I guess that'd work (at least you'd avoid the NPE) - but you still end up
with a flat molecule. So the final surface area would be incorrect
On Fri, Feb 26, 2016 at 6:36 PM, Yannick .Djoumbou <y.djoum...@gmail.com>
wrote:
> 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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>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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