Dear Rajarshi,
Exception in thread "main" java.lang.NullPointerException
at
org.openscience.cdk.geometry.surface.NumericalSurface.calculateSurface(NumericalSurface.java:113)
at testSurface.main(testSurface.java:68)
lines 67 and 68 of testSurface.java:
surface = new NumericalSurface(container);
surface.calculateSurface();
About the molecule being flat or not:
The SD File I would like to deal with contains 2D structures
without hydrogen atoms.
The benzene.sdf file I provided in my first mail is the simplest
example I had that causes the problem.
Does the surface calculation depend on atom coordinates
or does it only depend on atom connectivity?
Best regards,
Jean-Marc Nuzillard
Message de Rajarshi Guha <rajarshi.g...@gmail.com>:
> The whole stack trace would be useful. Is this a flat molecule?
>
> On Tue, May 18, 2010 at 10:46 AM, JEAN MARC NUZILLARD
> <jm.nuzill...@univ-reims.fr> wrote:
>> Dear Egon,
>>
>> Message de Egon Willighagen <egon.willigha...@gmail.com>:
>>
>>> Dear Jean-Marc,
>>>
>>> On Mon, May 17, 2010 at 11:02 PM, JEAN MARC NUZILLARD
>>> <jm.nuzill...@univ-reims.fr> wrote:
>>>> The code generates an exception during the surface calculation
>>>> and I would like to know for
>>>> which reason and what could be done as a remedy.
>>>
>>> Can you give us the Exception too, please?
>>
>> Sure. The NullPointerException is thrown,
>> and the "Error in surface area calculation" message is displayed.
>> I have checked that the container is not empty and contains
>> the expected number of atoms.
>>
>> Jean-Marc Nuzillard
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>
>
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
>
------------------------------------------------------------------------------
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
