Martin,
Following John's comments, I've realized you might consider writing SMARTS
via SmartsHelper.toSmarts() method from ambit2-smarts package (takes
QueryAtomContainer )
http://ambit.sourceforge.net/AMBIT2-LIBS/ambit2-smarts/apidocs/ambit2/smarts/SmartsHelper.html#toSmarts(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer)
Regards,
Nina
On 2 December 2014 at 21:47, John May <john.wilkinson...@gmail.com> wrote:
> Just to clarify you can write SMILES in CDK you’re writing SMILES and then
> interpreting this as SMARTS. CDK doesn’t have the ability to write a
> SMARTS. As well as hydrogens you may also have trouble with aromaticity,
> charges, and isotopes.
>
> c(c[cH])c[cH]
>
>
> Is probably better as [#6]([#6][#6])[#6][#6].
>
> The reason you’re having trouble in CDK 1.5 is SMILES IO now correctly
> handles the valence.
>
> Anyways, There are a couple of solutions
>
> 1) reset the hydrogen counts to default (i.e atom typing) this will work
> for your examples but will also mean you would lose aromaticity flags (i.e.
> the example above isn’t a ring) and this wouldn’t fix nitrogens which also
> have H displayed when aromatic. I would not recommend this.
> 2) set all hydrogen counts to 0 (not null!) before generating the SMILES
> you may also want to do charge and mass. Simply loop over the MCS and set
> the implicitH count to 0. removeHydrogens has no effect because they’re not
> explicit -
> http://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/
> .
> 3) after parsing the SMILES as SMARTS, traverse the expression tree of
> each atom and replace the And(<OtherSmartsAtom>, HydrogenCount) with
> <OtherSmartsAtom>.
> 4) load the SMILES as a SMILES and do a normal subgraph match opposed to
> SMARTS.
>
> Also
> - make sure you use the new SMSD (not part of CDK) the CDK packages are
> quite old
> - avoid using the DefaultChemObjectBuilder and use SilentChemObjectBuilder
> (the naming is the wrong way round but actually Silent is better as it
> doesn’t fire off events).
> - you’re generating canonical SMILES when this isn’t needed use
> SmilesGenerator.generic().aromatic() when creating the SmilesGenerator.
>
> J
>
> On Dec 2, 2014, at 11:04 AM, Martin Gütlein <guetl...@posteo.de> wrote:
>
> Hi,
>
> any help with this issue would be very much appreciated,
>
> Kind regards,
> Martin
>
> -------- Originalnachricht --------
> Betreff: Re: how to print SMARTS pattern without hydrogens
> Datum: 02.12.2014 12:00
> On 30 September 2014 at 09:30, Martin Guetlein
> <martin.guetl...@googlemail.com> wrote:
>
> Hi,
>
> I am currently migrating from cdk1.4 to 1.5. I am mining the maximum
> common subgraph of two compounds and then print the resulting fragment
> as SMARTS. This is working in 1.4, however in 1.5 the SmilesGenerator
> is adding unwanted Hydrogens. How can I get rid of the Hydrogens?
> See example below.
> See also
> https://www.mail-archive.com/cdk-user@lists.sourceforge.net/msg02597.html
>
> Thanks and kind regards,
> Martin
>
> The following code prints "mcs: c(c[cH])c[cH]" instead of "mcs: ccccc"
> [[
> SmilesParser sp = new
> SmilesParser(DefaultChemObjectBuilder.getInstance());
> IAtomContainer mol1 = sp.parseSmiles("c1ccccc1NC");
> IAtomContainer mol2 = sp.parseSmiles("c1cccnc1");
> org.openscience.cdk.smsd.Isomorphism mcsFinder = new
> org.openscience.cdk.smsd.Isomorphism(
> org.openscience.cdk.smsd.interfaces.Algorithm.DEFAULT, true);
> mcsFinder.init(mol1, mol2, true, true);
> mcsFinder.setChemFilters(true, true, true);
>
> mol1 = mcsFinder.getReactantMolecule();
> IAtomContainer mcsmolecule =
> DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class,
> mol1);
> List<IAtom> atomsToBeRemoved = new ArrayList<IAtom>();
> for (IAtom atom : mcsmolecule.atoms())
> {
> int index = mcsmolecule.getAtomNumber(atom);
> if (!mcsFinder.getFirstMapping().containsKey(index))
> atomsToBeRemoved.add(atom);
> }
> for (IAtom atom : atomsToBeRemoved)
> mcsmolecule.removeAtomAndConnectedElectronContainers(atom);
>
> // has no effect
> // mcsmolecule = AtomContainerManipulator.removeHydrogens(mcsmolecule);
>
> SmilesGenerator g = new SmilesGenerator().aromatic();
> System.out.println("mcs: " + g.create(mcsmolecule));
> ]]
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 8442 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> guetl...@informatik.uni-freiburg.de
>
>
>
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