>
> Although this produces bit-fingerprints and not any String-representation
> of the signatures if I'm reading this correctly?
Yes but notice it also gives you the atom indexes, this is much more
powerful that just giving the String. We actually have a utility to get the
SMARTS for the atoms. Won't give you stereo but it's pretty easy to make it
do that if you were so inclined, would be easy to output stereo as SMILES
instead of SMARTS:
> SmilesParser smipar = new
> SmilesParser(SilentChemObjectBuilder.getInstance());
> IAtomContainer mol = smipar.parseSmiles("CCCCCC[C@H](C)CO");
> CircularFingerprinter fp = new
> CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6);
> fp.calculate(mol);
>
SmartsFragmentExtractor smafrag = new SmartsFragmentExtractor(mol);
for (int i = 0; i < fp.getFPCount(); i++)
> System.out.println(smafrag.generate(fp.getFP(i).atoms));
Result:
[CH3v4X4+0]
> [CH2v4X4+0]
> [CH2v4X4+0]
> [CH2v4X4+0]
> [CH2v4X4+0]
> [CH2v4X4+0]
> [CH1v4X4+0]
> [CH3v4X4+0]
> [CH2v4X4+0]
> [OH1v2X2+0]
> [CH3v4X4+0][CH2v4X4+0]
> [CH3v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]
> [CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0]
> [CH1v4X4+0][CH3v4X4+0]
> [CH1v4X4+0][CH2v4X4+0][OH1v2X2+0]
> [CH2v4X4+0][OH1v2X2+0]
> [CH3v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH3v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0]
> [CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0][OH1v2X2+0]
> [CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0][OH1v2X2+0]
> [CH3v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0]
>
> [CH3v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]
>
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0]
>
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0][OH1v2X2+0]
>
> [CH2v4X4+0][CH2v4X4+0][CH2v4X4+0][CH1v4X4+0]([CH3v4X4+0])[CH2v4X4+0][OH1v2X2+0]
However, I have done some experiments comparing the circular fingerprints
> of enantiomers and also diastereomers, and they turn out to have 1.0
> tanimoto scores.
> What am I doing wrong?
Unfortunately the way it was written you currently need 2D coordinates.
It's an easy fix if you want to submit the patch, just need to pull the
tetrahedral rubric out of the IStereoElements - note the IStereoElement's
are created automatically on 2D/3D.
SmilesParser smipar = new
> SmilesParser(SilentChemObjectBuilder.getInstance());
> IAtomContainer mol1 = smipar.parseSmiles("CCCCCC[C@H](C)CO");
> IAtomContainer mol2 = smipar.parseSmiles("CCCCCC[C@@H](C)CO");
> CircularFingerprinter fp = new
> CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6);
> System.out.println(Tanimoto.calculate(fp.getFingerprint(mol1),
> fp.getFingerprint(mol2)));
> // 1.0
> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
> sdg.generateCoordinates(mol1);
> sdg.generateCoordinates(mol2);
> System.out.println(Tanimoto.calculate(fp.getFingerprint(mol1),
> fp.getFingerprint(mol2)));
> // 0.77
On 21 July 2017 at 12:25, Christoph Steinbeck <
[email protected]> wrote:
> CircularFingerprinter.getBitFingerprint().asBitString().toString();
>
> or
>
> Integer.toString(CircularFingerprinter.getFP())
>
> Did not test this.
>
> Kind regards,
>
> Chris
>
>
> —
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> Phone Secretariat: +49-3641-948171
> http://orcid.org/0000-0001-6966-0814
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
> > On 21 Jul 02017, at 13:09, Staffan Arvidsson <
> [email protected]> wrote:
> >
> > OK thanks! Although this produces bit-fingerprints and not any
> String-representation of the signatures if I'm reading this correctly?
> Currently all our code requires the Signatures to be Strings. Would require
> a large rewrite to get this to work for us. Because the javadoc says that
> method getRawFingerprint is not correct so I should not use it? (Even
> though this would be something more like what we want)
> >
> > Best,
> > Staffan
> >
> > 2017-07-21 11:59 GMT+02:00 John Mayfield <[email protected]>:
> > Yes,
> >
> > Use the CircularFingerprinter, it encodes stereochemistry, the relevant
> method is CircularFingerprinter.getFP() which will give you the atoms
> involved and the hashed value. IIRC the first atom in the list is the
> 'root'.
> >
> > John
> >
> > On 21 July 2017 at 09:39, Staffan Arvidsson <[email protected]>
> wrote:
> > Hi all,
> >
> > I wonder if there is any way of producing atom signatures with
> stereoinformation? Currently we're using
> >
> > String signature = new AtomSignature(atom, height,
> molecule).toCanonicalString();
> >
> > to produce the signatures.
> >
> >
> > Best,
> > Staffan
> >
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