Package org.openscience.cdk.tools
Class CDKHydrogenAdder
- java.lang.Object
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- org.openscience.cdk.tools.CDKHydrogenAdder
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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:
- main
- Belongs to CDK module:
- valencycheck
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Method Detail
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getInstance
public static CDKHydrogenAdder getInstance(IChemObjectBuilder builder)
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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
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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 addedatom
- IAtom to set the implicit hydrogen count for- Throws:
CDKException
- Throws if insufficient information is present
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