How to determine if structural coordinates are zero

Hi,





I am creating a mol file from a SMILES.





MolHandler mh=new MolHandler();


mh.setMolecule("c1ccccc1Cl");


Molecule mole=mh.getMolecule();


//mole.clean(2,null)


String molFile=mole.toFormat("mol");





The mol file from this algorithm has no coordinates (all coordinates are zero) unless I call the clean method before I obtain the molFile. But I can only find this if I look into the mol file itself.





My question is: how can I programmatically tell whether the coordinates of the molecule object are zero or not?





Thank you.





Ben Li


Neurogen Corporation

Try this:

Code:

Molecule mole=mh.getMolecule(); if(mole.getDim() < 2) {     mole.clean(2,null); }

Hi,





I found solution for my own question.





int dim=mole.getDim();





if dim is zero, that means the melecule has not been cleaned in 2D or 3D.





Correct me if I am wrong.





Ben Li

Exactly.