So the problem is in the exact mass - it is always null. I took a look at
the unit test for the descriptor and I see
IAtomContainer ac = (IAtomContainer) cList.get(0);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
After this code, the exact mass should be non-null, but in fact every atom
in the molecule has a null value for exact mass. This leads to the center
of mass being null and there for the final descriptor value is NaN
It looks like this is happening for all the LoB unit tests.
So the question is - why is exact mass null after atom typing? Or is there
a new way to configure the exact mass?
On Thu, Oct 23, 2014 at 6:03 PM, Zheng Shi <[email protected]> wrote:
> Here is an example of one molecule. The Z coordinate is not 0. But the
> result is still NaN.
>
> On Thu, Oct 23, 2014 at 6:43 AM, Rajarshi Guha <[email protected]>
> wrote:
>
>> As Yannick pointed out, toString() is not the right way to access the
>> values. But more importantly, it expects 3D coordinates. While it throws an
>> exception if 3D coordinates are not available, it might generate NaN if the
>> Z coordinate is set to 0 (flat molecule) or else if the covalent radius for
>> an element is not available. A reproducible example would be helpful
>>
>> On Tue, Oct 21, 2014 at 5:11 PM, Zheng Shi <[email protected]> wrote:
>>
>>> Hi,
>>>
>>> I have puzzles regarding calculating LengthOverBreadthDescriptors with
>>> cdk. When I use the class to calculate, I just get two "NaN""NaN" as the
>>> result. Why is it? I get confused. I use the following class. Why is it?
>>> Thanks for your help.
>>>
>>> LengthOverBreadthDescriptor le=new LengthOverBreadthDescriptor();
>>> String s=le.calculate(molecule).getValue().toString();
>>>
>>>
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>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>
>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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