Egon,
I am glad that you are looking at this.
We need to work on it together, because there are still many things that I
do not understand about crystal cells.
- my terminology may be wrong
- it may be too specific to .pdb files
- I may be doing some things it incorrectly
But with your help we can get it cleaned up.
> I've tried to figure out how I can get a CDK Crystal object displayed in
> HEAD... What it does right now, in CDKJmolAdapter, is convert the
> fractional coordinates into cartesian coordinates using the
> cdk.geometry.CrystalGeometryTools...
We no longer need to convert the unit cell into cartesian coordinates.
It is best to keep the crystal cell as fractional coordinates. That way we
will be in a better position to show a 2x2 or MxN representation of the
unit cell.
> and then it shows atoms in the
> display... but 'set unitcell on' does not work yet because I need to put
> the unit cell info somewhere too...
Keep reading ...
> - - Did I do it right, to create cartesian coordinates, or does Jmol
> handle fractional coordinates internally too?
Jmol now knows how to handle fractional coordinates for the unitcell.
There are a set of new routines to handle crystal unit cells:
getNotionalUnitcell()
returns null or a float[6] which is the notional unitcell
This is the terminology that you were using in CDK.
getCrystalScaleMatrix()
returns null or a float[9] which is the 3x3 scale matrix
for converting cartesian to fractional coordinates.
This is essentially the three SCALEn records out of .pdb
If it is too specific to .PDB then we should change it and
make it more general.
getCrystalScaleTranslate()
This is null or a float[3]
It is the translation component that is used to translate
the orthogonal coordinates to the fractional coordinates.
This is the U component from the SCALEn records from .pdb
Again, if this is too specific to PDB then we should
generalize it.
> - - How should I set the unit cell info in CDKJmolAdapter?
Change the CDKJmolModelAdapter so that it implements
float[] getNotionalUnitcell(...) {
...
return new float[] {a, b, c, alpha, beta, gamma};
}
Q: What is the difference between "Notional Unit Cell" and "fractional
coordinates"?
> Egon
>
> - --
> [EMAIL PROTECTED]
> PhD on Molecular Representation in Chemometrics
> Nijmegen University
> http://www.cac.sci.kun.nl/people/egonw/
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