Dear Egon,
Thank you for your response. > Can you say some words on the data model you are using? Does it > support only molecules, or also protein structures (PDB files)? Is it > based on a simple chemical graph, or doing something more Dietz like? Sorry, I do not know what Dietz model is. Our code base supports only molecules represented as undirected graphs, and reactions represented as a collections of reactants and products with additional data like reaction flags and AAM. > * support reading and writing of Chemical Markup Language? Not yet... we support (reaction) SMILES, Molfiles, and Rxnfiles so far. InChI support is the next. But thank you for pointing us on CML, we will think about that. > * use the Blue Obelisk Data Repository for isotope properties? We once imported the values of relative atomic mass, isotopic composition, and standard atomic weight from the NIST website: http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&ascii=ascii&isotype=all Using the Blue Obelisk Data Repository is possible. What are the pros and cons? > * use the Algorithm Dictionary, so that we can GPLv3/C++ > implementations of common cheminformatics algorithms? I am not sure I understand the question... I looked up the list of algorithms on http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml Indigo has original implementations of some algorithms listed there, namely layoutMolecule, graphSpanningTree, graphPartitioning, alignmentKabsch As far as I get the idea, we could assign the "blueobelisk:algorithmName" labels to our source code and index it in Google it be found by the "Search Implementations" link on the site. Is this all about that, or is there anything else we can do in this direction? > * have a library of unit tests? No, sorry. We do have integration tests for each project, but these tests are somewhat hard to deploy so we decided not to put them in the GPL release. With best regards, Dmitry ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
