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[Cdk-commits] SF.net SVN: cdk: [10341] branches/miguelrojasch/charges/src
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From: <eg...@us...> - 2008-03-06 16:03:59
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Revision: 10341
http://cdk.svn.sourceforge.net/cdk/?rev=10341&view=rev
Author: egonw
Date: 2008-03-06 08:03:34 -0800 (Thu, 06 Mar 2008)
Log Message:
-----------
Applied patch 9901: 'All class in the charges module now implement IPartialChargeCalculator; some other code clean up'
Modified Paths:
--------------
branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/InductivePartialCharges.java
branches/miguelrojasch/charges/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java
branches/miguelrojasch/charges/src/test/org/openscience/cdk/charges/InductivePartialChargesTest.java
Modified: branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
===================================================================
--- branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2008-03-06 15:42:28 UTC (rev 10340)
+++ branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2008-03-06 16:03:34 UTC (rev 10341)
@@ -28,6 +28,7 @@
import java.util.List;
import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
@@ -65,7 +66,8 @@
* @cdk.keyword PEPE
* @see GasteigerMarsiliPartialCharges
*/
-public class GasteigerPEPEPartialCharges {
+public class GasteigerPEPEPartialCharges implements IPartialChargeCalculator {
+
/** max iterations */
private double MX_ITERATIONS = 8;
/** max number of resonance structures to be searched*/
@@ -96,9 +98,11 @@
*
*@param iters The new maxGasteigerIters value
*/
- public void setMaxGasteigerIters(double iters) {
- MX_ITERATIONS = iters;
+ public GasteigerPEPEPartialCharges(double iters, int numbReson) {
+ MX_ITERATIONS = iters;
+ MX_RESON = numbReson;
}
+
/**
* Sets the maximum resonance structures to be searched
*
@@ -117,7 +121,7 @@
*@return AtomContainer with partial charges
*@exception Exception Possible Exceptions
*/
- public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception {
+ public double[] calculatePartialCharges(IAtomContainer ac) throws Exception {
// logger.debug("smiles1: "+(new SmilesGenerator()).createSMILES((IMolecule) ac));
IAtomContainerSet setHI = null;
@@ -146,8 +150,10 @@
// logger.debug("isetTT: "+iSet.getAtomContainerCount());
}
if(iSet.getAtomContainerCount() < 2)
- return ac;
+ return new double[ac.getAtomCount()];
+ double[] finalCharges = new double[ac.getAtomCount()];
+
/*2: search whose atoms which don't keep their formal charge and set flags*/
double[][] sumCharges = new double[iSet.getAtomContainerCount()][ac.getAtomCount( )];
for(int i = 1; i < iSet.getAtomContainerCount() ; i++){
@@ -279,13 +285,14 @@
double chargeT = 0.0;
chargeT = charge + gasteigerFactors[k][STEP_SIZE * i + i + 5];
// logger.debug("i<|"+chargeT+"=c:" +charge + "+g: "+gasteigerFactors[k][STEP_SIZE * i + i + 5]);
- ac.getAtom(i).setCharge(chargeT);
+// ac.getAtom(i).setCharge(chargeT);
+ finalCharges[i] = chargeT;
}
}
}// iterations
- return ac;
+ return finalCharges;
}
/**
@@ -467,6 +474,7 @@
*
*@return STEP_SIZE
*/
+ @TestMethod("testGetStepSize")
public int getStepSize(){
return STEP_SIZE;
}
Modified: branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/InductivePartialCharges.java
===================================================================
--- branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/InductivePartialCharges.java 2008-03-06 15:42:28 UTC (rev 10340)
+++ branches/miguelrojasch/charges/src/main/org/openscience/cdk/charges/InductivePartialCharges.java 2008-03-06 16:03:34 UTC (rev 10341)
@@ -24,18 +24,24 @@
*/
package org.openscience.cdk.charges;
+import java.io.IOException;
+import java.util.Iterator;
+
+import javax.vecmath.Point3d;
+
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import javax.vecmath.Point3d;
-import java.io.IOException;
-
/**
* The calculation of the inductive partial atomic charges and equalization of
* effective electronegativities is based on {@cdk.cite CHE03}.
@@ -49,7 +55,7 @@
* @cdk.keyword electronegativity
*/
@TestClass("org.openscience.cdk.charges.InductivePartialChargesTest")
-public class InductivePartialCharges {
+public class InductivePartialCharges implements IPartialChargeCalculator {
private static double[] pauling;
private IsotopeFactory ifac = null;
@@ -85,14 +91,17 @@
*@exception Exception Description of the Exception
*/
@TestMethod("testInductivePartialCharges")
- public IAtomContainer assignInductivePartialCharges(IAtomContainer ac) throws Exception {
+ public double[] calculatePartialCharges(IAtomContainer ac) throws Exception {
if (factory == null) {
factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt",
ac.getBuilder());
}
+ if (ifac == null) {
+ ifac = IsotopeFactory.getInstance(ac.getBuilder());
+ }
int stepsLimit = 9;
- org.openscience.cdk.interfaces.IAtom[] atoms = AtomContainerManipulator.getAtomArray(ac);
+ IAtom[] atoms = AtomContainerManipulator.getAtomArray(ac);
double[] pChInch = new double[atoms.length * (stepsLimit + 1)];
double[] ElEn = new double[atoms.length * (stepsLimit + 1)];
double[] pCh = new double[atoms.length * (stepsLimit + 1)];
@@ -117,7 +126,13 @@
//logger.debug("DONE step " + s + ", atom " + atoms[a].getSymbol() + ", ch " + tmp1 + ", ee " + tmp2);
}
}
- return ac;
+ double[] finalCharges = new double[atoms.length];
+ double[] effectiveEnegs = new double[atoms.length];
+ for (int a = 0; a < atoms.length; a++) {
+ finalCharges[a] = pCh[a + (9 * atoms.length)]; // 9, because that's the last s in above
+ effectiveEnegs[a] = ElEn[a + (9 * atoms.length)];
+ }
+ return finalCharges;
}
@@ -131,64 +146,59 @@
*@exception Exception Description of the Exception
*/
@TestMethod("testGetPaulingElectronegativities")
- public double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified) throws CDKException {
+ public double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified) throws Exception {
+ if (ifac == null) {
+ ifac = IsotopeFactory.getInstance(ac.getBuilder());
+ }
double[] paulingElectronegativities = new double[ac.getAtomCount()];
IElement element = null;
String symbol = null;
int atomicNumber = 0;
- try {
- ifac = IsotopeFactory.getInstance(ac.getBuilder());
- for (int i = 0; i < ac.getAtomCount(); i++) {
- IAtom atom = ac.getAtom(i);
- symbol = ac.getAtom(i).getSymbol();
- element = ifac.getElement(symbol);
- atomicNumber = element.getAtomicNumber();
- if (modified) {
- if (symbol.equals("Cl")) {
- paulingElectronegativities[i] = 3.28;
- } else if (symbol.equals("Br")) {
- paulingElectronegativities[i] = 3.13;
- } else if (symbol.equals("I")) {
- paulingElectronegativities[i] = 2.93;
- } else if (symbol.equals("H")) {
- paulingElectronegativities[i] = 2.10;
- } else if (symbol.equals("C")) {
- if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
- // Csp3
- paulingElectronegativities[i] = 2.20;
- } else if (ac.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
- paulingElectronegativities[i] = 2.31;
- } else {
- paulingElectronegativities[i] = 3.15;
- }
- } else if (symbol.equals("O")) {
- if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
- // Osp3
- paulingElectronegativities[i] = 3.20;
- } else if (ac.getMaximumBondOrder(atom) != IBond.Order.SINGLE) {
- paulingElectronegativities[i] = 4.34;
- }
- } else if (symbol.equals("Si")) {
- paulingElectronegativities[i] = 1.99;
- } else if (symbol.equals("S")) {
- paulingElectronegativities[i] = 2.74;
- } else if (symbol.equals("N")) {
- paulingElectronegativities[i] = 2.59;
- } else {
- paulingElectronegativities[i] = pauling[atomicNumber];
- }
+ for (int i = 0; i < ac.getAtomCount(); i++) {
+ IAtom atom = ac.getAtom(i);
+ symbol = ac.getAtom(i).getSymbol();
+ element = ifac.getElement(symbol);
+ atomicNumber = element.getAtomicNumber();
+ if (modified) {
+ if (symbol.equals("Cl")) {
+ paulingElectronegativities[i] = 3.28;
+ } else if (symbol.equals("Br")) {
+ paulingElectronegativities[i] = 3.13;
+ } else if (symbol.equals("I")) {
+ paulingElectronegativities[i] = 2.93;
+ } else if (symbol.equals("H")) {
+ paulingElectronegativities[i] = 2.10;
+ } else if (symbol.equals("C")) {
+ if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
+ // Csp3
+ paulingElectronegativities[i] = 2.20;
+ } else if (ac.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
+ paulingElectronegativities[i] = 2.31;
} else {
- paulingElectronegativities[i] = pauling[atomicNumber];
+ paulingElectronegativities[i] = 3.15;
}
+ } else if (symbol.equals("O")) {
+ if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
+ // Osp3
+ paulingElectronegativities[i] = 3.20;
+ } else if (ac.getMaximumBondOrder(atom) != IBond.Order.SINGLE) {
+ paulingElectronegativities[i] = 4.34;
+ }
+ } else if (symbol.equals("Si")) {
+ paulingElectronegativities[i] = 1.99;
+ } else if (symbol.equals("S")) {
+ paulingElectronegativities[i] = 2.74;
+ } else if (symbol.equals("N")) {
+ paulingElectronegativities[i] = 2.59;
+ } else {
+ paulingElectronegativities[i] = pauling[atomicNumber];
}
- return paulingElectronegativities;
- } catch (Exception ex1) {
- logger.debug(ex1);
- throw new CDKException("Problems with IsotopeFactory due to " + ex1.toString(), ex1);
+ } else {
+ paulingElectronegativities[i] = pauling[atomicNumber];
+ }
}
- }
-
-
+ return paulingElectronegativities;
+ }
/**
* Gets the atomicSoftnessCore attribute of the InductivePartialCharges object
@@ -199,11 +209,16 @@
*@exception CDKException Description of the Exception
*/
// this method returns the result of the core of the equation of atomic softness
- // that can be used for qsar descriptors and during the iterative calculation
+ // that can be used for QSAR descriptors and during the iterative calculation
// of effective electronegativity
@TestMethod("testGetAtomicSoftness")
public double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition) throws CDKException {
- org.openscience.cdk.interfaces.IAtom target = null;
+ if (factory == null) {
+ factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt",
+ ac.getBuilder());
+ }
+
+ IAtom target = null;
double core = 0;
double radiusTarget = 0;
target = ac.getAtom(atomPosition);
@@ -225,7 +240,7 @@
throw new CDKException("Problems with AtomTypeFactory due to " + ex1.toString());
}
- java.util.Iterator atoms = ac.atoms();
+ Iterator<IAtom> atoms = ac.atoms();
while (atoms.hasNext()) {
IAtom atom = (IAtom)atoms.next();
if (!target.equals(atom)) {
@@ -375,7 +390,7 @@
*@param atom2 second atom
*@return squared distance between the 2 atoms
*/
- private double calculateSquaredDistanceBetweenTwoAtoms(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2) {
+ private double calculateSquaredDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2) {
double distance = 0;
double tmp = 0;
Point3d firstPoint = atom1.getPoint3d();
Modified: branches/miguelrojasch/charges/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java
===================================================================
--- branches/miguelrojasch/charges/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java 2008-03-06 15:42:28 UTC (rev 10340)
+++ branches/miguelrojasch/charges/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java 2008-03-06 16:03:34 UTC (rev 10341)
@@ -128,9 +128,9 @@
throw new CDKException("The parameter must be of type Integer");
maxResonStruc = (Integer) params[2];
}
+ pepe = new GasteigerPEPEPartialCharges(maxIterations, maxResonStruc);
}
-
/**
* Gets the parameters attribute of the PartialPiChargeDescriptor object
*
@@ -164,14 +164,10 @@
lpcheck.saturate(ac);
}
if (!isCachedAtomContainer(ac)) {
- if(maxIterations != -1)
- pepe.setMaxGasteigerIters(maxIterations);
- if(maxResonStruc != -1)
- pepe.setMaxResoStruc(maxResonStruc);
try {
for (int i=0; i<ac.getAtomCount(); i++)
ac.getAtom(i).setCharge(0.0);
- pepe.assignGasteigerPiPartialCharges(ac, true);
+ pepe.calculatePartialCharges(ac);
for (int i=0; i<ac.getAtomCount(); i++) {
// assume same order, so mol.getAtom(i) == ac.getAtom(i)
cacheDescriptorValue(ac.getAtom(i), ac, new DoubleResult(ac.getAtom(i).getCharge()));
@@ -181,7 +177,13 @@
}
}
return getCachedDescriptorValue(atom) != null
- ? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), getCachedDescriptorValue(atom))
+ ? new DescriptorValue(
+ getSpecification(),
+ getParameterNames(),
+ getParameters(),
+ getCachedDescriptorValue(atom),
+ new String[] {"piCharge"}
+ )
: null;
}
Modified: branches/miguelrojasch/charges/src/test/org/openscience/cdk/charges/InductivePartialChargesTest.java
===================================================================
--- branches/miguelrojasch/charges/src/test/org/openscience/cdk/charges/InductivePartialChargesTest.java 2008-03-06 15:42:28 UTC (rev 10340)
+++ branches/miguelrojasch/charges/src/test/org/openscience/cdk/charges/InductivePartialChargesTest.java 2008-03-06 16:03:34 UTC (rev 10341)
@@ -25,22 +25,20 @@
package org.openscience.cdk.charges;
+import javax.vecmath.Point3d;
+
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
-import org.openscience.cdk.charges.InductivePartialCharges;
+import org.openscience.cdk.NewCDKTestCase;
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.NewCDKTestCase;
-import javax.vecmath.Point3d;
-import java.io.IOException;
-
/**
* TestSuite that runs a test for the MMFF94PartialCharges.
*
@@ -89,7 +87,17 @@
*/
@Test
public void testInductivePartialCharges() throws java.lang.Exception {
- double [] testResult={0.197,-0.492,0.051,0.099,0.099};
+ double [] testResult={0.197,-0.492,0.051,0.099,0.099};
+ Molecule mol = create3DMolecule();
+ InductivePartialCharges ipc = new InductivePartialCharges();
+ double[] charges = ipc.calculatePartialCharges(mol);
+ for (int i = 0; i < mol.getAtomCount(); i++) {
+ Assert.assertEquals(testResult[i], charges[i], 0.1);
+ //logger.debug("CHARGE AT " + ac.getAtomAt(i).getSymbol() + " " + ac.getAtomAt(i).getProperty("MMFF94charge"));
+ }
+ }
+
+ private Molecule create3DMolecule() {
Point3d c_coord=new Point3d(1.392, 0.0, 0.0);
Point3d f_coord=new Point3d(0.0, 0.0, 0.0);
Point3d h1_coord=new Point3d(1.7439615035767404, 1.0558845107302222, 0.0);
@@ -122,19 +130,13 @@
mol.addBond(0, 2, IBond.Order.SINGLE); // 1
mol.addBond(0, 3, IBond.Order.SINGLE); // 1
mol.addBond(0, 4, IBond.Order.SINGLE); // 1
- InductivePartialCharges ipc = new InductivePartialCharges();
- ipc.assignInductivePartialCharges(mol);
- for (int i = 0; i < mol.getAtomCount(); i++) {
- Assert.assertEquals(testResult[i], ((Double)mol.getAtom(i).getProperty("InductivePartialCharge")).doubleValue(), 0.1);
- //logger.debug("CHARGE AT " + ac.getAtomAt(i).getSymbol() + " " + ac.getAtomAt(i).getProperty("MMFF94charge"));
- }
+ return mol;
}
@Test
public void testGetPaulingElectronegativities() throws Exception, ClassNotFoundException {
InductivePartialCharges ipc = new InductivePartialCharges();
double[] eneg = ipc.getPaulingElectronegativities(mol, true);
- long[] expected = {};
Assert.assertEquals("Error in C electronegativity", 2.20, eneg[0], 0.01);
Assert.assertEquals("Error in Cl electronegativity", 3.28, eneg[1], 0.01);
Assert.assertEquals("Error in Br electronegativity", 3.13, eneg[2], 0.01);
@@ -143,9 +145,10 @@
}
@Test
- public void testGetAtomicSoftness() throws IOException, ClassNotFoundException, CDKException {
+ public void testGetAtomicSoftness() throws Exception {
InductivePartialCharges ipc = new InductivePartialCharges();
- double softness = ipc.getAtomicSoftnessCore(mol, 0);
+ Molecule mol = create3DMolecule();
+ ipc.getAtomicSoftnessCore(mol, 0);
Assert.fail("Not validated - need known values");
}
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