How to fuse() with good spacing but no reorientation?

Hi,

If I fuse() two molecules and then run a standardizer "clean" on the result, the fused structures are very close together .. but if I run a standardizer "clean:full" on the result, the fused structures show better spacing but they are now reoriented.  Is there a way to increase the spacing between fused moecules without reorienting the molecules?

Thanks for any advice,

Andrew

Hi,

Do you need a Java API solution to increase the spacing betweent the two fragments of the molecule?

Zsolt

Yes .. a Java API solution for increasing the spacing between any number of molecules that have been fuse()'d into the same molecule .. that would be very helpful!

Thanks.

Hi,

I think arrangeMolecules(..) is the API call you need. Fragment your molecule using molecule.findFrags(SelectionMolecule.class, type) then call arrangeMolecules on the fragments.

Eg:

MoleculeGraph[] frags = mol.findFrags(
                        SelectionMolecule.class, 
                        MoleculeGraph.FRAG_KEEPING_MULTICENTERS);


CleanUtil.arrangeMolecules(frags, 2, -1);

I hope this helps.

Works perfectly!  Thanks very much -- Andrew