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[Cdk-commits] SF.net SVN: cdk: [11177] cdk/trunk/src
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From: <eg...@us...> - 2008-05-27 05:06:10
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Revision: 11177
http://cdk.svn.sourceforge.net/cdk/?rev=11177&view=rev
Author: egonw
Date: 2008-05-26 22:06:03 -0700 (Mon, 26 May 2008)
Log Message:
-----------
Partial rewrite to make use of IAtomType.Hybridization, but it seems not all atom types have proper hybrid info yet??
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java 2008-05-26 22:51:33 UTC (rev 11176)
+++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java 2008-05-27 05:06:03 UTC (rev 11177)
@@ -27,6 +27,7 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
@@ -157,67 +158,24 @@
@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer container) throws CDKException
{
- IAtomType atomType = findMatchingAtomType(container, atom);
-
- double bondOrderSum = container.getBondOrderSum(atom);
- Integer charge = atom.getFormalCharge() == CDKConstants.UNSET ? 0 : atom.getFormalCharge();
- Integer hcount = atom.getHydrogenCount() == CDKConstants.UNSET ? 0 : atom.getHydrogenCount();
- int valency = atomType.getValency();
- double nLonePair = (valency - ( hcount + bondOrderSum ) - charge) / 2;
-
- int hybridization = (int)nLonePair + ( hcount + container.getConnectedAtomsList(atom).size() );
-
- logger.debug("ATOM : bondOrderSum " + bondOrderSum + ", charge " + charge + ", hcount " + hcount +
- ", valency " + valency + ", nLonePair " + nLonePair + ", hybridization " + hybridization);
-
- int hybridizationCDK = 0;
- switch (hybridization)
- {
- case 2:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP1;break;
- case 3:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP2;break;
- case 4:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3;break;
- case 5:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D1;break;
- case 6:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D2;break;
- case 7:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D3;break;
- case 8:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D4;break;
- case 9:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D5;break;
- default:
- hybridizationCDK = CDKConstants.HYBRIDIZATION_UNSET;break;
+ IAtomType atomType = CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom);
+ if (atomType == null) {
+ return new DescriptorValue(
+ getSpecification(), getParameterNames(), getParameters(),
+ new IntegerResult((int)Double.NaN), // does that work??
+ new String[]{"hybr"}
+ );
}
-
- return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(hybridizationCDK));
+ int hybridizationCDK =
+ atomType.getHybridization() == null ? 0 : atomType.getHybridization().ordinal();
+
+ return new DescriptorValue(
+ getSpecification(), getParameterNames(), getParameters(),
+ new IntegerResult(hybridizationCDK),
+ new String[]{"hybr"}
+ );
}
-
-
- private IAtomType findMatchingAtomType(IAtomContainer container, org.openscience.cdk.interfaces.IAtom atom) throws CDKException
- {
- try {
- if(atomATF==null)
- atomATF = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/valency2_atomtypes.xml",
- container.getBuilder());
-
- // take atomtype for the given element...
- return atomATF.getAtomType(atom.getSymbol());
-
- } catch (Exception ex1)
- {
- logger.error(ex1.getMessage());
- logger.debug(ex1);
- throw new CDKException("Problems with AtomTypeFactory due to " + ex1.toString(), ex1);
- }
- }
-
-
-
/**
* Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
*
Modified: cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java 2008-05-26 22:51:33 UTC (rev 11176)
+++ cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java 2008-05-27 05:06:03 UTC (rev 11177)
@@ -29,13 +29,12 @@
import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
-import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.LonePairElectronChecker;
@@ -80,11 +79,11 @@
molecule.addBond(b1);
molecule.addBond(b2);
- assertEquals(CDKConstants.HYBRIDIZATION_SP2, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP2.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP2, ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP2.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP3, ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
}
/**
@@ -109,11 +108,11 @@
molecule.addBond(b1);
molecule.addBond(b2);
- assertEquals(CDKConstants.HYBRIDIZATION_SP1, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP1.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP1, ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP1.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP3, ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
}
/**
@@ -140,11 +139,11 @@
molecule.addBond(b1);
molecule.addBond(b2);
- assertEquals(CDKConstants.HYBRIDIZATION_SP2, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP2.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP3, ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(1),molecule).getValue()).intValue());
- assertEquals(CDKConstants.HYBRIDIZATION_SP3, ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(2),molecule).getValue()).intValue());
}
/**
@@ -171,7 +170,7 @@
molecule.addBond(b2);
molecule.addBond(b3);
- assertEquals(CDKConstants.HYBRIDIZATION_SP2, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP2.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
}
@@ -203,7 +202,7 @@
molecule.addBond(b3);
molecule.addBond(b4);
- assertEquals(CDKConstants.HYBRIDIZATION_SP3D2, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3D2.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
}
@@ -228,7 +227,7 @@
molecule.addBond(b1);
molecule.addBond(b2);
- assertEquals(CDKConstants.HYBRIDIZATION_SP3D1, ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
+ assertEquals(IAtomType.Hybridization.SP3D1.ordinal(), ((IntegerResult)descriptor.calculate(molecule.getAtom(0),molecule).getValue()).intValue());
}
/**
@@ -236,7 +235,11 @@
*/
public void testAtomHybridizationVSEPRDescriptorTest_7() throws ClassNotFoundException, CDKException, java.lang.Exception
{
- int[] testResult = {CDKConstants.HYBRIDIZATION_SP3,CDKConstants.HYBRIDIZATION_SP2,CDKConstants.HYBRIDIZATION_SP2};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
+ int[] testResult = {
+ IAtomType.Hybridization.SP3.ordinal(),
+ IAtomType.Hybridization.SP2.ordinal(),
+ IAtomType.Hybridization.SP2.ordinal()
+ }; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
AtomHybridizationVSEPRDescriptor descriptor = new AtomHybridizationVSEPRDescriptor();
@@ -257,7 +260,11 @@
*/
public void testAtomHybridizationVSEPRDescriptorTest_8() throws ClassNotFoundException, CDKException, java.lang.Exception
{
- int[] testResult = {CDKConstants.HYBRIDIZATION_SP2,CDKConstants.HYBRIDIZATION_SP2,CDKConstants.HYBRIDIZATION_SP3};
+ int[] testResult = {
+ IAtomType.Hybridization.SP2.ordinal(),
+ IAtomType.Hybridization.SP2.ordinal(),
+ IAtomType.Hybridization.SP3.ordinal()
+ };
AtomHybridizationVSEPRDescriptor descriptor = new AtomHybridizationVSEPRDescriptor();
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