Re: [Cdk-devel] NumericalSurface returns different results after rigid alignment

[Rajarshi G. <raj...@gm...>]

You're good! Stared at this for an hour last night and missed it :(

Yes, the else clause should be adding the atom index. With that the surface
areas are much more similar - 411.00944 vs 410.45645 - but not identical as
I would expect they should be.

You're probably right about the order of operations. Also probably should
look at Tesselate

On Mon, Feb 20, 2017 at 9:33 AM, John Mayfield <joh...@gm...>
wrote:

> Not tested but I think the problem is here: https://github.com/cdk/
> cdk/blob/master/descriptor/qsarmolecular/src/main/java/
> org/openscience/cdk/geometry/surface/NeighborList.java#L55-L61
>
> Shouldn't the else also add the atom to the list?
>
> A shorter, more efficient and less error prone idiom is:
>
> List<IAtom> atoms = this.boxes.get(key);
>> if (atoms == null)
>>   this.boxes.put(key, atoms = new ArrayList<>());
>> atoms.add(atom);
>
>
> Notice we do a single get, then iff the value was null we create a new one
> and add it. We always add the atom to the atoms array.
>
> I can see that some people may find the assignment in the put confusing
> (in C++ the put would do a copy so the atoms.add looks like a no-op).
>
> John
>
> On 20 February 2017 at 13:57, Rajarshi Guha <raj...@gm...>
> wrote:
>
>> Here's some sample code https://gist.github.com/r
>> ajarshi/86389392173191ee15cef7b76d994ae5 and the SD files are available
>> at https://www.dropbox.com/sh/xu548wx8brqx9z9/AABloecWNrSXAE
>> cwud7ZSV-Oa?dl=0
>>
>> Poking around I found our that the neighbor lists for a given atom differ
>> between the aligned and non-aligned cases.
>>
>> On Mon, Feb 20, 2017 at 4:59 AM, John Mayfield <
>> joh...@gm...> wrote:
>>
>>> Have you got the molecule/usage? My money is on either order of
>>> operations / Tesselate.java.
>>>
>>> John
>>>
>>> On 20 February 2017 at 02:54, Rajarshi Guha <raj...@gm...>
>>> wrote:
>>>
>>>> Hi, a user pointed out a bug in the CPSA descriptor that is generating
>>>> different results for the same molecule after a rigid alignment.
>>>>
>>>> It turns out that the bug arises due to NumericalSurface giving
>>>> different total surface area values for the molecule before alignment and
>>>> after alignment.
>>>>
>>>> I confirmed that the relative positions of the atoms are identical in
>>>> the two versions of the molecule (pairwise distance matrix is the same to
>>>> four decimal places).
>>>>
>>>> Does anybody have any immediate ideas about why a rigid alignment would
>>>> lead to a difference in the computed surface area?
>>>>
>>>> --
>>>> Rajarshi Guha | http://blog.rguha.net
>>>> NIH Center for Advancing Translational Science
>>>>
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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