Dear Janette, Please send future RDKit questions to the rdkit-discuss mailing list. I prefer to have things archived so others can benefit from questions and answers. You can find information about subscribing to the mailing list here: https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
On Thu, Feb 3, 2011 at 4:30 PM, Jani Nickel <[email protected]> wrote: > Hello Greg Landrum, > > I am a student at the University of Frankfurt am Main (Germany) and found > out that you're an expert with RDKit. Maybe you can help me because so far > no one else could. I hope I don't annoy you :) no worries. :-) > I have some problems with the rdkit one component reaction node in knime. > > For example I have a molecule CCOc1cc([N+]([O-])=O)ccc1*C(=O)O and a > reaction SMARTS discribing this reaction [*]C(=O)O>>[*]C(=O)Cl but the > product molecule is [*]C(=O)Cl . I expected the whole molecule ( > CCOc1cc([N+]([O-])=O)ccc1*C(=O)Cl ) as the product molecule instead of > [*]C(=O)Cl as the product. My question is now, how can I achieve that the > whole molecule is the result of the output? Is the syntax of my SMARTS > wrong? I used rxn-files and converted them with OpenBabel into rsmi and used > them as my SMARTS because I thought that valid SMILES are also valid SMARTS. The problem at the moment is that you aren't really providing reaction smarts as the RDKit understands it. The format is a bit odd, and unique to the RDKit. There's some documentation here that may help you understand how to use it: http://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk/Docs/Book/RDKit_Book.pdf For the reaction above, what you probably want is something like: [C:1](=[O:2])O>>[C:1](=[O:2])Cl > Another question: Is it possible that these reactions could work without > wildcards? Or would the result be that the fitting molecules would be > matched: c1ccccc1>>CC(=O)c1ccccc1 The above example should work. > And at last: Some of my SMARTS have a dot "." just like > *C(*)*.[OH]>>*C(O)* Is there a possibility to deal with them in the rdkit > one component reaction node or can i just use them with the rdkit two > component reaction node? The dot is used in reactions to separate reactants (or products) from each other, so you would need to use the two-component reaction node if you want to include a dot. I'm a bit confused about what you're trying to describe with that reaction though. -greg ------------------------------------------------------------------------------ The modern datacenter depends on network connectivity to access resources and provide services. The best practices for maximizing a physical server's connectivity to a physical network are well understood - see how these rules translate into the virtual world? http://p.sf.net/sfu/oracle-sfdevnlfb _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
