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 ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
