Implementing MarvinJS webservices in JRuby with JChem

User a50c3bcf44

13-08-2015 11:11:59

Hi,


Apologies if this is the incorrect forum section for posting this.


I'm currently replicating the MarvinJS support webservices in JRuby (we have a pre-exsting JRuby/Sintra API for a legacy application) using an older version of JChem 5.7.3). The majority have been fairly trivial, but I've hit a snag with CIP Stereo analysis.


I'm using the chemaxon.core.calculations.stereo.CIPStereoRecognizer, which returns a HashSet of descriptors, but I think I'm missing a further rule set which interprets these properly. Iterating over the Hashset, parsing and returning to the MarvinJS is giving me incorrect results against Marvin Sketch and the MarvinJS demo site.


I've not managed to integrate the CIPStereoDescriptorIface in JRuby -  the missing step?


Thanks for your help,


Nathan

ChemAxon f052bdfe3c

18-08-2015 10:26:10

Hi Nathan,


 


I am sorry for the late reply. We have discussed this issue with the developers and they suggest to use getChirality function directly, that way you will get an integer for each atom. Please see the documentation on this page https://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/struc/MoleculeGraph.html#getChirality(int)


Please let us know whether this solution work for you. 


Best regards,


Efi

User a50c3bcf44

18-08-2015 10:54:36

Hi Efi,


Thanks for your reply. I also meant to post again since I discovered and implemented the same solution using .getChirality() and .getStereo2() - it pays to read the documentation well!


Thanks and regards,


Nathan