Hey guys, I have a general question to the working of the method getAtomNumber(). What are the criteria an atom is chosen in the IAtomContainer?
For example I have following test code: Created a AtomContainer from following smiles: [Z]O // in this case the [Z] is a placeholder for the link position of the fragment in the main substance So I take the Atom at index position 1 in the Fragment. When I print the Symbol it is the O. Now I want to get the Index in the complete substance and it is sure that O is in the substance present. I get the index -1 so I think the method cannot find the Atom. The complete substance I use for my test is CHEMBL501674. If I do getAtom(0) on the substance it returns an O Atom. So the general Question is, is it impossible to get the Atomposition in this way in the original substance with a fragment created from a smiles string? Or how does the method correctly work, on the documentation I was not able to find a detailed information and I had not the time to watch in the code, also I thought if it is the wrong way you can tell it me much more faster. I want to realise the idea of John to get the starting position of the fragment in the specific molecule on this way. Thanks for your help again. Cheers Niko ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
