Fabian, > 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? Well, as I worked on it more I changed the API.
It is no longer called enumDelta. Probably the call you want to use is either Bspt.enumSphere(Bspt.Tuple center, double radius) or Bspt.enumHemiSphere(Bspt.Tuple center, double radius) The hemisphere version will only return half of the points. This is good enough if you are going to iterate over all the atoms. If you don't want a sphere, then let me know. There is another iterator which is available. Look at the code in ChemFrame.java to see how the tree is constructed and how to use the iterators. I'll be glad to help. Send me more questions. Miguel > > 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]> -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Pe�a Primera 11-13 esc dcha 6B 37002 Salamanca Espa�a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- 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
