprecated or retrained. These are used in the IPAtomicHOSEDescriptor.IPdb and ProtonAffinityHOSEDescriptor.Affinitydb as well as several cdk-reaction classes - RadicalSiteHrBetaReaction...
We need to include Guava and Math3 since CDK no longer depends on these. All tests passing OK.
This patch provides the generic/low-level data structures and representations to describe a molecular transform. A conveient way of describing transforms is the SMIRKS syntax which is supported via functionality in...
The newer Apache JENA (cdk-iordf) version pulls in a lot of dependencies which ultimately means our "cdk-bundle" size is nearly double. A neat trick to work out where bloat is...
During deployment I get warnings about xercesImpl. While one option is to upgrade a longer term option would be to try and replace it
Fixes #971. Also removes the property reading from the Iterating Reader since the base readers now do it. We can do a little better with the IteratingSDFReader loop - will...
Abbreviations on attachment points is broken. 
Currently it is not possible to write ```C:C```. Which makes sense, however we may "want" to write this. Adding a non-default, "expert" mode would allow this.