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 want to store the BitSet BS1 representation of my mol in MySQL
> database?
>
> So that I can pull the BitSet representation of mol out of my mySQL
> database and compare my query molecule BitSet BS2 against BS1 as an
> initial screen before doing a more deep substrcuture search.
A possible way would be:
-create 16 columns in the mysql database of type bigint.
-create the 16 figures to save in here with a code similar to this:
/**
*Gets a BigIntger value representation of the Fingerprint bitset
*
* @param bs Fingerprint bitset
* @param num A number between 63 and 1023 representing one of the 16
sectors of the Fingerprint
* @return The BigInteger representations of the specified Fingerprint
sector
*/ public static BigInteger getBigIntegerValue(BitSet bs, int num) {
BigInteger bi = new BigInteger("0");
for (int i = 0; i < 64; i++) {
if (bs.get(i + (num * 64))) {
bi = bi.add(new BigInteger("2").pow(i));
}
}
return bi;
-write the values to db with a normal update/insert statement, using
getBigIntegerValue().longValue()
-so a search like select from where fingerprintcolumn1 &
searchfingerprint1=searchfingerprint1 and fingerprintcolumn2 ...
Stefan
>
>
> Anyone got ideas how to do this.
>
>
>
> CSL Bioinformatics Internet Pages at http://bioinformatics.csl.gov.uk
> ----------------------------------------------------------------------
> Robert Stones MRes, BSc Phone: +44 (0)1904 462675
> Higher Bioinformatics Specialist GTN: 5129 2675
> Central Science Laboratory Fax: +44 (0)1904 462111
> Sand Hutton Email: [EMAIL PROTECTED]
> York YO41 1LZ Web: http://www.csl.gov.uk
> ----------------------------------------------------------------------
>
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--
Stefan Kuhn BSc MA
IPB Halle
AG Bioinformatik & Massenspektrometrie
Weinberg 3
06120 Halle
http://www.ipb-halle.de http://msbi.bic-gh.de
[EMAIL PROTECTED] +49 (0) 345 5582 1474 Fax.+49 (0) 345 5582 1409
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