[MMTK] object or module for molecule-centered grid

Andrew D. Fant fant at pobox.com
Thu Mar 23 21:23:19 CET 2006

konrad.hinsen at cea.fr wrote:
> On 10.03.2006, at 21:00, Andrew D. Fant wrote:
>>     Is there code in MMTK, or has anyone written any, that will  take
>> a molecule,
>> orient it to the usual standards (center of gravity, aligned to 
>> principal
>> moments of inertia) and generate a uniformly-spaced set of grid 
>> points to
>> surround it?  I'll admit to being a novice, so I apologize if this  is
>> already in
> The first part is straightforward:
>     molecule.normalizeConfiguration()
> will do the alignment that you want to have. As for generating a 
> uniformly spaces set of grid points around the molecule, it all  depends
> on what exactly you need and what you want to do with it.  Here is one
> approach that should be fine:
>     from MMTK.Geometry import SCLattice
>     cell_size = 0.1*Units.nm
>     grid_size = 10  # 10 cells in each direction
>     grid_origin = -(grid_size/2) * cell_size
>     for point in SCLattice(cell_size, grid_size):
>         print point + origin
> You could also calculate the grid size as a function of 
> molecule.boundingBox(), for example.

   Thanks for the pointers. This is beginning to make sense to me now.  I do
have a follow-on question in 2 parts.

Are there any special routines to allow a set of points from that lattice to be
accessed as a single entity?  For example to treat the set of grid points that
are within the VdW radius of the nearest atom (plus or minus some reasonable
epsilon) as a "surface" that can be used for further computation.

Alternately, is there a good way to use the surface objects that are defined
elsewhere as the basis for a lattice as defined above?  Most of the interesting
things I am reading on molecular superposition seem to be happiest working on
grids/lattices approximating the steric boundaries.

Thanks again,

Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant at pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself

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