[Cdk-user] Murcko Framework / aromaticity

Hi, I would like to generate Murcko framework for my library (a big Zinc subset). But for now, I'm just trying to do it for a few smiles :) After a bit of googling and java initiation (not so easy for me :) - thanks to Rajarshi, Egon, Christian and other who let some pieces of code there and

Re: [Cdk-user] Murcko Framework / aromaticity

Hi again, I progressed a bit in my code, and now I would like to print the molecule name. But the following code only prints null... Anybody could tell me where I am wrong? Thanks! Input smiles: tmp.smi: CCCNCC1=CC(CC2CC2)=CC=C1 molec1 CCCNCc1(CC2CC2)c1 molec2 Code below. Regads, Pascal

Re: [Cdk-user] Murcko Framework / aromaticity

Hi Pascal, Ah. After a bit of testing, and looking at the IteratingSmilesReader code, it seems like you actually need: mol.getProperty(CDKConstants.TITLE) as that is what the IteratingSMILESReader is doing. It would be great if you could file a feature request:

Re: [Cdk-user] Murcko Framework / aromaticity

Hi Pascal, for the CDK, we decided that we want it to behave like a Lego construction set. Each of the components should only do the minimal promised work, which gives maximum flexibility in wiring things together as you like them. In your example, you would always need to do aromaticity

Re: [Cdk-user] Murcko Framework / aromaticity

If I remember correctly the Murcko framework code in the CDK is broken. I have been working on an updated package for fragmentation but, of course, the real world slows things down ... On Sep 30, 2010, at 7:31 AM, Pascal Muller wrote: Hi, Each of the components should only do the minimal

[Cdk-user] CDK fingerprints

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

Re: [Cdk-user] CDK fingerprints

Hi Adel, On Thu, Sep 30, 2010 at 4:23 PM, Adel Golovin golo...@ebi.ac.uk wrote: 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

Re: [Cdk-user] CDK fingerprints

Hi Egon, I use cdk-1.3.4 Thanks, Adel. Egon Willighagen wrote: Hi Adel, On Thu, Sep 30, 2010 at 4:23 PM, Adel Golovin golo...@ebi.ac.uk wrote: Thank you for an excellent opensource chemical package. However I write to report an issue :( I have come across a problem with fingerprints.

Re: [Cdk-user] CDK fingerprints

On Thu, Sep 30, 2010 at 5:08 PM, Adel Golovin golo...@ebi.ac.uk wrote: cdk-1.3.4 Good. On the bus home I wrote four new unit tests for the fingerprinter, and using the AtomContainerAtomPermutor and AtomContainerBondPermutor on two molecules, and that showed no problems. If you send me your file

Re: [Cdk-user] CDK fingerprints

Thanks Egon, I made a few other experiments with the same compound and it looked Okay. I need to investigate the matter a bit deeper myself. I'll write the results. Adel. Egon Willighagen wrote: On Thu, Sep 30, 2010 at 5:08 PM, Adel Golovin golo...@ebi.ac.uk wrote: cdk-1.3.4 Good.