Hi Rajarshi,
How about bringing CDK to read the molecules in the SDF file as with 3D
coordinates, but using the following Property:
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
IteratingSDFReader sdfr = new IteratingSDFReader(new FileReader(
pathToInputFile),bldr);
Properties prop = new Properties();
prop.setProperty("ForceReadAs3DCoordinates", "true");
PropertiesListener listener = new PropertiesListener(prop);
sdfr.addChemObjectIOListener(listener);
Regards,
On Fri, Feb 26, 2016, 3:00 PM Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> 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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