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

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

Here's some sample code
https://gist.github.com/rajarshi/86389392173191ee15cef7b76d994ae5 and the
SD files are available at
https://www.dropbox.com/sh/xu548wx8brqx9z9/AABloecWNrSXAEcwud7ZSV-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