TopologyAnalyser fusedAromaticRings

Hi all,





I noticed the latest functionality of TopologyAnalyser which can be very handy however when I try run the following code:

Code:

Molecule mol = MolImporter.importMol("c1ccc2ccccc2c1", "smiles");       TopologyAnalyser tp = new TopologyAnalyser();       tp.setMolecule(mol);       int[][] aromRingSystems = tp.fusedAromaticRings();       for(int[] ringSystem : aromRingSystems) {          System.out.println(Arrays.toString(ringSystem));       }

I get an exception

Code:

Exception in thread "main" java.lang.NullPointerException    at chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(TopologyAnalyser.java:1613)    at chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(TopologyAnalyser.java:1592)

accoring to java doc the fusedAromaticRings() function should return the atom indexes of the fused aromatic rings in the molecule and for the case above the indexes for naphthalene ring system





I am using JChem 5.2 and Java 1.6





Oleg.

I cannot reproduce the error, the code works perfectly on my computer with version 5.2. These are the results:


[1, 2, 3, 8, 9, 0]


[4, 5, 6, 7, 8, 3]





I will ask my colleague to investigate this problem further.

It seems, that the problem is caused by the static importMol function, that returns null! We will investigate the issue, until that I suggest you use something like this:

Code:

BufferedInputStream is = new BufferedInputStream(new FileInputStream(args[0])); MolInputStream mis = new MolInputStream(is); MolImporter imp = new chemaxon.formats.MolImporter(mis); Molecule m; while ((m = imp.read()) != null) {     // your code here }

Hi Gyuri,





I tried your suggested code with the same naphthalene structure as before and still I get the same Exception

Code:

BufferedInputStream is = new BufferedInputStream(new FileInputStream(args[0]));       MolInputStream mis = new MolInputStream(is);       MolImporter molReader = new MolImporter(mis);       Molecule mol;       TopologyAnalyser tp = new TopologyAnalyser();       while((mol = molReader.read()) != null) {          tp.setMolecule(mol);           int[][] aromRingSystems = tp.fusedAromaticRings();           for(int[] ringSystem : aromRingSystems) {              System.out.println(Arrays.toString(ringSystem));           }       }        molReader.close();

the exception

Code:

Exception in thread "main" java.lang.NullPointerException    at chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(TopologyAnalyser.java:1613)    at chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(TopologyAnalyser.java:1592)

the exception is thrown at code line

Code:

int[][] aromRingSystems = tp.fusedAromaticRings();

the input file (args[0]) contains

Code:

c1ccc2ccccc2c1

I tried this on windows and linux with Java 1.6 and the same results.





Oleg.

I am sorry, I do not know what I mixed, but it is really the fault of TopologyAnalyser. It will be corrected in the next bugfix version.

It has been fixed, so the upcoming new release (5.5) will contain it.