Daniel,
I would suppose you would need the set of vertex positions, vertex values,
and faces. Then you would need some sort of algorithm that would give you
the integration across a triangle that has three different values, one on
each vertex. Summing over all the faces would give you the integral.
You can use getProperty("isosurfaceInfo") to get all that:
$ x = getProperty("isosurfaceInfo")
$ print x.keys
haveQuads
id
polygonCount
polygons
vertexCount
vertexValues
vertices
but I don't know what exactly you would use to integrate each face. Is
there a standard way of doing that? If you do, then I'd be very happy to
add that to Jmol.
Bob Hanson
On Sat, Jun 23, 2012 at 8:04 AM, Daniel Aioanei <[email protected]> wrote:
> For a small molecule I can compute an electrostatic potential-mapped
> isosurface like this:
>
> isosurface <name> sasurface 1.4 map color range <min> <max>
> 'pymol-generated.dx' translucent .2
> zoom 40
>
> Once I have the surface, how can I compute the integral of an
> arbitrary function of the electrostatic potential on the surface
> accessible area? Needless to say, the integral should be independent
> of the color range chosen, and of the grid spacing chosen for the .dx
> file (as long as the spacing is fine enough).
>
> In particular, the function I would like to integrate is exp(-E_p *
> (k_B T) ^ {-1} * alpha), where alpha is a constant charge with unit of
> measurement e_c (the elementary positive charge), and E_p is the
> electrostatic potential from the .dx file (measured in k_B T / e_c).
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
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