I see.Thank you for clarifying that.
On Sat, Feb 27, 2016, 8:15 AM Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> 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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