Hi John,
seems like a good workaround. Thanks, will try it.
Best regards,
Christoph
--
Christoph Ruttkies
Group Bioinformatics & Mass Spectrometry
Leibniz Institute of Plant Biochemistry
Weinberg 3
06120 Halle, Germany
email: crutt...@ipb-halle.de
phone: +49-345-5582-1471
fax: +49-345-5582-1409
On 02/09/2016 10:42 AM, John M wrote:
> Hi Christoph, > > We don't currently have a SMARTS writer but if you want to
> write
aromatic SMILES you just need to tell the generator. It takes exactly
what you put it, so I can set the arom flags myself on a substrcture and
then create the SMILES: > > * IAtomContainer mol = new
AtomContainer(); > ** IAtom a1 = new Atom("C"); >
** a1.setImplicitHydrogenCount(0); > **
a1.setIsAromatic(true); > ** IAtom a2 = new Atom("O"); >
** a2.setImplicitHydrogenCount(0); > **
a2.setIsAromatic(true); > ** IAtom a3 = new Atom("C"); >
** a3.setImplicitHydrogenCount(0); > **
a3.setIsAromatic(true); > ** IBond b1 = new Bond(a1, a2);
> ** b1.setIsAromatic(true); > ** IBond b2 = new
Bond(a2, a3); > ** b2.setIsAromatic(true); > **
mol.addAtom(a1); > ** mol.addAtom(a2); > **
mol.addAtom(a3); > ** mol.addBond(b1); > **
mol.addBond(b2);** > ** SmilesGenerator smigen =
SmilesGenerator.generic() >
** .aromatic(); >
** String smi = smigen.create(mol);* > > > [c]o[c] > > > Note
you have to watch out for hydrogens! *[nH]1ccc2c1cccc2 *is indole but as
a SMARTS won't match Cn1ccc2c1cccc2. > > Thanks, > John > > Regards, >
John W May > john.wilkinson...@gmail.com
<mailto:john.wilkinson...@gmail.com> > > On 9 February 2016 at 08:42,
cruttkie <crutt...@ipb-halle.de <mailto:crutt...@ipb-halle.de>> wrote: >
> Hi, > > I am using CDK to find substructures within an
AtomContainer and write > them out as SMILES. The problem I have
with this workflow is related to > the loss of aromaticity
information when writing those substructure > SMILES in case the
substructure has matched within an aromatic ring for > example. >
> Is there a way to write out SMARTS instead of SMILES? If not, do
you > think it is a nice idea to adapt the SmilesGenerator to write
out SMARTS > including aromaticity information? > > Best
regards, > Christoph > > -- > > Christoph Ruttkies >
Group Bioinformatics & Mass Spectrometry > Leibniz Institute of
Plant Biochemistry > Weinberg 3 > 06120 Halle, Germany > >
email: crutt...@ipb-halle.de <mailto:crutt...@ipb-halle.de> > phone:
+49-345-5582-1471 <tel:%2B49-345-5582-1471> > fax:
+49-345-5582-1409 <tel:%2B49-345-5582-1409> > > >
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