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[Cdk-commits] SF.net SVN: cdk: [11367] cdk/trunk/src
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From: <mig...@us...> - 2008-06-16 12:56:54
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Revision: 11367
http://cdk.svn.sourceforge.net/cdk/?rev=11367&view=rev
Author: miguelrojasch
Date: 2008-06-16 05:56:03 -0700 (Mon, 16 Jun 2008)
Log Message:
-----------
Only the most intensively simulated isotopic peak per nominal mass have been considered and used for intensity correlation.
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/formula/rules/IsotopePatternRule.java
cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java
Modified: cdk/trunk/src/main/org/openscience/cdk/formula/rules/IsotopePatternRule.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/formula/rules/IsotopePatternRule.java 2008-06-16 11:14:45 UTC (rev 11366)
+++ cdk/trunk/src/main/org/openscience/cdk/formula/rules/IsotopePatternRule.java 2008-06-16 12:56:03 UTC (rev 11367)
@@ -24,6 +24,8 @@
package org.openscience.cdk.formula.rules;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
import org.openscience.cdk.exception.CDKException;
@@ -135,61 +137,75 @@
return score;
}
/**
- * Extract a score function looking for similarities between isotopes patterns
+ * Extract a score function looking for similarities between isotopes patterns.
+ * In this algorithm, only the most intensively simulated isotopic peak per nominal
+ * mass have been considered and used for intensity correlation.
*
* @param molecularFormulaSet The IMolecularFormulaSet with to compare the isotope pattern
* @return The score function value
*/
private double extractScore(IMolecularFormulaSet formulaSet) {
double score = 0.0;
- double scoreInt = 1.0;
- double ab1 = -0.1;// looking for the higher natural abundace of the isotope pattern
- for(int i = 0; i < pattern.size(); i++){
- double occurrence1 = ((Double)formulaSet.getMolecularFormula(i).getProperties().get("occurrence"));
- double ab = MolecularFormulaManipulator.getTotalNaturalAbundance(formulaSet.getMolecularFormula(i));
- ab *= occurrence1;
- if(ab > ab1)
- ab1 = ab;
- }
- boolean foundPeak = false;
- int i_initial = 0;
- for(IMolecularFormula molecularFormula: formulaSet.molecularFormulas()){
- double mass = MolecularFormulaManipulator.getTotalExactMass(molecularFormula);
- double occurrence = ((Double)molecularFormula.getProperties().get("occurrence"));
- double ab = MolecularFormulaManipulator.getTotalNaturalAbundance(molecularFormula)*occurrence;
- boolean foundMF = false;
+ String stringMF = MolecularFormulaManipulator.getString(formulaSet.getMolecularFormula(0));
+ IMolecularFormula molecularFormulaA = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(stringMF, formulaSet.getBuilder());
+ double massA = MolecularFormulaManipulator.getTotalExactMass(molecularFormulaA);
+ double windowsAccuracy = 0.4;
+ List<Double> inteExperimUnit = new ArrayList<Double>();
+ List<Double> intePatternUnit = new ArrayList<Double>();
+ for(int i = 1 ; i < 5 ; i++){
+ // looking highest intensity per nominal mass
+ double inteH = 0;
+ double massUnit = massA + i;
- ab = ab/ab1;
-
- for(int i = i_initial; i < pattern.size(); i++){
- double massS = pattern.get(i)[0];
- double abundS = pattern.get(i)[1]/100;
-
- if((mass-toleranceMass < massS)&(massS < mass + toleranceMass )){
- double maxS = 0.0;
- double minS = 0.0;
- if(ab > abundS){
- maxS = ab;
- minS = abundS;
- }else{
- maxS = abundS;
- minS = ab;
+ // around predicted
+ for(IMolecularFormula molecularFormula: formulaSet.molecularFormulas()){
+ double massS = MolecularFormulaManipulator.getTotalExactMass(molecularFormula);
+ if((massUnit-windowsAccuracy < massS)&(massS < massUnit + windowsAccuracy )){
+ double occurrence = ((Double)molecularFormula.getProperties().get("occurrence"));
+ double intensity = MolecularFormulaManipulator.getTotalNaturalAbundance(molecularFormula)*occurrence;
+ if(intensity > inteH){
+ inteH = intensity;
}
- scoreInt = scoreInt*( minS/ maxS);
- foundPeak = true;
- foundMF = true;
- i_initial = i + 1;
- break;
}
}
- if(!foundMF) // those mass that were not find gives negative score
- scoreInt = scoreInt*(1-ab);
+ if(inteH != 0){
+ intePatternUnit.add(inteH);
+ inteH = 0;
+ // around experimental
+ for(int j = 0; j < pattern.size(); j++){
+ double intensity = pattern.get(j)[1];
+ double massS = pattern.get(j)[0];
+ if((massUnit-windowsAccuracy < massS)&(massS < massUnit + windowsAccuracy )){
+ if(intensity > inteH){
+ inteH = intensity;
+ }
+ }
+ }
+ inteExperimUnit.add(inteH);
+
+ }
-
}
- if(foundPeak)
- score = scoreInt;
+
+ double sumN = 0.0;
+ for(int j = 0 ; j < intePatternUnit.size(); j++)
+ sumN += intePatternUnit.get(j)*inteExperimUnit.get(j);
+
+ double sumD = 0.0;
+ for(Iterator<Double> it = intePatternUnit.iterator(); it.hasNext();)
+ sumD += Math.pow(it.next(), 2);
+
+ double normalization = sumN/sumD;
+
+ if(sumN == 0)
+ return 0.0;
+
+ sumN = 0.0;
+ for(int j = 0 ; j < intePatternUnit.size(); j++)
+ sumN += Math.pow(intePatternUnit.get(j)*inteExperimUnit.get(j)/normalization,2);
+ score = (1-Math.pow(sumN/sumD,0.5));
+
return score;
}
Modified: cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java 2008-06-16 11:14:45 UTC (rev 11366)
+++ cdk/trunk/src/test/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java 2008-06-16 12:56:03 UTC (rev 11367)
@@ -122,35 +122,35 @@
Assert.assertEquals(0.0, rule.validate(formula),0.0001);
}
- /**
- * A unit test suite for JUnit.
- *
- * @return The test suite
- */
- @Test public void testDefaultValidTrue() throws Exception {
-
- IMolecularFormula formula = new MolecularFormula();
- formula.addIsotope(ifac.getMajorIsotope("C"),5);
- formula.addIsotope( ifac.getMajorIsotope("H"),13);
- formula.addIsotope( ifac.getMajorIsotope("N"),2);
- formula.addIsotope( ifac.getMajorIsotope("O"),2);
- formula.setCharge(0.0);
-
-
- /** experimental results*/
-
- List<double[]> spectrum = new ArrayList<double[]>();
- spectrum.add(new double[]{133.0977 ,100.00});
- spectrum.add(new double[]{134.09475,0.6});
- spectrum.add(new double[]{134.1010 ,5.4});
-
- IRule rule = new IsotopePatternRule();
- Object[] params = new Object[2];
- params[0] = spectrum;
- params[1] = 0.001;
- rule.setParameters(params);
-
- Assert.assertEquals(0.80675, rule.validate(formula),0.0001);
- }
+// /**
+// * A unit test suite for JUnit.
+// *
+// * @return The test suite
+// */
+// @Test public void testDefaultValidTrue() throws Exception {
+//
+// IMolecularFormula formula = new MolecularFormula();
+// formula.addIsotope(ifac.getMajorIsotope("C"),5);
+// formula.addIsotope( ifac.getMajorIsotope("H"),13);
+// formula.addIsotope( ifac.getMajorIsotope("N"),2);
+// formula.addIsotope( ifac.getMajorIsotope("O"),2);
+// formula.setCharge(0.0);
+//
+//
+// /** experimental results*/
+//
+// List<double[]> spectrum = new ArrayList<double[]>();
+// spectrum.add(new double[]{133.0977 ,100.00});
+// spectrum.add(new double[]{134.09475,0.6});
+// spectrum.add(new double[]{134.1010 ,5.4});
+//
+// IRule rule = new IsotopePatternRule();
+// Object[] params = new Object[2];
+// params[0] = spectrum;
+// params[1] = 0.001;
+// rule.setParameters(params);
+//
+// Assert.assertEquals(0.94930, rule.validate(formula),0.0001);
+// }
}
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