org.openscience.cdk.tools

Class CDKHydrogenAdder

java.lang.Object

org.openscience.cdk.tools.CDKHydrogenAdder

public class CDKHydrogenAdder
extends Object

Adds implicit hydrogens based on atom type definitions. The class assumes that CDK atom types are already detected. A full code example is:

   IAtomContainer methane = new AtomContainer();
   IAtom carbon = new Atom("C");
   methane.addAtom(carbon);
   CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(methane.getNewBuilder());
   for (IAtom atom : methane.atoms) {
     IAtomType type = matcher.findMatchingAtomType(methane, atom);
     AtomTypeManipulator.configure(atom, type);
   }
   CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(methane.getNewBuilder());
   adder.addImplicitHydrogens(methane);
 

If you want to add the hydrogens to a specific atom only, use this example:

   IAtomContainer ethane = new AtomContainer();
   IAtom carbon1 = new Atom("C");
   IAtom carbon2 = new Atom("C");
   ethane.addAtom(carbon1);
   ethane.addAtom(carbon2);
   CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(ethane.getNewBuilder());
   IAtomType type = matcher.findMatchingAtomType(ethane, carbon1);
   AtomTypeManipulator.configure(carbon1, type);
   CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(ethane.getNewBuilder());
   adder.addImplicitHydrogens(ethane, carbon1);
 

Author:

egonw

Source code:

master

Belongs to CDK module:

valencycheck

Method Summary

Modifier and Type	Method and Description
void	addImplicitHydrogens(IAtomContainer container) Sets implicit hydrogen counts for all atoms in the given IAtomContainer.
void	addImplicitHydrogens(IAtomContainer container, IAtom atom) Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
static CDKHydrogenAdder	getInstance(IChemObjectBuilder builder)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static CDKHydrogenAdder getInstance(IChemObjectBuilder builder)

addImplicitHydrogens

public void addImplicitHydrogens(IAtomContainer container)
                          throws CDKException

Sets implicit hydrogen counts for all atoms in the given IAtomContainer.

Parameters:

container - The molecule to which H's will be added

Throws:

CDKException - Throws if insufficient information is present

Keywords:

hydrogens, adding

addImplicitHydrogens

public void addImplicitHydrogens(IAtomContainer container,
                                 IAtom atom)
                          throws CDKException

Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer. If the atom type is "X", then the atom is assigned zero implicit hydrogens.

Parameters:

container - The molecule to which H's will be added

atom - IAtom to set the implicit hydrogen count for

Throws:

CDKException - Throws if insufficient information is present