[Cdk-commits] SF.net SVN: cdk:[12155] cdk/trunk/src/main/org/openscience/cdk/qsar/ descriptors/molecular/BCUTDescriptor.java

[<raj...@us...>]

Revision: 12155
          http://cdk.svn.sourceforge.net/cdk/?rev=12155&view=rev
Author:   rajarshi
Date:     2008-09-03 21:17:20 +0000 (Wed, 03 Sep 2008)

Log Message:
-----------
Some code cleanup

Modified Paths:
--------------
    cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java

Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java	2008-09-03 21:11:11 UTC (rev 12154)
+++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java	2008-09-03 21:17:20 UTC (rev 12155)
@@ -29,7 +29,6 @@
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
-import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
 import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
 import org.openscience.cdk.charges.GasteigerPEPEPartialCharges;
 import org.openscience.cdk.charges.Polarizability;
@@ -37,9 +36,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.graph.PathTools;
 import org.openscience.cdk.graph.matrix.AdjacencyMatrix;
-import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.qsar.DescriptorSpecification;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.IMolecularDescriptor;
@@ -50,10 +47,7 @@
 import org.openscience.cdk.tools.LoggingTool;
 import org.openscience.cdk.tools.LonePairElectronChecker;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 
-import java.util.Iterator;
-
 /**
  * Eigenvalue based descriptor noted for its utility in chemical diversity.
  * Described by Pearlman et al. {@cdk.cite PEA99}.
@@ -316,13 +310,7 @@
 
         // add H's in case they're not present
         try {
-            CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
-            Iterator<IAtom> atoms = molecule.atoms().iterator();
-            while (atoms.hasNext()) {
-                IAtom atom = atoms.next();
-                IAtomType type = matcher.findMatchingAtomType(molecule, atom);
-                AtomTypeManipulator.configure(atom, type);
-            }
+            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);            
             CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(molecule.getBuilder());
             hAdder.addImplicitHydrogens(molecule);
             AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);


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