Hello together,

i have several questions/annotations to some features in the CDK.

The first depends on the UniversalIsomorphismTester class. Let me begin with an example code:

try {
      SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
      IAtomContainer atomContainer = sp.parseSmiles("CCCNCCC");
      IAtomContainer SMILESquery = sp.parseSmiles("CNC");
      IQueryAtomContainer query = QueryAtomContainerCreator.createBasicQueryContainer(SMILESquery);
      List<List<RMap>> maps =
            UniversalIsomorphismTester.getSubgraphMaps(atomContainer, query);
} catch (Exception e) {
      // Do...

If I test the two example molecules the getSubgraphMaps() method returns two RMaps but it should be one. In my eyes is this behaviour a bug because the first molecule contains the query structure only once.

The second thing is a feature request which would be nice if it could be implemented in further versions of the CDK/JChemPaint. It would be nice if you could paint an additional bond type to show the user a broken/made bond (e.g. a reaction centre). It could be visualized with a snake like line which cuts the bond into two parts. Furthermore the MDLReader/MDLwriter class must be adapted to support this feature. The bond property (bond made/broken) should be saved in the bond block “reaction center status” field of the mol files (I think it is not supported at this time).

My last problem is that the Java2Drenderer class does not paint rest labels of pseudo atoms anymore. The corresponding code fragment is commented out in the CDK sources version 1.2.0. (I know you are working on JChemPaint).

I need this features in context of my bachelor thesis and I would help to implement some of the features. But I have no idea how to start with. The programming side should be no problem but how to submit the source changes and how to work with git/subversion is a problem. Perhaps anyone could give me a short introduction to this.