Here's how you can convert the atom indices to a SMILES with stereo,
2.1-SNAPSHOT cleans up the stereo API avoids the cast and actually makes
this a lot easier, done quick and dirty here but you get the idea.
public static String toSmiles(CircularFingerprinter.FP fp,
IAtomContainer mol) throws CDKException
{
IAtomContainer part = mol.getBuilder().newAtomContainer();
Set<IAtom> aset = new HashSet<>();
for (int idx : fp.atoms) {
aset.add(mol.getAtom(idx));
part.addAtom(mol.getAtom(idx));
}
for (IBond bond : mol.bonds()) {
if (aset.contains(bond.getBegin()) &&
aset.contains(bond.getEnd()))
part.addBond(bond);
}
for (IStereoElement se : mol.stereoElements()) {
if (se instanceof ITetrahedralChirality) {
ITetrahedralChirality tc = (ITetrahedralChirality) se;
if (aset.contains(tc.getChiralAtom()) &&
aset.contains(tc.getLigands()[0]) &&
aset.contains(tc.getLigands()[1]) &&
aset.contains(tc.getLigands()[2]) &&
aset.contains(tc.getLigands()[3]))
part.addStereoElement(tc);
}
}
return SmilesGenerator.isomeric().create(part);
}
On 21 July 2017 at 13:12, John Mayfield <[email protected]> wrote:
> 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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>> >
>> >
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>>
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