Change of bond representations by addExplicitHydrogens

 

Hi,

 

In order to standardize drawings, I perform these commands on all user structures:

 

mol.addExplicitHydrogens(0);

mol.implicitizeHydrogens(MolAtom.ALL_H & ~MolAtom.LONELY_H & ~MolAtom.ISOTOPE_H & ~MolAtom.CHARGED_H & ~MolAtom.RADICAL_H & ~MolAtom.MAPPED_H & ~MolAtom.HCONNECTED_H & ~MolAtom.CTSPECIFIC_H  );

 

I call addExplicitHydrogens(0) in case user draw already as implicit any H's I would prefer to be explicit.

 

However, addExplicitHydrogens(0) (and also Marvin) can change bond representation (see attached pdf).

 

Is there a way to prevent the change in bond representation?

 

Thank you for any advice.

 

Best regards,

 

Andrew

 

 

Hi,

Try calling mol.addExplicitHydrogens(0) with MoleculeGraph.OMIT_POSTCLEAN instead of 0.

http://www.chemaxon.com/marvin/help/developer/core/hydrogens.html

 

I hope that will work for you.

Yes, that works well!  Thank you!