From: <eg...@us...> - 2007-05-29 11:59:10
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Revision: 8339 http://svn.sourceforge.net/cdk/?rev=8339&view=rev Author: egonw Date: 2007-05-29 04:59:08 -0700 (Tue, 29 May 2007) Log Message: ----------- Added help on how to add hydrogens to ions Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/tools/HydrogenAdder.java Modified: trunk/cdk/src/org/openscience/cdk/tools/HydrogenAdder.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/tools/HydrogenAdder.java 2007-05-29 11:31:58 UTC (rev 8338) +++ trunk/cdk/src/org/openscience/cdk/tools/HydrogenAdder.java 2007-05-29 11:59:08 UTC (rev 8339) @@ -37,9 +37,12 @@ import java.util.HashMap; /** - * Provides methods for adding missing hydrogen atoms. + * Provides methods for adding missing hydrogen atoms. Make sure to correctly + * instantiate the HydrogenAdder for the type of molecule you are using. If + * your molecule has charges, or requires atomic hybridization information to + * derive, you need the parameterized constructor, as explained below. * - * <p>An example: + * <p>An example, for a neutral molecule: * <pre> * Molecule methane = new Molecule(); * Atom carbon = new Atom("C"); @@ -76,8 +79,13 @@ * </pre> * * <p>This class skips adding hydrogens for radicals, i.e IAtom's that - * have an associated ISingleAtom. + * have an associated ISingleAtom. Use the following code, if your molecule + * has charged atoms: * + * <pre> + * HydrogenAdder adder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker"); + * </pre> + * * @cdk.keyword hydrogen, adding * @cdk.module valencycheck * @cdk.bug 1575269 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |