One way out is to compute the approximate surface area described by Labute
(which is based on a lookup table). I have an implementation at
https://github.com/rajarshi/personal/blob/master/CDKPersonal/src/net/guha/apps/VSA.java
but will probably need some updating for the latest CDK
On Fri, Feb 26, 2016 at 2:59 PM, Zheng Shi <zs...@ualberta.ca> wrote:
> Thank you. If so, what APIs can I use in cdk to deal with this situation?
> That is to say, how can I calculate the surface for this kind of molecule
> with cdk? Thanks.
>
> On Thu, Feb 25, 2016 at 6:59 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
> wrote:
>
>> It's failing because it doesn't have 3d coordinates
>>
>> On Thu, Feb 25, 2016 at 6:47 PM, Zheng Shi <zs...@ualberta.ca> wrote:
>>
>>> Hi, all,
>>>
>>> I'm using cdk to calculate numerical surface. I use the following code,
>>> but it throws exception for some molecule. What's the problem? Does anyone
>>> have ideas for this? Thanks.
>>>
>>> Below is my code and an example molecule with such exception. Any
>>> suggestions? Thanks.
>>>
>>> IAtomcontainer container=...; //get from somewhere
>>> NumericalSurface ns = new NumericalSurface(container);
>>> ns.calculateSurface();
>>> double ASA = ns.getTotalSurfaceArea();
>>>
>>>
>>>
>>>
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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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