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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