Did you perform explicit aromaticity detection and atom typing (I don't recall whether the MDLReader does this by default)
On Thu, Sep 30, 2010 at 10:23 AM, Adel Golovin <[email protected]> wrote: > Dear CDK developers, > Thank you for an excellent opensource chemical package. > However I write to report an issue :( > I have come across a problem with fingerprints. > The fingerprints depend on the order of atoms in the MDL file. > The example molecule is 1FH (kind of a heme) from PDB. > > the code I use to generate fingerprints: > > org.openscience.cdk.io.MDLReader cdkmdl = new > org.openscience.cdk.io.MDLReader(); > StringReader r = new StringReader(strMOL); > cdkmdl.setReader(r); > Molecule mol = new Molecule(); > cdkmdl.read(mol); > Fingerprinter f = new Fingerprinter(); > fingerprinter = f.getFingerprint(mol); > > > > here strMOL is a string containing a molecule in MDL format. > > Best regards, > Adel Golovin, > PDBe / EMBL-EBI > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
