Hi,
Our Chemists pointed out that sometimes our chemical images were
incorrectly rendering stereo chemistry bonds when non were present.
Rather than always calling .setStereoElements() for our rendering code...
atomContainer.setStereoElements(
StereoElementFactory.using3DCoordinates(atomContainer)
.createAll());
I noticed we had to check if three dimensional points were present before
calling .setStereoElements()
if( checkHas3D( atomContainer ) ){
atomContainer.setStereoElements(
StereoElementFactory.using3DCoordinates(atomContainer)
.createAll());
}
private boolean checkHas3D( IAtomContainer atomContainer ) {
boolean has3D = false;
for( int i = 0 ; i < atomContainer.getAtomCount() ; i++ ){
IAtom atom = atomContainer.getAtom( i );
Point3d point3d = atom.getPoint3d();
if( ( null != point3d) && point3d.z != 0d ){
has3D = true;
break;
}
}
return has3D;
}
This cleaned up the image for our chemists. It seems that we should be
able to call .setStereoElements() and not have to worry about the 3D check
- it should just work.
Are we not using the API correctly or have we stumbled on a bug?
The issue was initially identified in version 1.5.11. Although we have
since upgraded to version 1.5.13 as I indicated separately, we have not
retested with the new version.
- steve
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