in my CrystalFrame code, I have to rebond the atoms lying in the "bond box". So far, I use the n(n-1) rebonding method but I would like to use your bew method. However I can't find your enumDelta(...) method you are talking about hier below (in b6 or head?). Could you give more information?
Fabian
On Fri, 2003-05-23 at 09:02, Miguel wrote:
Egon et al,
To solve the "rebonding" problem I built a prototype of a binary space
partitioning tree to hold the points. This is an effecient data structure
which provides access to points which are "near" other points.
It has not yet been integrated into cdk/jmol, but is a standalone prototype.
In our case, the BSP tree divides the 3-space into little blocks. You can
then use an iterator to enumerate all the points within those blocks.
The API is currently
Enumeration enumDelta(Point3D center, double delta)
This enumerator is returns all the points that are within the cube defined
by:
center.x +/- delta
center.y +/- delta
center.z +/- delta
Two points
1) this is a cube, not a sphere
2) because of way the data structure works, some points outside
this cube are returned also ... basically the contents of all
little boxes defined by the bsp tree.
It would be easy for me to make another variant of this iterator which
restricts to all the points that are within the sphere. But this may not
be worth it if we are going to turn around and do some more distance
calculations with the result.
Questions:
Does the auto-bonding distance depend upon the types of the atoms involved?
*Should* it depend upon the types of the atoms involved?
Gracias,
Miguel
-------------------------------------------------------
This SF.net email is sponsored by: ObjectStore.
If flattening out C++ or Java code to make your application fit in a
relational database is painful, don't do it! Check out ObjectStore.
Now part of Progress Software. http://www.objectstore.net/sourceforge
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
|
-- Fabian Dortu <[EMAIL PROTECTED]> |
signature.asc
Description: This is a digitally signed message part
