On Wednesday 20 June 2007 04:00, Rajarshi Guha wrote:
> On Jun 19, 2007, at 11:17 AM, Robert Stones wrote:
> > I have a molecule mol = sp.parseSmiles("CCC");
> >
> > Fingerprinter fingerprinter = new Fingerprinter();
> >
> > Using CDK fingerprinter.getFingerprint(mol);
> >
> > Java BitSet repres
On Jun 19, 2007, at 11:17 AM, Robert Stones wrote:
> I have a molecule mol = sp.parseSmiles("CCC");
>
> Fingerprinter fingerprinter = new Fingerprinter();
>
> Using CDK fingerprinter.getFingerprint(mol);
>
> Java BitSet representation:
> BitSet BS1 = fingerprinter.getFingerprint(mol);
>
> I no
On Tuesday 19 June 2007 17:17, Robert Stones wrote:
> I have a molecule mol = sp.parseSmiles("CCC");
>
> Fingerprinter fingerprinter = new Fingerprinter();
>
> Using CDK fingerprinter.getFingerprint(mol);
>
> Java BitSet representation:
> BitSet BS1 = fingerprinter.getFingerprint(mol);
>
> I now
I have a molecule mol = sp.parseSmiles("CCC");
Fingerprinter fingerprinter = new Fingerprinter();
Using CDK fingerprinter.getFingerprint(mol);
Java BitSet representation:
BitSet BS1 = fingerprinter.getFingerprint(mol);
I now want to store the BitSet BS1 representation of my mol in MySQL
dat
--- Robert Stones <[EMAIL PROTECTED]> wrote:
> Sorry - yes thats what I am interested in a
> bitstring stored in a
> database for every molecule that can be searched
> first before doing
> substructure searching.
If you're interested in databases and the Web, you
might be interested in Rails. I
Sorry - yes thats what I am interested in a bitstring stored in a
database for every molecule that can be searched first before doing
substructure searching.
Thanks
>I think the idea is to have the bit strings precalculated for a set
>of molecules. Then rather than doing a substructure search
Stefan Kuhn <[EMAIL PROTECTED]> wrote:
> On Monday 11 June 2007 15:34, Rajarshi Guha wrote:
> > On Jun 11, 2007, at 9:20 AM, sushil ronghe wrote:
> > > Therefore a fast bistring comparision to rule out most
> > > structures (e.g. has it got an aromatic ring represented in the
> > > bitstring) b
On Monday 11 June 2007 15:34, Rajarshi Guha wrote:
> On Jun 11, 2007, at 9:20 AM, sushil ronghe wrote:
> > Therefore a fast bistring comparision to rule out most
> > structures (e.g. has it got an aromatic ring represented in the
> > bitstring) before the more deep substructure matching would be ve
On Jun 11, 2007, at 9:20 AM, sushil ronghe wrote:
> Therefore a fast bistring comparision to rule out most
> structures (e.g. has it got an aromatic ring represented in the
> bitstring) before the more deep substructure matching would be very
> beneficial.
>
> This is absolutely fantastic idea.
>
there any libraries to convert mol structures into a
bitstring representation.
Fingerprinter class is solution for this question.
But here i you are missing something
if the query is a substructure of any molecule in the
database.
Substructure searching is the only way out for this.
I a
Right - and the respective cdk.test.FingerPrinterTest, which shows how
to use it.
Cheers,
Chris
Stefan Kuhn wrote:
>> Is there anything in CDK or any other open source libraries out there ?
> See the Fingerprinter class.
>> Regards
>>
>> CSL Bioinformatics Internet Pages at http://bioinformatics
> Is there anything in CDK or any other open source libraries out there ?
See the Fingerprinter class.
>
> Regards
>
> CSL Bioinformatics Internet Pages at http://bioinformatics.csl.gov.uk
> --
> Robert Stones MRes, BSc
Hi
I was wondering are there any libraries to convert mol structures into a
bitstring representation.
I am thinking for trying to match a query mol against a database of
molecules to find if the query is a substructure of any molecule in the
database.
The substructure CDK matching algorithm
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