I'm trying to add bonds explicitly to a structure loaded in .xyz format.
The structure intentionally has unrealistic atom positions.
The structure is loaded like so:
myAppConsole.execute("set autobond OFF");
myViewer.loadInline(molAsXyz);
The problem is that the viewer loads N atoms as N molecules, and each
molecule lists an atom count of zero:
# xyz:4
No comment.
C 3.952 2.132 3.339
C 0.321 1.781 2.229
C 0.490 1.193 2.953
C 2.701 1.473 0.464
// Java:final int nMols =
myViewer.getModelSet().getMolecules().length;for (int i = 0; i <
nMols; ++i) {
System.out.println(String.format("Mol %d - Atom count
%d",i,viewer.getModelSet().getMolecules()[i].atomCount));
}// output:// Mol 0 - Atom count 0// Mol 1 - Atom count 0// Mol
2 - Atom count 0// Mol 3 - Atom count 0
The viewer is displaying the four atoms in their correct positions.
How can I force the .xyz to load into a single molecule such that I may add
in bonds like so:
Bond[] bonds = new Bond[knownBondCount];// ...
bonds[i] = new Bond(atom1,atom2,1,(short)0,(short)0);// ...
JmolMolecule mol = myViewer.getModelSet().getMolecules()[0];for (int i
= 0; i < mol.atomCount; ++i) {
final Atom atom = (Atom)mol.nodes[i];
atom.setBonds(bonds); // of course the 'bonds' value passed
changes for each atom in reality.
}
Is there a format better suited for this purpose than .xyz?
David
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