Adding a proton to a given Atom

Hi,

How do I connect a proton to a given atom in the molecule to create a protonated species using API.

Suppose I have a molecule and the index of the atom to which I want to connect the proton..

Thanks.

Hi, 

 

You want to add a charge to an atom or you want to attach an explicit H+  atom to the molecule?

Explicit H+ or add a Hydrogen and change charge to +1..either way

Then the following code should work:

 

MolAtom hydrogen = new MolAtom(1);


hydrogen.setCharge(1);


MolAtom bondTo = molecule.getAtom(index);


MolBond bond = new MolBond(bondTo, hydrogen);


molecule.add(hydrogen);


molecule.add(bond);


molecule.valenceCheck();

 

First, I create a new atom with atomic number 1, and I set it's charge to 1. Then I create a bond between the Hydrogen and the atom in the molecule I want to bond it. Finally, I add the new atom and the bond to the molecule and run valenceCheck to clean up the implicit Hydrogen count on the atom I added a new bond to.

Best regards, 

Peter