Hi, "Egon Willighagen" <[EMAIL PROTECTED]> wrote:
> On Feb 8, 2008 1:46 PM, Nina Jeliazkova <[EMAIL PROTECTED]> wrote: > > My experience with the latest code says that if you parse an aromatic > > smiles (as below), all the aromatic bonds will correctly have aromatic > > flag turned on, but the bond order will be single everywhere. This > > causes lot of confusion for further processing, and could be the reason > > inchi is not generated. > > If this is indeed the problem, please try the use of the DeduceBondSystemTool: > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/smiles/DeduceBondSystemTool.html > > ... to create a kekule representation. Actually, I can't get it working. Even for benzene, all the bonds stay single after using DeduceBondSystemTool. public void testDeduceBondOrders() throws Exception { SmilesParser p = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IMolecule m = p.parseSmiles("c1ccccc1"); boolean b = CDKHueckelAromaticityDetector.detectAromaticity(m); assertTrue(b); DeduceBondSystemTool dbst = new DeduceBondSystemTool(); IMolecule m1 = dbst.fixAromaticBondOrders(m); int single_bonds = 0; int double_bonds = 0; int aromatic_bonds = 0; for (int i=0; i<m1.getBondCount();i++) { Order o = m1.getBond(i).getOrder(); if (o.equals(Order.DOUBLE)) double_bonds++; if (o.equals(Order.SINGLE)) single_bonds++; if (m1.getBond(i).getFlag(CDKConstants.ISAROMATIC)) aromatic_bonds++; } assertEquals(6,aromatic_bonds); assertEquals(3,single_bonds); assertEquals(3,double_bonds); } Do this work for others and I am misusing the code somehow? Regards, Nina > > Egon ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
