Hi everybody,
I want to select atoms graphically, save that atoms
(something like atom[i] = selected...) and use them for further
calculations within my code. Primarily I need to know which of the
selected atoms are bonded together (something like isBond(atom1,
atom2)), the coordinates of the atoms and other atoms which are bonded
to this atoms. I have no idea how to do this...
I´m using Jmol jmol-10.9.76 and the CdkJmolAdapter. What I did so far is:
I read in a SDF File ,
eval the String "select none;set picking atom;set display selected;";
select some atoms by clicking.
I know I can get the coordinates of the SELECTED atoms like this:
Vector atomInfo = (Vector)viewer.getProperty("object", "atomList",
"selected");
for(int i = 0; i< atomInfo.size(); i++){
int x = (Integer) atomInfo.elementAt(i);
coord = viewer.getAtomPoint3f(x);
}
I can also get the mol file viewer.getProperty("String",
"extractModel","selected");
But how can I get the atoms or ask something like "aBond(atomList[1],
atomList[2])?".And can I save these selected atoms in a "model" so that
I can convert them into a CDK AtomContainer?
I tried to get the selected BitSet, but getSelectedSet is private, also
SelectionManager or ModelManager (I had a look how the bonds and atoms
are extracted for "modelExtract"), so I´m not allowed to use them.
Kind regards,
Tina
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