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[Cdk-commits] SF.net SVN: cdk: [7185] trunk/cdk/src/org/openscience/cdk
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From: <mig...@us...> - 2006-10-25 13:36:22
|
Revision: 7185
http://svn.sourceforge.net/cdk/?rev=7185&view=rev
Author: miguelrojasch
Date: 2006-10-25 06:35:55 -0700 (Wed, 25 Oct 2006)
Log Message:
-----------
classes which are qsar.descriptors.bond implements IBondDescriptor
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java
trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java
trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/ResonancePositiveChargeDescriptorTest.java
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -249,9 +249,7 @@
results[0][1]= new Double(((DoubleResult)descriptor2.calculate(positionC,atomContainer).getValue()).doubleValue());
/*2*/
BondPartialSigmaChargeDescriptor descriptor3 = new BondPartialSigmaChargeDescriptor();
- params[0] = new Integer(atomContainer.getBondNumber(bond));
- descriptor3.setParameters(params);
- results[0][2]= new Double(((DoubleResult)descriptor3.calculate(atomContainer).getValue()).doubleValue());
+ results[0][2]= new Double(((DoubleResult)descriptor3.calculate(bond, atomContainer).getValue()).doubleValue());
/*3*/
SigmaElectronegativityDescriptor descriptor4 = new SigmaElectronegativityDescriptor();
results[0][3]= new Double(((DoubleResult)descriptor4.calculate(positionX, atomContainer).getValue()).doubleValue());
@@ -260,9 +258,7 @@
results[0][4]= new Double(((DoubleResult)descriptor5.calculate(positionX, atomContainer).getValue()).doubleValue());
/*5*/
ResonancePositiveChargeDescriptor descriptor6 = new ResonancePositiveChargeDescriptor();
- params[0] = new Integer(atomContainer.getBondNumber(bond));
- descriptor6.setParameters(params);
- DoubleArrayResult dar = ((DoubleArrayResult)descriptor6.calculate(atomContainer).getValue());
+ DoubleArrayResult dar = ((DoubleArrayResult)descriptor6.calculate(bond, atomContainer).getValue());
double datT = (dar.get(0)+dar.get(1))/2;
results[0][5] = new Double(datT);
@@ -271,24 +267,24 @@
}
return results;
}
- /**
- * Gets the parameterNames attribute of the IPAtomicDescriptor object
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "targetPosition";
- return params;
- }
- /**
- * Gets the parameterType attribute of the IPAtomicDescriptor object
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- return new Integer(0);
- }
+ /**
+ * Gets the parameterNames attribute of the IPAtomicDescriptor object.
+ *
+ * @return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ return new String[0];
+ }
+
+
+ /**
+ * Gets the parameterType attribute of the IPAtomicDescriptor object.
+ *
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
+ */
+ public Object getParameterType(String name) {
+ return null;
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -27,12 +27,13 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
+import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* The calculation of bond-pi Partial charge is calculated
@@ -60,9 +61,8 @@
* @cdk.dictref qsar-descriptors:bondPartialPiCharge
* @see PartialPiChargeDescriptor
*/
-public class BondPartialPiChargeDescriptor implements IMolecularDescriptor {
+public class BondPartialPiChargeDescriptor implements IBondDescriptor {
- private int bondPosition = 0;
private PartialPiChargeDescriptor descriptor;
@@ -88,34 +88,21 @@
"The Chemistry Development Kit");
}
-
/**
- * Sets the parameters attribute of the BondPartialPiChargeDescriptor object
- *
- *@param params The new parameters value
- *@exception CDKException Description of the Exception
+ * This descriptor does have any parameter.
*/
public void setParameters(Object[] params) throws CDKException {
- if (params.length > 2) {
- throw new CDKException("BondPartialPiChargeDescriptor only expects two parameter");
- }
- if (!(params[0] instanceof Integer)) {
- throw new CDKException("The parameter 1 must be of type Integer");
- }
- bondPosition = ((Integer) params[0]).intValue();
}
/**
- * Gets the parameters attribute of the BondPartialPiChargeDescriptor object
+ * Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
*
*@return The parameters value
+ * @see #setParameters
*/
public Object[] getParameters() {
- // return the parameters as used for the descriptor calculation
- Object[] params = new Object[1];
- params[0] = new Integer(bondPosition);
- return params;
+ return new Object[0];
}
@@ -127,8 +114,8 @@
*@return return the sigma electronegativity
*@exception CDKException Possible Exceptions
*/
- public DescriptorValue calculate(IAtomContainer ac) throws CDKException {
- IAtom[] atoms = BondManipulator.getAtomArray(ac.getBond(bondPosition));
+ public DescriptorValue calculate(IBond bond, IAtomContainer ac) throws CDKException {
+ IAtom[] atoms = BondManipulator.getAtomArray(bond);
double[] results = new double[2];
Integer[] params = new Integer[1];
@@ -143,30 +130,24 @@
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result));
}
+ /**
+ * Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.
+ *
+ * @return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ return new String[0];
+ }
- /**
- * Gets the parameterNames attribute of the BondPartialPiChargeDescriptor
- * object
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "bondPosition";
- return params;
- }
-
- /**
- * Gets the parameterType attribute of the BondPartialPiChargeDescriptor
- * object
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- // since both params are of Integer type, we don't need to check
- return new Integer(0);
- }
+ /**
+ * Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
+ *
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
+ */
+ public Object getParameterType(String name) {
+ return null;
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -28,12 +28,13 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
+import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* The calculation of bond-sigma Partial charge is calculated
@@ -61,9 +62,8 @@
* @cdk.dictref qsar-descriptors:bondPartialSigmaCharge
* @see PartialSigmaChargeDescriptor
*/
-public class BondPartialSigmaChargeDescriptor implements IMolecularDescriptor {
+public class BondPartialSigmaChargeDescriptor implements IBondDescriptor {
- private int bondPosition = 0;
private PartialSigmaChargeDescriptor descriptor;
@@ -89,34 +89,21 @@
"The Chemistry Development Kit");
}
-
/**
- * Sets the parameters attribute of the BondPartialSigmaChargeDescriptor object
- *
- *@param params The new parameters value
- *@exception CDKException Description of the Exception
+ * This descriptor does have any parameter.
*/
public void setParameters(Object[] params) throws CDKException {
- if (params.length > 2) {
- throw new CDKException("BondPartialSigmaChargeDescriptor only expects two parameter");
- }
- if (!(params[0] instanceof Integer)) {
- throw new CDKException("The parameter 1 must be of type Integer");
- }
- bondPosition = ((Integer) params[0]).intValue();
}
/**
- * Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object
+ * Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
*
*@return The parameters value
+ * @see #setParameters
*/
public Object[] getParameters() {
- // return the parameters as used for the descriptor calculation
- Object[] params = new Object[1];
- params[0] = new Integer(bondPosition);
- return params;
+ return new Object[0];
}
@@ -128,9 +115,9 @@
*@return return the sigma electronegativity
*@exception CDKException Possible Exceptions
*/
- public DescriptorValue calculate(IAtomContainer ac) throws CDKException {
+ public DescriptorValue calculate(IBond bond, IAtomContainer ac) throws CDKException {
Molecule mol = new Molecule(ac);
- IAtom[] atoms = BondManipulator.getAtomArray(mol.getBond(bondPosition));
+ IAtom[] atoms = BondManipulator.getAtomArray(bond);
double[] results = new double[2];
Integer[] params = new Integer[1];
@@ -145,30 +132,24 @@
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result));
}
+ /**
+ * Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
+ *
+ * @return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ return new String[0];
+ }
- /**
- * Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor
- * object
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "bondPosition";
- return params;
- }
-
- /**
- * Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor
- * object
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- // since both params are of Integer type, we don't need to check
- return new Integer(0);
- }
+ /**
+ * Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
+ *
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
+ */
+ public Object getParameterType(String name) {
+ return null;
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -27,9 +27,10 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.manipulator.BondManipulator;
@@ -60,9 +61,8 @@
* @see org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
* @see org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
*/
-public class BondPartialTChargeDescriptor implements IMolecularDescriptor {
+public class BondPartialTChargeDescriptor implements IBondDescriptor {
- private int bondPosition = 0;
private PartialTChargePEOEDescriptor descriptor;
@@ -88,37 +88,22 @@
"The Chemistry Development Kit");
}
-
/**
- * Sets the parameters attribute of the BondPartialTChargeDescriptor object
- *
- *@param params The new parameters value
- *@exception CDKException Description of the Exception
+ * This descriptor does have any parameter.
*/
public void setParameters(Object[] params) throws CDKException {
- if(params.length > 1) {
- throw new CDKException("BondPartialTChargeDescriptor only expects one parameter");
- }
- if (!(params[0] instanceof Integer)) {
- throw new CDKException("The parameter 1 must be of type Integer");
- }
- bondPosition = ((Integer) params[0]).intValue();
}
/**
- * Gets the parameters attribute of the BondPartialTChargeDescriptor object
+ * Gets the parameters attribute of the BondPartialTChargeDescriptor object.
*
*@return The parameters value
+ * @see #setParameters
*/
public Object[] getParameters() {
- // return the parameters as used for the descriptor calculation
- Object[] params = new Object[1];
- params[0] = new Integer(bondPosition);
- return params;
+ return new Object[0];
}
-
-
/**
* The method calculates the bond total Partial charge of a given bond
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
@@ -127,8 +112,8 @@
*@return return the sigma electronegativity
*@exception CDKException Possible Exceptions
*/
- public DescriptorValue calculate(IAtomContainer ac) throws CDKException {
- IAtom[] atoms = BondManipulator.getAtomArray(ac.getBond(bondPosition));
+ public DescriptorValue calculate(IBond bond, IAtomContainer ac) throws CDKException {
+ IAtom[] atoms = BondManipulator.getAtomArray(bond);
double[] results = new double[2];
Integer[] params = new Integer[1];
@@ -141,31 +126,24 @@
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result));
}
-
-
- /**
- * Gets the parameterNames attribute of the BondPartialTChargeDescriptor
- * object
+ /**
+ * Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.
*
- *@return The parameterNames value
+ * @return The parameterNames value
*/
public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "bondPosition";
- return params;
+ return new String[0];
}
/**
- * Gets the parameterType attribute of the BondPartialTChargeDescriptor
- * object
+ * Gets the parameterType attribute of the BondPartialTChargeDescriptor object.
*
- *@param name Description of the Parameter
- *@return The parameterType value
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
*/
public Object getParameterType(String name) {
- // since both params are of Integer type, we don't need to check
- return new Integer(0);
+ return null;
}
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -27,9 +27,10 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.manipulator.BondManipulator;
@@ -59,9 +60,8 @@
* @cdk.dictref qsar-descriptors:bondSigmaElectronegativity
* @see SigmaElectronegativityDescriptor
*/
-public class BondSigmaElectronegativityDescriptor implements IMolecularDescriptor {
+public class BondSigmaElectronegativityDescriptor implements IBondDescriptor {
- private int bondPosition = 0;
private SigmaElectronegativityDescriptor descriptor;
@@ -87,37 +87,22 @@
"The Chemistry Development Kit");
}
-
/**
- * Sets the parameters attribute of the BondSigmaElectronegativityDescriptor object
- *
- *@param params The new parameters value
- *@exception CDKException Description of the Exception
+ * This descriptor does have any parameter.
*/
public void setParameters(Object[] params) throws CDKException {
- if (params.length > 1) {
- throw new CDKException("BondSigmaElectronegativityDescriptor only expects two parameter");
- }
- if (!(params[0] instanceof Integer)) {
- throw new CDKException("The parameter 1 must be of type Integer");
- }
- bondPosition = ((Integer) params[0]).intValue();
}
/**
- * Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object
+ * Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.
*
*@return The parameters value
+ * @see #setParameters
*/
public Object[] getParameters() {
- // return the parameters as used for the descriptor calculation
- Object[] params = new Object[1];
- params[0] = new Integer(bondPosition);
- return params;
+ return new Object[0];
}
-
-
/**
* The method calculates the sigma electronegativity of a given bond
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
@@ -126,9 +111,9 @@
*@return return the sigma electronegativity
*@exception CDKException Possible Exceptions
*/
- public DescriptorValue calculate(IAtomContainer ac) throws CDKException {
+ public DescriptorValue calculate(IBond bond, IAtomContainer ac) throws CDKException {
- IAtom[] atoms = BondManipulator.getAtomArray(ac.getBond(bondPosition));
+ IAtom[] atoms = BondManipulator.getAtomArray(bond);
double[] results = new double[2];
Integer[] params = new Integer[1];
@@ -142,31 +127,24 @@
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result));
}
-
-
- /**
- * Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor
- * object
+ /**
+ * Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.
*
- *@return The parameterNames value
+ * @return The parameterNames value
*/
public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "bondPosition";
- return params;
+ return new String[0];
}
/**
- * Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor
- * object
+ * Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.
*
- *@param name Description of the Parameter
- *@return The parameterType value
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
*/
public Object getParameterType(String name) {
- // since both params are of Integer type, we don't need to check
- return new Integer(0);
+ return null;
}
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -229,9 +229,7 @@
/* */
ResonancePositiveChargeDescriptor descriptor5 = new ResonancePositiveChargeDescriptor();
- params[0] = new Integer(atomContainer.getBondNumber(bond));
- descriptor5.setParameters(params);
- DoubleArrayResult dar = ((DoubleArrayResult)descriptor5.calculate(atomContainer).getValue());
+ DoubleArrayResult dar = ((DoubleArrayResult)descriptor5.calculate(bond, atomContainer).getValue());
results[0][4] = new Double(dar.get(0));
results[0][5] = new Double(dar.get(1));
@@ -241,25 +239,24 @@
}
return results;
}
-
- /**
- * Gets the parameterNames attribute of the IPBondDescriptor object
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "set";
- return params;
- }
- /**
- * Gets the parameterType attribute of the IPBondDescriptor object
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- return new Integer(0);
- }
+ /**
+ * Gets the parameterNames attribute of the IPBondDescriptor object.
+ *
+ * @return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ return new String[0];
+ }
+
+
+ /**
+ * Gets the parameterType attribute of the IPBondDescriptor object.
+ *
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
+ */
+ public Object getParameterType(String name) {
+ return null;
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -25,7 +25,6 @@
package org.openscience.cdk.qsar.descriptors.bond;
import java.util.ArrayList;
-import java.util.Iterator;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.charges.GasteigerPEPEPartialCharges;
@@ -33,26 +32,23 @@
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReactionSet;
-import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.reaction.type.BreakingBondReaction;
-import org.openscience.cdk.smiles.SmilesGenerator;
-import org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.tools.StructureResonanceGenerator;
-import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* <p>The calculation of Resonance stabilization of a positive charge of an heavy
@@ -79,9 +75,8 @@
* @cdk.dictref qsar-descriptors:resonancePositiveCharge
* @see GasteigerPEPEPartialCharges
*/
-public class ResonancePositiveChargeDescriptor implements IMolecularDescriptor {
+public class ResonancePositiveChargeDescriptor implements IBondDescriptor {
- private int bondPosition = 0;
private PiElectronegativityDescriptor pielectronegativity = null;
@@ -108,33 +103,20 @@
/**
- * Sets the parameters attribute of the ResonancePositiveChargeDescriptor
- * object
- *
- *@param params Bond position
- *@exception CDKException Description of the Exception
+ * This descriptor does have any parameter.
*/
public void setParameters(Object[] params) throws CDKException {
- if (params.length > 1) {
- throw new CDKException("ResonancePositiveChargeDescriptor only expects one parameter");
- }
- if (!(params[0] instanceof Integer)) {
- throw new CDKException("The parameter 1 must be of type Integer");
- }
- bondPosition = ((Integer) params[0]).intValue();
}
/**
- * Gets the parameters attribute of the ResonancePositiveChargeDescriptor object
+ * Gets the parameters attribute of the VdWRadiusDescriptor object.
*
*@return The parameters value
+ * @see #setParameters
*/
public Object[] getParameters() {
- // return the parameters as used for the descriptor calculation
- Object[] params = new Object[1];
- params[0] = new Integer(bondPosition);
- return params;
+ return new Object[0];
}
@@ -148,7 +130,10 @@
* which belong to the bond.
*@exception CDKException Possible Exceptions
*/
- public DescriptorValue calculate(IAtomContainer acI) throws CDKException {
+ public DescriptorValue calculate(IBond bond, IAtomContainer acI) throws CDKException {
+
+ cleanFlagReactiveCenter((IMolecule) acI);
+
DoubleArrayResult dar = new DoubleArrayResult(2);
IAtomContainer ac;
try {
@@ -156,42 +141,39 @@
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IAtomContainer!", e);
}
- ArrayList result1 = new ArrayList();
+
+ ArrayList result1 = new ArrayList();
ArrayList distance1 = new ArrayList();
ArrayList result2 = new ArrayList();
ArrayList distance2 = new ArrayList();
- IAtom[] atoms = BondManipulator.getAtomArray(ac.getBond(bondPosition));
-
- /* RESTRICTION: only possible to break H or doble bonds*/
-// if(ac.getBond(bondPosition).getOrder() < 2)
-// if(!atoms[0].getSymbol().equals("H") && !atoms[1].getSymbol().equals("H")){
-// DoubleArrayResult dar = new DoubleArrayResult();
-// dar.add(0.0);dar.add(0.0);
-// System.out.println("return 0.0");
-// return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),dar);
-// }
+ IAtom atom0 = bond.getAtom(0);
+ int atomPos0 = acI.getAtomNumber(atom0);
+ IAtom atom1 = bond.getAtom(1);
+ int atomPos1 = acI.getAtomNumber(atom1);
+
+ ac.getAtom(atomPos0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ ac.getAtom(atomPos1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ ac.getBond(acI.getBondNumber(bond)).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+
/*break bond*/
- if(ac.getSingleElectronSum(atoms[0]) > 0 || ac.getSingleElectronSum(atoms[1]) > 0){
+ if(ac.getSingleElectronSum(atom0) > 0 || ac.getSingleElectronSum(atom1) > 0){
dar.add(0.0);
dar.add(0.0);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),dar);
}
+
BreakingBondReaction type = new BreakingBondReaction();
- atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);
- int atomPos0 = ac.getAtomNumber(atoms[0]);
- atoms[1].setFlag(CDKConstants.REACTIVE_CENTER,true);
- int atomPos1 = ac.getAtomNumber(atoms[1]);
- ac.getBond(bondPosition).setFlag(CDKConstants.REACTIVE_CENTER,true);
-
+
Object[] paramsR = {Boolean.TRUE};
type.setParameters(paramsR);
IMoleculeSet setOfReactants = ac.getBuilder().newMoleculeSet();
setOfReactants.addMolecule((IMolecule) ac);
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
-
+
/*search resonance for each product obtained. Only 2*/
for(int i = 0 ; i < 2; i++){
if(setOfReactions.getReaction(i) == null)
@@ -302,29 +284,36 @@
}
- /**
- * Gets the parameterNames attribute of the ResonancePositiveChargeDescriptor
- * object
- *
- *@return The parameterNames value
- */
- public String[] getParameterNames() {
- String[] params = new String[1];
- params[0] = "bondPosition";
- return params;
- }
+ /**
+ * Gets the parameterNames attribute of the ResonancePositiveChargeDescriptor object.
+ *
+ * @return The parameterNames value
+ */
+ public String[] getParameterNames() {
+ return new String[0];
+ }
+
+ /**
+ * Gets the parameterType attribute of the ResonancePositiveChargeDescriptor object.
+ *
+ * @param name Description of the Parameter
+ * @return An Object of class equal to that of the parameter being requested
+ */
+ public Object getParameterType(String name) {
+ return null;
+ }
/**
- * Gets the parameterType attribute of the ResonancePositiveChargeDescriptor
- * object
- *
- *@param name Description of the Parameter
- *@return The parameterType value
- */
- public Object getParameterType(String name) {
- Integer[] object = {new Integer(0), new Integer(0)};
- return object;
- }
+ * clean the flags CDKConstants.REACTIVE_CENTER from the molecule
+ *
+ * @param mol
+ */
+ public void cleanFlagReactiveCenter(IMolecule molecule){
+ for(int j = 0 ; j < molecule.getAtomCount(); j++)
+ molecule.getAtom(j).setFlag(CDKConstants.REACTIVE_CENTER, false);
+ for(int j = 0 ; j < molecule.getBondCount(); j++)
+ molecule.getBond(j).setFlag(CDKConstants.REACTIVE_CENTER, false);
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -484,15 +484,15 @@
IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
double[] testResult = {0.0,0.25,0.0,0.0,0.0,0.25,0.0,0.0,0.0,0.0,0.0,0.0,}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
SmilesParser sp = new SmilesParser();
- Molecule mol = sp.parseSmiles("[H]C([H])=C([H])C([H])([H])C#[O+]");
- mol.addElectronContainer(new SingleElectron(mol.getAtom(9)));
- mol.addElectronContainer(new LonePair(mol.getAtom(9)));
+ Molecule mol = sp.parseSmiles("[H]=C=C=O");
+// mol.addElectronContainer(new SingleElectron(mol.getAtom(0)));
+ mol.addElectronContainer(new LonePair(mol.getAtom(3)));
Object[] object = {new Integer(6),new Boolean(false)};
descriptor.setParameters(object);
- for (int i = 3 ; i < 4 ; i++){
+ for (int i = 0 ; i < mol.getAtomCount() ; i++){
double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
-
+ System.out.println(mol.getAtom(i).getSymbol()+",result: "+result);
// if(testResult[i] == 0.0)
// assertTrue(result == 0.0);
// else {
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -25,9 +25,10 @@
import junit.framework.Test;
import junit.framework.TestSuite;
+
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
@@ -42,7 +43,7 @@
public class BondPartialPiChargeDescriptorTest extends CDKTestCase {
- private IMolecularDescriptor descriptor;
+ private IBondDescriptor descriptor;
/**
* Constructor for the BondPartialPiChargeDescriptorTest object
*
@@ -65,17 +66,13 @@
descriptor = new BondPartialPiChargeDescriptor() ;
double [] testResult={0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CF");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.01);
}
@@ -87,18 +84,13 @@
descriptor = new BondPartialPiChargeDescriptor() ;
double [] testResult={0.0022,0.0011,0.0011,0.0011,0.0011,0.0,0.0,0.0}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCBr");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.03);
}
}
@@ -109,15 +101,12 @@
descriptor = new BondPartialPiChargeDescriptor() ;
double testResult = 0.0 ; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Object[] params = {new Integer(0)};
- descriptor.setParameters(params);
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C(C)(C)CCI");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
- for (int i = 0 ; i < mol.getAtomCount() ; i++){
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ for (int i = 0 ; i < 6 ; i++){
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult,result,0.001);
}
}
@@ -127,7 +116,6 @@
public void testBondPiElectronegativityDescriptor_Allyl_mercaptan() throws ClassNotFoundException, CDKException, java.lang.Exception {
descriptor = new BondPartialPiChargeDescriptor() ;
double [] testResult={0.0006,0.0003,0.0003,0.0003,0.0003,0.0,0.0,0.0,0.0}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCS");
@@ -135,9 +123,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 9 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.03);
}
}
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -25,9 +25,10 @@
import junit.framework.Test;
import junit.framework.TestSuite;
+
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
@@ -42,7 +43,7 @@
public class BondPartialSigmaChargeDescriptorTest extends CDKTestCase {
- private IMolecularDescriptor descriptor;
+ private IBondDescriptor descriptor;
public BondPartialSigmaChargeDescriptorTest() {
descriptor = new BondPartialSigmaChargeDescriptor() ;
@@ -57,7 +58,6 @@
public void testBondSigmaElectronegativityDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.3323,0.0218 };/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[2];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CF");
@@ -65,10 +65,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- params[1] = new Integer(6);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.01);
}
@@ -80,17 +77,12 @@
public void testBondSigmaElectronegativityDescriptor_Methyl_chloride() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.2137,0.0075};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[2];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CCl");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- params[1] = new Integer(6);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.05);
}
}
@@ -100,19 +92,13 @@
public void testBondSigmaElectronegativityDescriptor_Allyl_bromide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0265,0.1268,0.1872,0.1564,0.1564,0.1347,0.0013,0.0013}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[2];
-
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCBr");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- params[1] = new Integer(6);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.03);
}
}
@@ -122,15 +108,12 @@
public void testBondSigmaElectronegativityDescriptor_Isopentyl_iodide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double testResult = 0.0165 ; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Object[] params = {new Integer(0)};
- descriptor.setParameters(params);
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C(C)(C)CCI");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(0),mol).getValue()).doubleValue();
assertEquals(testResult,result,0.001);
}
/**
@@ -139,7 +122,6 @@
public void testBondSigmaElectronegativityDescriptor_Ethoxy_ethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0864,0.4262,0.4262,0.0864,0.0662,0.0662,0.0662,0.0104,0.0104}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[2];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CCOCC");
@@ -147,10 +129,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- params[1] = new Integer(6);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.002);
}
}
@@ -160,18 +139,13 @@
public void testBondSigmaElectronegativityDescriptor_Ethanolamine() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.3463,0.0274,0.448,0.448,0.448}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[2];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("NCCO");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 5 ; i++){
- params[0] = new Integer(i);
- params[1] = new Integer(6);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.06);
}
}
@@ -180,7 +154,6 @@
*/
public void testBondSigmaElectronegativityDescriptor_Allyl_mercaptan() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0203,0.0921,0.1835,0.1569,0.3593,8.5917}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCS");
@@ -188,9 +161,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 4 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.005);
}
}
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -25,9 +25,10 @@
import junit.framework.Test;
import junit.framework.TestSuite;
+
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
@@ -43,7 +44,7 @@
public class BondPartialTChargeDescriptorTest extends CDKTestCase {
- private IMolecularDescriptor descriptor;
+ private IBondDescriptor descriptor;
/**
* Constructor for the BondPartialTChargeDescriptorTest object
*
@@ -65,8 +66,6 @@
public void testBondTElectronegativityDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.3323,0.0218 };/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CF");
@@ -77,9 +76,7 @@
lpcheck.newSaturate(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.01);
}
@@ -90,8 +87,6 @@
public void testBondTElectronegativityDescriptor_Allyl_bromide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0243,0.1279,0.1872,0.1553,0.1553,0.1358,0.0013,0.0013}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCBr");
HydrogenAdder hAdder = new HydrogenAdder();
@@ -100,9 +95,7 @@
lpcheck.newSaturate(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.035);
}
}
@@ -112,14 +105,11 @@
public void testBondTElectronegativityDescriptor_Isopentyl_iodide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double testResult = 0.0165 ; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Object[] params = {new Integer(0)};
- descriptor.setParameters(params);
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C(C)(C)CCI");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(0),mol).getValue()).doubleValue();
assertEquals(testResult,result,0.001);
}
/**
@@ -127,7 +117,6 @@
*/
public void testBondTElectronegativityDescriptor_Allyl_mercaptan() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0197,0.0924,0.1835,0.1566,0.1566,0.1412,0.0323,0.0323,0.2761}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCS");
@@ -135,9 +124,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 9 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.03);
}
}
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java 2006-10-25 13:35:55 UTC (rev 7185)
@@ -25,9 +25,10 @@
import junit.framework.Test;
import junit.framework.TestSuite;
+
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
@@ -43,7 +44,7 @@
public class BondSigmaElectronegativityDescriptorTest extends CDKTestCase {
- private IMolecularDescriptor descriptor;
+ private IBondDescriptor descriptor;
public BondSigmaElectronegativityDescriptorTest() {
descriptor = new BondSigmaElectronegativityDescriptor() ;
@@ -58,8 +59,6 @@
public void testBondSigmaElectronegativityDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={2.5882,1.1894};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CF");
HydrogenAdder hAdder = new HydrogenAdder();
@@ -68,9 +67,7 @@
lpcheck.newSaturate(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.01);
}
@@ -82,16 +79,12 @@
public void testBondSigmaElectronegativityDescriptor_Methyl_chloride() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={2.1612,0.8751};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CCl");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 2 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.05);
}
}
@@ -101,18 +94,13 @@
public void testBondSigmaElectronegativityDescriptor_Allyl_bromide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.2396,0.3635,1.7086,0.3635,0.338,0.574,0.969,0.969}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCBr");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.03);
}
}
@@ -122,15 +110,12 @@
public void testBondSigmaElectronegativityDescriptor_Isopentyl_iodide() throws ClassNotFoundException, CDKException, java.lang.Exception {
double testResult = 0.1482; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Object[] params = {new Integer(0)};
- descriptor.setParameters(params);
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C(C)(C)CCI");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(0),mol).getValue()).doubleValue();
assertEquals(testResult,result,0.001);
}
/**
@@ -139,17 +124,13 @@
public void testBondSigmaElectronegativityDescriptor_Ethoxy_ethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.7939,1.0715,1.0715,0.7939,0.2749,0.2749,0.2749,0.8796,0.8796}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("CCOCC");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 8 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.002);
}
}
@@ -159,17 +140,13 @@
public void testBondSigmaElectronegativityDescriptor_Ethanolamine() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.0074,0.3728,0.8547,0.2367,0.2367}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
-
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("NCCO");
HydrogenAdder hAdder = new HydrogenAdder();
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 5 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.06);
}
}
@@ -178,7 +155,6 @@
*/
public void testBondSigmaElectronegativityDescriptor_Allyl_mercaptan() throws ClassNotFoundException, CDKException, java.lang.Exception {
double [] testResult={0.1832,0.0143,0.5307,0.3593,0.3593,8.5917}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
- Integer[] params = new Integer[1];
SmilesParser sp = new SmilesParser();
Molecule mol = sp.parseSmiles("C=CCS");
@@ -186,9 +162,7 @@
hAdder.addExplicitHydrogensToSatisfyValency(mol);
for (int i = 0 ; i < 4 ; i++){
- params[0] = new Integer(i);
- descriptor.setParameters(params);
- double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue();
+ double result= ((DoubleResult)descriptor.calculate(mol.getBond(i),mol).getValue()).doubleValue();
assertEquals(testResult[i],result,0.005);
}
}
Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/ResonancePositiveChargeDescriptorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/ResonancePositiveChargeDescriptorTest.java 2006-10-25 13:29:22 UTC (rev 7184)
+++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/ResonancePositiveChargeDescriptor...
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