The NumericalSurface class requires 3D coordinates.
Labute (https://www.chemcomp.com/journal/vsadesc.htm) described an
approximation to the surface area using only connectivity. I thought this
had been included in the CDK.
Some older code to compute this can be found at
https://github.com/rajarshi/personal/blob/master/CDKPersonal/src/net/guha/apps/VSA.java
but will need to be updated for the latest version of the CDK
On Mon, Jan 18, 2016 at 5:39 PM, Zheng Shi <zs...@ualberta.ca> wrote:
> Hi, all,
>
> I'm trying to calculate the numerical surface for some molecules. I use
> the following code with CDK.
>
> NumericalSurface ns = new NumericalSurface(mol);
> ns.calculateSurface();
> double ASA = ns.getTotalSurfaceArea();
>
> For some molecules which don't have 3-D coordinates. how can I get the
> surface area? Below I provide two molecules, I can find ways to calculate
> surface for the first one as it has partial coordinates, but I don't know
> how to do for the second one. It seems the second one doesn't have any
> coordinates. Any ideas? Thanks.
>
>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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