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[Cdk-commits] SF.net SVN: cdk: [10259] branches/miguelrojasch/removemfa/src
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From: <mig...@us...> - 2008-02-26 16:44:22
|
Revision: 10259
http://cdk.svn.sourceforge.net/cdk/?rev=10259&view=rev
Author: miguelrojasch
Date: 2008-02-26 08:43:29 -0800 (Tue, 26 Feb 2008)
Log Message:
-----------
updated all methods to MolecularFormulaManipulator. Removed the MFAnalyser.
Modified Paths:
--------------
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/applications/jchempaint/JChemPaintModel.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/config/IsotopeFactory.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/io/ShelXWriter.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/DeAromatizationTool.java
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/modulesuites/MformulaTests.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
Removed Paths:
-------------
branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/MFAnalyser.java
branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/MFAnalyserTest.java
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/applications/jchempaint/JChemPaintModel.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/applications/jchempaint/JChemPaintModel.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/applications/jchempaint/JChemPaintModel.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -35,13 +35,13 @@
import javax.swing.event.ChangeListener;
import javax.swing.event.EventListenerList;
-import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.controller.Controller2DModel;
import org.openscience.cdk.event.ICDKChangeListener;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.renderer.Renderer2DModel;
-import org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
/**
@@ -227,11 +227,11 @@
else if (position == 1) {
// depict bruto formula
IAtomContainer wholeModel = model.getBuilder().newAtomContainer();
- Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
+ Iterator<IAtomContainer> containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
while (containers.hasNext()) {
- wholeModel.add((IAtomContainer)containers.next());
+ wholeModel.add(containers.next());
}
- String formula = new MFAnalyser(wholeModel,true).getHTMLMolecularFormulaWithCharge();
+ String formula = MolecularFormulaManipulator.getHTML(MolecularFormulaManipulator.getMolecularFormula(wholeModel),true,false);
int impliciths=0;
for(int i=0;i<wholeModel.getAtomCount();i++){
if(wholeModel.getAtom(i).getHydrogenCount()==null)
@@ -244,7 +244,7 @@
// depict brutto formula of the selected molecule or part of molecule
if (rendererModel.getSelectedPart() != null) {
IAtomContainer selectedPart = rendererModel.getSelectedPart();
- String formula = new MFAnalyser(selectedPart,true).getHTMLMolecularFormulaWithCharge();
+ String formula = MolecularFormulaManipulator.getHTML(MolecularFormulaManipulator.getMolecularFormula(selectedPart),true,false);
status = "<html>" + formula + "</html>";
}
}
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/config/IsotopeFactory.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/config/IsotopeFactory.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/config/IsotopeFactory.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -335,6 +335,26 @@
configure(container.getAtom(f));
}
}
+ /**
+ * Gets the natural mass of this element, defined as average of masses of isotopes,
+ * weighted by abundance.
+ *
+ * @param element Description of the Parameter
+ * @return The natural mass value
+ */
+ @TestMethod("testGetNaturalMass_IElement")
+ public double getNaturalMass(IElement element){
+ IIsotope[] isotopes = getIsotopes(element.getSymbol());
+ double summedAbundances = 0;
+ double summedWeightedAbundances = 0;
+ double getNaturalMass = 0;
+ for (int i = 0; i < isotopes.length; i++) {
+ summedAbundances += isotopes[i].getNaturalAbundance();
+ summedWeightedAbundances += isotopes[i].getNaturalAbundance() * isotopes[i].getExactMass();
+ getNaturalMass = summedWeightedAbundances / summedAbundances;
+ }
+ return getNaturalMass;
+ }
}
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -24,16 +24,16 @@
*/
package org.openscience.cdk.fingerprint;
+import java.util.BitSet;
+
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.AllRingsFinder;
-import org.openscience.cdk.tools.MFAnalyser;
-import java.util.BitSet;
-
/**
* Generates an extended fingerprint for a given AtomContainer, that
* extends the Fingerprinter with additional bits describing ring
@@ -107,8 +107,7 @@
public BitSet getFingerprint(IAtomContainer ac, IRingSet rs) throws Exception {
BitSet bs = fingerprinter.getFingerprint(ac);
int size = this.getSize();
- MFAnalyser mfa=new MFAnalyser(ac);
- float weight=mfa.getNaturalMass();
+ double weight = MolecularFormulaManipulator.getTotalNaturalAbundance(MolecularFormulaManipulator.getMolecularFormula(ac));
for(int i=1;i<11;i++){
if(weight>(100*i))
bs.set(size-26+i); // 26 := RESERVED_BITS+1
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/io/ShelXWriter.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/io/ShelXWriter.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/io/ShelXWriter.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -36,14 +36,16 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.formula.IMolecularFormula;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.geometry.CrystalGeometryTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.ICrystal;
+import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.ShelXFormat;
import org.openscience.cdk.tools.FormatStringBuffer;
-import org.openscience.cdk.tools.MFAnalyser;
/**
* <p>Serializes a MoleculeSet or a Molecule object to ShelX code.
@@ -169,15 +171,17 @@
write("SYMM -X , 1/2+Y , 1/2-Z\n");
write("SYMM 1/2-X , -Y , 1/2+Z\n");
}
- MFAnalyser mfa = new MFAnalyser(crystal);
+// MFAnalyser mfa = new MFAnalyser(crystal);
String elemNames = "";
String elemCounts = "";
- List asortedElements = mfa.getElements();
- Iterator elements = asortedElements.iterator();
+ IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(crystal);
+ List<IElement> asortedElements = MolecularFormulaManipulator.elements(formula);
+ Iterator<IElement> elements = asortedElements.iterator();
while (elements.hasNext()) {
- String symbol = (String)elements.next();
+ IElement element = elements.next();
+ String symbol = element.getSymbol();
elemNames += symbol + " ".substring(symbol.length());
- String countS = new Integer(mfa.getAtomCount(symbol)).toString();
+ String countS = new Integer(MolecularFormulaManipulator.getElementCount(formula, element)).toString();
elemCounts += countS + " ".substring(countS.length());
}
write("SFAC " + elemNames + "\n");
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -20,6 +20,9 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;
+import org.openscience.cdk.ChemObject;
+import org.openscience.cdk.Element;
+import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.matrix.TopologicalMatrix;
import org.openscience.cdk.interfaces.IAtomContainer;
@@ -30,7 +33,6 @@
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
-import org.openscience.cdk.tools.MFAnalyser;
/**
* This class calculates ATS autocorrelation descriptor, where the weight equal
@@ -56,7 +58,8 @@
private static double scaledAtomicMasses(IElement element)
throws java.io.IOException, ClassNotFoundException {
- double realmasses = MFAnalyser.getNaturalMass(element);
+ IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
+ double realmasses = isofac.getNaturalMass(new Element("H"));
return (realmasses / CARBON_MASS);
}
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -23,6 +23,8 @@
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.formula.IMolecularFormula;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.DescriptorSpecification;
@@ -32,7 +34,6 @@
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.MFAnalyser;
import Jama.EigenvalueDecomposition;
import Jama.Matrix;
@@ -231,10 +232,10 @@
// finally get the radius of gyration
double pri = 0.0;
- MFAnalyser mfa = new MFAnalyser(container);
+ IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(container);
if (Math.abs(eval[2]) > eps) pri = Math.pow(eval[0] * eval[1] * eval[2], 1.0 / 3.0);
- else pri = Math.sqrt(eval[0] * ccf / mfa.getMass());
- retval.add(Math.sqrt(Math.PI * 2 * pri * ccf / mfa.getMass()));
+ else pri = Math.sqrt(eval[0] * ccf / MolecularFormulaManipulator.getTotalNaturalAbundance(formula));
+ retval.add(Math.sqrt(Math.PI * 2 * pri * ccf / MolecularFormulaManipulator.getTotalNaturalAbundance(formula)));
String[] names = {
"MOMI-X", "MOMI-Y", "MOMI-Z",
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -31,7 +31,7 @@
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
-import org.openscience.cdk.tools.MFAnalyser;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* Vertex adjacency information (magnitude):
@@ -113,8 +113,7 @@
*@exception CDKException Possible Exceptions
*/
public DescriptorValue calculate(IAtomContainer atomContainer) throws CDKException {
- MFAnalyser formula = new MFAnalyser(atomContainer);
- int magnitude = formula.getHeavyAtoms().size();
+ int magnitude = AtomContainerManipulator.getHeavyAtoms(atomContainer).size();
double vadjMa = 0;
if (magnitude > 0) {
vadjMa += (Math.log(magnitude) / Math.log(2)) + 1;
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -25,6 +25,8 @@
import java.util.ArrayList;
import java.util.List;
+import org.openscience.cdk.formula.IMolecularFormula;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
@@ -32,7 +34,6 @@
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.structgen.IStructureGenerationListener;
import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.MFAnalyser;
/**
@@ -117,7 +118,6 @@
numberOfSetFragment=0;
numberOfStructures=0;
logger.debug(mf);
- MFAnalyser mfa = new MFAnalyser(mf, builder.newAtomContainer());
molecularFormula=new int[12];
numberOfBasicUnit=new int[23];
numberOfBasicFragment=new int[34];
@@ -129,7 +129,7 @@
else structureout = null;
initializeParameters();
- analyseMolecularFormula(mfa);
+ analyseMolecularFormula(MolecularFormulaManipulator.getMolecularFormula(mf));
}
@@ -256,19 +256,19 @@
*
* @param mfa MFAnalyser object to operate the molecular formula
*/
- public void analyseMolecularFormula(MFAnalyser mfa) throws java.lang.Exception
+ public void analyseMolecularFormula(IMolecularFormula formula) throws java.lang.Exception
{
- molecularFormula[1]=mfa.getAtomCount("C");
- molecularFormula[2]=mfa.getAtomCount("H");
- molecularFormula[3]=mfa.getAtomCount("O");
- molecularFormula[4]=mfa.getAtomCount("N");
- molecularFormula[5]=mfa.getAtomCount("S");
- molecularFormula[6]=mfa.getAtomCount("P");
- molecularFormula[7]=mfa.getAtomCount("Si");
- molecularFormula[8]=mfa.getAtomCount("F");
- molecularFormula[9]=mfa.getAtomCount("Cl");
- molecularFormula[10]=mfa.getAtomCount("Br");
- molecularFormula[11]=mfa.getAtomCount("I");
+ molecularFormula[1]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("C"));
+ molecularFormula[2]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("H"));
+ molecularFormula[3]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("O"));
+ molecularFormula[4]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("N"));
+ molecularFormula[5]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("S"));
+ molecularFormula[6]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("P"));
+ molecularFormula[7]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Si"));
+ molecularFormula[8]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("F"));
+ molecularFormula[9]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Cl"));
+ molecularFormula[10]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Br"));
+ molecularFormula[11]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("I"));
molecularFormula[0]=2*molecularFormula[1]+molecularFormula[4]+molecularFormula[6]+
2*molecularFormula[7]+2-molecularFormula[2]-molecularFormula[8]-molecularFormula[9]-
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/DeAromatizationTool.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/DeAromatizationTool.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/DeAromatizationTool.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -28,16 +28,18 @@
*/
package org.openscience.cdk.tools;
+import java.util.Iterator;
+
import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.Element;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.formula.IMolecularFormula;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRing;
-import java.util.Iterator;
-import java.util.Map;
-
/**
* Methods that takes a ring of which all bonds are aromatic, and assigns single
* and double bonds. It does this in a non-general way by looking at the ring
@@ -75,18 +77,19 @@
ring.getBond(i).setOrder(IBond.Order.SINGLE);
}
boolean result = false;
- Map elementCounts = new MFAnalyser(ring).getFormulaHashtable();
+ IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(ring);
+// Map elementCounts = new MFAnalyser(ring).getFormulaHashtable();
if (ring.getRingSize() == 6) {
- if (((Integer)elementCounts.get("C")).intValue() == 6) {
+ if (MolecularFormulaManipulator.getElementCount(formula, new Element("C")) == 6) {
result = DeAromatizationTool.deAromatizeBenzene(ring);
- } else if (((Integer)elementCounts.get("C")).intValue() == 5 &&
- ((Integer)elementCounts.get("N")).intValue() == 1) {
+ } else if (MolecularFormulaManipulator.getElementCount(formula, new Element("C")) == 5 &&
+ MolecularFormulaManipulator.getElementCount(formula, new Element("N")) == 1) {
result = DeAromatizationTool.deAromatizePyridine(ring);
}
}
if (ring.getRingSize() == 5) {
- if (((Integer)elementCounts.get("C")).intValue() == 4 &&
- ((Integer)elementCounts.get("N")).intValue() == 1) {
+ if (MolecularFormulaManipulator.getElementCount(formula, new Element("C")) == 4 &&
+ MolecularFormulaManipulator.getElementCount(formula, new Element("N")) == 1) {
result= deAromatizePyrolle(ring);
}
}
Deleted: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/MFAnalyser.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/MFAnalyser.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/MFAnalyser.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -1,708 +0,0 @@
-/* $Revision$ $Author$ $Date$
- *
- * Copyright (C) 2002-2007 Christoph Steinbeck
- *
- * Contact: cdk...@li...
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.openscience.cdk.tools;
-
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.config.AtomTypeFactory;
-import org.openscience.cdk.config.IsotopeFactory;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.formula.IMolecularFormula;
-import org.openscience.cdk.interfaces.*;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-
-import java.io.IOException;
-import java.util.*;
-
-/**
- * Analyses a molecular formula given in String format and builds
- * an AtomContainer with the Atoms in the molecular formula.
- *
- * About implict H handling: By default the methods to calculate formula, natural and canonical mass
- * use the explicit Hs and only the explicit Hs if there is at least one in the molecule, implicit Hs are
- * ignored. If there is no explicit H and only then the implicit Hs are used. If you use the constructor
- * MFAnalyser(IAtomContainer ac, boolean useboth) and set useboth to true, all explicit Hs and all implicit Hs are used,
- * the implicit ones also on atoms with explicit Hs.
- *
- * @author Christoph Steinbeck
- * @author Stefan Kuhn
- * @author Egon Willighagen
- * @cdk.created MFAnalyser
- * @cdk.module formula
- * @cdk.svnrev $Revision$
- * @cdk.keyword molecule, molecular mass
- * @cdk.keyword molecule, molecular formula
- * @cdk.keyword molecule, double bond equivalents
- */
-public class MFAnalyser {
-
- private final static String H_ELEMENT_SYMBOL = "H";
-
- private String stringMF;
- private IMolecularFormula molecularFormula;
- private IAtomContainer atomContainer;
- private int HCount = 0;
- private boolean useboth=false;
-
- private LoggingTool logger = new LoggingTool(MFAnalyser.class);
-
-
- /**
- * Construct an instance of MFAnalyser, initialized with a molecular
- * formula string. The string is immediatly analysed and a set of Nodes
- * is built based on this analysis
- *
- * @param stringMF Description of the Parameter
- * @param target TODO
- */
- public MFAnalyser(String stringMF, IAtomContainer target) {
- this.stringMF = stringMF;
- this.atomContainer = analyseMF(stringMF, target);
- }
-
-
- /**
- * Construct an instance of MFAnalyser, initialized with a set of Nodes
- * The set is analysed and a molecular formular is constructed
- * based on this analysis
- *
- * @param ac Description of the Parameter
- */
- public MFAnalyser(IAtomContainer ac) {
- this(ac,false);
- }
-
- /**
- * Construct an instance of MFAnalyser, initialized with a set of Nodes
- * The set is analysed and a molecular formular is constructed
- * based on this analysis
- *
- * @param ac Description of the Parameter
- * @param useboth true=implicit and explicit hs will be used, false=explicit used, implicit only if no explicit
- */
- public MFAnalyser(IAtomContainer ac, boolean useboth) {
- this.useboth=useboth;
- this.atomContainer = ac;
- this.stringMF = analyseAtomContainer(ac);
- }
-
-
- /**
- * returns the complete set of Nodes, as implied by the molecular
- * formula, including all the hydrogens.
- *
- * @return The atomContainer value
- */
- public IAtomContainer getAtomContainer() {
- return atomContainer;
- }
-
-
- /**
- * Returns the complete set of Nodes, as implied by the molecular
- * formula, including all the hydrogens.
- *
- * @return The molecularFormula value
- * @see #getHTMLMolecularFormula()
- */
- public String getMolecularFormula() {
- return stringMF;
- }
-
-
- /**
- * Returns the string representation of the molecule formula with
- * numbers wrapped in <sub></sub> tags. Useful for displaying
- * formulae in Swing components or on the web.
- *
- * @return A HTML representation of the molecular formula.
- */
- public String getHTMLMolecularFormula() {
- boolean lastCharacterWasDigit = false;
- boolean currentCharacterIsDigit;
- StringBuffer htmlString = new StringBuffer(stringMF);
-
- for (int characterCounter = 0; characterCounter <= htmlString.length(); characterCounter++) {
- try {
- currentCharacterIsDigit = Character.isDigit(htmlString.charAt(characterCounter));
- } catch (StringIndexOutOfBoundsException oobe) {
- currentCharacterIsDigit = false;
- }
-
- if (currentCharacterIsDigit && !lastCharacterWasDigit) {
- //Insert an opening sub and move the counter beyond it
- htmlString.insert(characterCounter, "<sub>");
- characterCounter += 5;
- } else if (lastCharacterWasDigit && !currentCharacterIsDigit) {
- //Insert a closing sub and move the counter beyond it
- htmlString.insert(characterCounter, "</sub>");
- characterCounter += 6;
- }
-
- lastCharacterWasDigit = currentCharacterIsDigit;
- }
-
- return htmlString.toString();
- }
-
-
- /**
- * Returns the number of double bond equivalents in this molecule.
- *
- * @return The number of DBEs
- * @cdk.keyword DBE
- * @cdk.keyword double bond equivalent
- */
- public float getDBE() throws IOException, ClassNotFoundException, CDKException{
- int valencies[]=new int[5];
- AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml", getAtomContainer().getBuilder());
- IAtomContainer ac = getAtomContainer();
- for (int f = 0; f < ac.getAtomCount(); f++) {
- IAtomType[] types = factory.getAtomTypes(ac.getAtom(f).getSymbol());
- if(types.length==0)
- throw new CDKException("Calculation of double bond equivalents not possible due to problems with element "+ac.getAtom(f).getSymbol());
- valencies[(int)types[0].getBondOrderSum().intValue()+ac.getAtom(f).getFormalCharge()]++;
- }
- return 1 + (valencies[4]) + (valencies[3] /2) - (valencies[1] /2);
- }
-
-
- /**
- * returns the exact mass for a given molecular formula, using major isotope for each element.
- *
- * @return The mass value
- */
- public float getMass() {
- float mass = 0;
- IIsotope i;
- IsotopeFactory si = null;
- try {
- si = IsotopeFactory.getInstance(getAtomContainer().getBuilder());
- } catch (Exception exception) {
- System.err.println("Could not instantiate the IsotopeFactory: " + exception.getMessage());
- }
- IAtomContainer ac = getAtomContainer();
- IIsotope h = si.getMajorIsotope(H_ELEMENT_SYMBOL);
- for (int f = 0; f < ac.getAtomCount(); f++) {
- i = si.getMajorIsotope(ac.getAtom(f).getSymbol());
- if (i != null) {
- mass += i.getExactMass();
- } else {
- return 0;
- }
- int hcount = 0;
- if (ac.getAtom(f).getHydrogenCount() != CDKConstants.UNSET) hcount = ac.getAtom(f).getHydrogenCount();
- mass += hcount * h.getExactMass();
- }
- return mass;
- }
-
-
- /**
- * Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
- *
- * @param element Description of the Parameter
- * @return The natural mass value
- * @exception java.io.IOException Description of the Exception
- * @exception ClassNotFoundException Description of the Exception
- */
- public static double getNaturalMass(IElement element) throws java.io.IOException, ClassNotFoundException {
- IIsotope[] isotopes = IsotopeFactory.getInstance(element.getBuilder()).getIsotopes(element.getSymbol());
- double summedAbundances = 0;
- double summedWeightedAbundances = 0;
- double getNaturalMass = 0;
- for (int i = 0; i < isotopes.length; i++) {
- summedAbundances += isotopes[i].getNaturalAbundance();
- summedWeightedAbundances += isotopes[i].getNaturalAbundance() * isotopes[i].getExactMass();
- getNaturalMass = summedWeightedAbundances / summedAbundances;
- }
- return getNaturalMass;
- }
-
- /**
- * returns the exact mass for a given molecular formula, using weighted average of isotopes.
- *
- * @return The naturalMass value
- * @exception java.io.IOException Description of the Exception
- * @exception ClassNotFoundException Description of the Exception
- */
- public float getNaturalMass() throws java.io.IOException, ClassNotFoundException {
- float mass = 0;
- IsotopeFactory si = null;
- try {
- si = IsotopeFactory.getInstance(getAtomContainer().getBuilder());
- } catch (Exception exception) {
- System.err.println("Could not instantiate the IsotopeFactory: " + exception.getMessage());
- }
- IAtomContainer ac = getAtomContainer();
- IIsotope h = si.getMajorIsotope("H");
- Map<String, Integer> symbols=this.getSymolMap(ac);
- Iterator<String> it = symbols.keySet().iterator();
- while (it.hasNext()) {
- String key = it.next();
- if (key.equals("H")){
- if(useboth){
- mass += MFAnalyser.getNaturalMass(h)*HCount;
- }else{
- if (symbols.get(key) != null) {
- mass += getNaturalMass(h)*symbols.get(key).intValue();
- } else {
- mass += getNaturalMass(h)*HCount;
- }
- }
- }else{
- IElement i = si.getElement(key);
- mass += getNaturalMass(i)*symbols.get(key).intValue();
- }
- }
- return mass;
- }
-
-
- /**
- * Produces an AtomContainer without explicit Hs but with H count from one with Hs.
- * Hs bonded to more than one heavy atom are preserved. The new molecule is a deep copy.
- *
- * @return The mol without Hs.
- * @cdk.keyword hydrogen, removal
- */
- public IAtomContainer removeHydrogensPreserveMultiplyBonded() {
- IAtomContainer ac = getAtomContainer();
-
- List<IAtom> h = new ArrayList<IAtom>();
- // H list.
- List<IAtom> multi_h = new ArrayList<IAtom>();
- // multiply bonded H
-
- // Find multiply bonded H.
- int count = ac.getBondCount();
- for (int i = 0;
- i < count;
- i++) {
- java.util.Iterator atoms = ac.getBond(i).atoms();
- while (atoms.hasNext()) {
- final IAtom atom = (IAtom)atoms.next();
- if (atom.getSymbol().equals(H_ELEMENT_SYMBOL)) {
- (h.contains(atom) ? multi_h : h).add(atom);
- }
- }
-
- // The short version (assumes atoms.length == 2 is always true).
-// (h.contains(atoms[0]) ? multi_h : h).add(atoms[0]);
-// (h.contains(atoms[1]) ? multi_h : h).add(atoms[1]);
- }
-
- return removeHydrogens(multi_h);
- }
-
-
- /**
- * Produces an AtomContainer without explicit Hs (except those listed) but with H count from one with Hs.
- * The new molecule is a deep copy.
- *
- * @param preserve a list of H atoms to preserve.
- * @return The mol without Hs.
- * @cdk.keyword hydrogen, removal
- */
- private IAtomContainer removeHydrogens(List<IAtom> preserve) {
- IAtomContainer ac = getAtomContainer();
-
- Map<IAtom,IAtom> map = new HashMap<IAtom,IAtom>();
- // maps original atoms to clones.
- List<IAtom> remove = new ArrayList<IAtom>();
- // lists removed Hs.
-
- // Clone atoms except those to be removed.
- IMolecule mol = ac.getBuilder().newMolecule();
- int count = ac.getAtomCount();
- for (int i = 0;
- i < count;
- i++) {
- // Clone/remove this atom?
- IAtom atom = ac.getAtom(i);
- if (!atom.getSymbol().equals(H_ELEMENT_SYMBOL) || preserve.contains(atom)) {
- IAtom a = null;
- try {
- a = (IAtom) atom.clone();
- } catch (CloneNotSupportedException e) {
- logger.error("Could not clone: ", atom);
- logger.debug(e);
- }
- a.setHydrogenCount(0);
- mol.addAtom(a);
- map.put(atom, a);
- } else {
- remove.add(atom);
- // maintain list of removed H.
- }
- }
-
- // Clone bonds except those involving removed atoms.
- count = ac.getBondCount();
- for (int i = 0;
- i < count;
- i++) {
- // Check bond.
- final IBond bond = ac.getBond(i);
- IAtom atom0 = bond.getAtom(0);
- IAtom atom1 = bond.getAtom(1);
- java.util.Iterator atoms = bond.atoms();
- boolean remove_bond = false;
- while (atoms.hasNext()){
- if (remove.contains((IAtom)atoms.next())) {
- remove_bond = true;
- break;
- }
- }
-
- // Clone/remove this bond?
- if (!remove_bond) {
- // if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
-
- IBond clone = null;
- try {
- clone = (IBond) ac.getBond(i).clone();
- } catch (CloneNotSupportedException e) {
- logger.error("Could not clone: ", ac.getBond(i));
- logger.debug(e);
- }
- clone.setAtoms(new IAtom[]{map.get(atom0), map.get(atom1)});
- mol.addBond(clone);
- }
- }
-
- // Recompute hydrogen counts of neighbours of removed Hydrogens.
- for (Iterator<IAtom> i = remove.iterator();
- i.hasNext(); ) {
- // Process neighbours.
- for (Iterator n = ac.getConnectedAtomsList(i.next()).iterator();
- n.hasNext(); ) {
- final IAtom neighb = map.get(n.next());
- neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
- }
- }
-
- return (mol);
- }
-
-
- /**
- * Returns a set of nodes excluding all the hydrogens
- *
- * @return The heavyAtoms value
- * @cdk.keyword hydrogen, removal
- */
- public List<IAtom> getHeavyAtoms() {
- List<IAtom> newAc = new ArrayList<IAtom>();
- IAtomContainer ac = getAtomContainer();
- for (int f = 0; f < ac.getAtomCount(); f++) {
- if (!ac.getAtom(f).getSymbol().equals(H_ELEMENT_SYMBOL)) {
- newAc.add(ac.getAtom(f));
- }
- }
- return newAc;
- }
-
-
- /**
- * Method that actually does the work of analysing the molecular formula
- *
- * @param MF molecular formula to create an AtomContainer from
- * @param ac AtomContainer in which the Atom's and Bond's will be stored
- * @return the filled AtomContainer
- */
- private IAtomContainer analyseMF(String MF, IAtomContainer ac) {
- char ThisChar;
- /*
- * Buffer for
- */
- String RecentElementSymbol = new String();
- String RecentElementCountString = new String("0");
- /*
- * String to be converted to an integer
- */
- int RecentElementCount;
-
- if (MF.length() == 0) {
- return null;
- }
-
- for (int f = 0; f < MF.length(); f++) {
- ThisChar = MF.charAt(f);
- if (f < MF.length()) {
- if (ThisChar >= 'A' && ThisChar <= 'Z') {
- /*
- * New Element begins
- */
- RecentElementSymbol = java.lang.String.valueOf(ThisChar);
- RecentElementCountString = "0";
- }
- if (ThisChar >= 'a' && ThisChar <= 'z') {
- /*
- * Two-letter Element continued
- */
- RecentElementSymbol += ThisChar;
- }
- if (ThisChar >= '0' && ThisChar <= '9') {
- /*
- * Two-letter Element continued
- */
- RecentElementCountString += ThisChar;
- }
- }
- if (f == MF.length() - 1 || (MF.charAt(f + 1) >= 'A' && MF.charAt(f + 1) <= 'Z')) {
- /*
- * Here an element symbol as well as its number should have been read completely
- */
- Integer RecentElementCountInteger = new Integer(RecentElementCountString);
- RecentElementCount = RecentElementCountInteger.intValue();
- if (RecentElementCount == 0) {
- RecentElementCount = 1;
- }
- for (int g = 0; g < RecentElementCount; g++) {
- ac.addAtom(ac.getBuilder().newAtom(RecentElementSymbol));
- }
- }
- }
- return ac;
- }
-
-
- /**
- * creates a sorted hash map of elementsymbol-count of this ac
- *
- * @param ac the atomcontainer to calculate with
- * @return the hashmap
- */
- private Map<String, Integer> getSymolMap(IAtomContainer ac){
- String symbol;
- SortedMap<String,Integer> symbols = new TreeMap<String,Integer>();
- IAtom atom = null;
- HCount=0;
- for (int f = 0; f < ac.getAtomCount(); f++) {
- atom = ac.getAtom(f);
- symbol = atom.getSymbol();
- if(useboth){
-
- }
- if (atom.getHydrogenCount() != CDKConstants.UNSET && atom.getHydrogenCount() > 0) {
- HCount += atom.getHydrogenCount();
- }
- if (symbols.get(symbol) != null) {
- symbols.put(symbol, symbols.get(symbol) + 1);
- } else {
- symbols.put(symbol, 1);
- }
- }
- if(useboth && symbols.get(H_ELEMENT_SYMBOL)!=null)
- HCount+=symbols.get(H_ELEMENT_SYMBOL).intValue();
- return symbols;
- }
-
- /**
- * Analyses a set of Nodes that has been changed or recently loaded
- * and returns a molecular formula
- *
- * @param ac Description of the Parameter
- * @return a string containing the molecular formula.
- */
- public String analyseAtomContainer(IAtomContainer ac) {
- String mf = "";
- Map<String, Integer> symbols = this.getSymolMap(ac);
- mf = addSymbolToFormula(symbols, "C", mf);
- if(useboth){
- if (HCount > 0)
- mf += H_ELEMENT_SYMBOL;
- if (HCount > 1) {
- mf += Integer.toString(HCount);
- }
- }else{
- if (symbols.get(H_ELEMENT_SYMBOL) != null) {
- mf = addSymbolToFormula(symbols, H_ELEMENT_SYMBOL, mf);
- } else {
- if (HCount > 0) {
- mf += H_ELEMENT_SYMBOL;
- if (HCount > 1) {
- mf += Integer.toString(HCount);
- }
- }
- }
- }
- mf = addSymbolToFormula(symbols, "N", mf);
- mf = addSymbolToFormula(symbols, "O", mf);
- mf = addSymbolToFormula(symbols, "S", mf);
- mf = addSymbolToFormula(symbols, "P", mf);
- Iterator<String> it = symbols.keySet().iterator();
- while (it.hasNext()) {
- Object key = it.next();
- if (!((String) key).equals("C") && !((String) key).equals(H_ELEMENT_SYMBOL) && !((String) key).equals("N") && !((String) key).equals("O") && !((String) key).equals("S") && !((String) key).equals("P")) {
- mf = addSymbolToFormula(symbols, (String) key, mf);
- }
- }
- return mf;
- }
-
-
- /**
- * Adds an element to a chemical formual string
- *
- * @param sm The map containing the elements
- * @param symbol The symbol to add
- * @param formula The chemical formula
- * @return Description of the Return Value
- */
- private String addSymbolToFormula(Map<String, Integer> sm, String symbol, String formula) {
- if (sm.get(symbol) != null) {
- formula += symbol;
- if (!sm.get(symbol).equals(new Integer(1))) {
- formula += sm.get(symbol).toString();
- }
- }
- return (formula);
- }
-
-
- /**
- * Checks a set of Nodes for the occurence of a particular
- * element.
- *
- * @param thisElement Description of the Parameter
- * @return The number of atoms for the particular element in the formula
- */
- public int getAtomCount(String thisElement) {
- int atomCount = 0;
- if (thisElement.equals(H_ELEMENT_SYMBOL) && HCount > 0) {
- return HCount;
- }
- for (int f = 0; f < atomContainer.getAtomCount(); f++) {
- if (atomContainer.getAtom(f).getSymbol().equals(thisElement)) {
- atomCount++;
- }
- }
- return atomCount;
- }
-
-
- /**
- * Returns a Vector (of Strings) with asorted element names.
- * The order is determined by ElementComparator.
- *
- * @return The elements value
- * @see ElementComparator
- */
- public List<String> getElements() {
- TreeSet<String> elements = new TreeSet<String>((Comparator<? super String>)new ElementComparator());
- for (int f = 0; f < atomContainer.getAtomCount(); f++) {
- String symbol = atomContainer.getAtom(f).getSymbol();
- if (!elements.contains(symbol)) {
- elements.add(symbol);
- }
- }
- List<String> results = new ArrayList<String>();
- Iterator<String> iter = elements.iterator();
- while (iter.hasNext()) {
- results.add(iter.next());
- }
- return results;
- }
-
-
- /**
- * Returns the number of distinct elements in the formula.
- *
- * @return The elementCount value
- */
- public int getElementCount() {
- return getElements().size();
- }
-
-
- /**
- * Gets a Molecule and an array of element symbols. Counts how many of each of these elements
- * the molecule contains. Then it returns the elements followed by their number as a string,
- * i.e. C15H8N3.
- *
- * @param mol The Molecule to be searched
- * @param elements Description of the Parameter
- * @return The element formula as a string
- */
- public static String generateElementFormula(IMolecule mol, String[] elements) {
- int num = elements.length;
- StringBuffer formula = new StringBuffer();
- int[] elementCount = new int[num];
- for (int i = 0; i < mol.getAtomCount(); i++) {
- for (int j = 0; j < num; j++) {
- if (elements[j].equals(mol.getAtom(i).getSymbol())) {
- elementCount[j]++;
- }
- }
- }
- for (int i = 0; i < num; i++) {
- formula.append(elements[i] + elementCount[i]);
- }
- return formula.toString();
- }
-
-
- /**
- * Builds the elemental formula of a given molecule as a Hashtable.
- * Keys are the elemental symbols (Strings) and values are the no. of occurrence (Integer objects).
- *
- * @return a Hashtable, keys are the elemental symbols and values are their no.
- */
- public Map<String, Integer> getFormulaHashtable() {
- Map<String, Integer> formula = new HashMap<String, Integer>();
- List<String> elements = this.getElements();
- for (int i = 0; i < elements.size(); i++) {
- Integer numOfAtom = new Integer(this.getAtomCount(elements.get(i)));
- formula.put(elements.get(i), numOfAtom);
- }
- return formula;
- }
-
- /**
- *
- * Returns the string representation of the molecule formula with
- * numbers wrapped in <sub></sub> tags and the total
- * charge of AtomContainer in <sup></sup> tags
- * Useful for displaying formulae in Swing components or on the web.
- *
- * @return The html-string representation of the sum formula with charge
- * @see #getHTMLMolecularFormula()
- */
- public String getHTMLMolecularFormulaWithCharge() {
- String formula = new MFAnalyser(atomContainer,useboth).getHTMLMolecularFormula();
- int charge = AtomContainerManipulator.getTotalFormalCharge(atomContainer);
- if (charge == 0)
- {
- return formula;
- } else if (charge < 0) {
- return formula + "<sup>" + charge * -1 + "-" + "</sup>";
- } else {
- return formula + "<sup>" + charge +"+" + "</sup>";
- }
- }
-}
-
-
Modified: branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
===================================================================
--- branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -572,10 +572,26 @@
return sum;
}
- @TestMethod("testGetMaxBondOrder")
+ @TestMethod("testGetMaxBondOrder_IAtomContainer")
public static IBond.Order getMaximumBondOrder(IAtomContainer container) {
return BondManipulator.getMaximumBondOrder(container.bonds());
}
+ /**
+ * Returns a set of nodes excluding all the hydrogens.
+ *
+ * @return The heavyAtoms value
+ * @cdk.keyword hydrogen, removal
+ */
+ @TestMethod("testGetHeavyAtoms_IAtomContainer")
+ public static List<IAtom> getHeavyAtoms(IAtomContainer container) {
+ List<IAtom> newAc = new ArrayList<IAtom>();
+ for (int f = 0; f < container.getAtomCount(); f++) {
+ if (!container.getAtom(f).getSymbol().equals("H")) {
+ newAc.add(container.getAtom(f));
+ }
+ }
+ return newAc;
+ }
}
Modified: branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java
===================================================================
--- branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -30,6 +30,7 @@
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.ChemObject;
+import org.openscience.cdk.Element;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.interfaces.IElement;
@@ -291,5 +292,9 @@
}
}
+ @Test public void testGetNaturalMass_IElement() throws Exception {
+ IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
+ Assert.assertEquals(1.0079760, isofac.getNaturalMass(new Element("H")), 0.1);
+ }
}
Modified: branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/modulesuites/MformulaTests.java
===================================================================
--- branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/modulesuites/MformulaTests.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/modulesuites/MformulaTests.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -35,7 +35,6 @@
import org.openscience.cdk.formula.MolecularFormulaSetManipulatorTest;
import org.openscience.cdk.formula.MolecularFormulaSetTest;
import org.openscience.cdk.formula.MolecularFormulaTest;
-import org.openscience.cdk.tools.MFAnalyserTest;
/**
* TestSuite that runs all the JUnit tests for the formula module.
@@ -58,7 +57,6 @@
suite.addTest(new JUnit4TestAdapter(MolecularFormulaSetManipulatorTest.class));
suite.addTest(new JUnit4TestAdapter(MolecularFormulaSetTest.class));
suite.addTest(new JUnit4TestAdapter(MolecularFormulaTest.class));
- suite.addTest(new JUnit4TestAdapter(MFAnalyserTest.class));
return suite;
}
Modified: branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java
===================================================================
--- branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -34,11 +34,10 @@
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.swing.MoleculeListViewer;
import org.openscience.cdk.applications.swing.MoleculeViewer2D;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.layout.StructureDiagramGenerator;
-import org.openscience.cdk.structgen.SingleStructureRandomGenerator;
import org.openscience.cdk.templates.MoleculeFactory;
-import org.openscience.cdk.tools.MFAnalyser;
/**
* @cdk.module test-structgen
@@ -57,7 +56,7 @@
ssrg = new SingleStructureRandomGenerator();
System.out.println("Assining unbonded set of atoms");
AtomContainer ac = getBunchOfUnbondedAtoms();
- mf = new MFAnalyser(ac).getMolecularFormula();
+ mf = MolecularFormulaManipulator.getString(MolecularFormulaManipulator.getMolecularFormula(ac));
System.out.println("Molecular Formula is: " + mf);
ssrg.setAtomContainer(ac);
}
Modified: branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java
===================================================================
--- branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -20,29 +20,41 @@
*/
package org.openscience.cdk.tools;
+import java.io.InputStream;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point2d;
+
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.openscience.cdk.*;
+
+import org.openscience.cdk.Atom;
+import org.openscience.cdk.Bond;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.ChemFile;
+import org.openscience.cdk.ChemObject;
+import org.openscience.cdk.Molecule;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.config.Elements;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.formula.IMolecularFormula;
+import org.openscience.cdk.formula.MolecularFormulaManipulator;
+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.IChemFile;
+import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.nonotify.NNAtom;
import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
-import org.openscience.cdk.CDKTestCase;
-import org.openscience.cdk.tools.CDKHydrogenAdder;
-import org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
-import javax.vecmath.Point2d;
-import java.io.InputStream;
-import java.util.Iterator;
-import java.util.List;
-
/**
* Tests CDK's hydrogen adding capabilities in terms of
* example molecules.
@@ -219,7 +231,8 @@
adder.addImplicitHydrogens(mol);
assertEquals(1, mol.getAtomCount());
- assertEquals(1, new MFAnalyser(mol).getAtomCount("H"));
+ IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(mol);
+ assertEquals(1, MolecularFormulaManipulator.getElementCount(formula,mol.getBuilder().newElement("H")));
assertEquals(0, mol.getConnectedBondsCount(proton));
assertNotNull(proton.getHydrogenCount());
assertEquals(0, proton.getHydrogenCount().intValue());
@@ -236,7 +249,8 @@
adder.addImplicitHydrogens(mol);
assertEquals(1, mol.getAtomCount());
- assertEquals(1, new MFAnalyser(mol).getAtomCount("H"));
+ IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(mol);
+ assertEquals(1, MolecularFormulaManipulator.getElementCount(formula,mol.getBuilder().newElement("H")));
assertEquals(0, mol.getConnectedBondsCount(proton));
assertNotNull(proton.getHydrogenCount());
assertEquals(1, proton.getHydrogenCount().intValue());
Deleted: branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/MFAnalyserTest.java
===================================================================
--- branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/MFAnalyserTest.java 2008-02-26 16:29:17 UTC (rev 10258)
+++ branches/miguelrojasch/removemfa/src/test/org/openscience/cdk/tools/MFAnalyserTest.java 2008-02-26 16:43:29 UTC (rev 10259)
@@ -1,276 +0,0 @@
-/* $Revision$ $Author$ $Date$
- *
- * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
- *
- * Contact: cdk...@li...
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.openscience.cdk.tools;
-
-import java.io.IOException;
-import java.util.Map;
-
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.Element;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.nonotify.NNAtomContainer;
-import org.openscience.cdk.smiles.SmilesParser;
-import org.openscience.cdk.templates.MoleculeFactory;
-import org.openscience.cdk.NewCDKTestCase;
-import org.openscience.cdk.tools.MFAnalyser;
-
-/**
- * @cdk.module test-formula
- */
-public class MFAnalyserTest extends NewCDKTestCase {
- static Molecule molecule;
-
- @BeforeClass
- public static void setUp()
- {
- molecule = MoleculeFactory.makeAlphaPinene();
- }
-
-
- @Test public void testMFAnalyser_String_IAtomContainer() {
- Assert.assertNotNull(new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer()));
- }
-
- @Test public void testMFAnalyser_IAtomContainer() {
- Assert.assertNotNull(new MFAnalyser(new org.openscience.cdk.AtomContainer()));
- }
-
- @Test public void testMFAnalyser_IAtomContainer_boolean() {
- Assert.assertNotNull(new MFAnalyser(new org.openscience.cdk.AtomContainer(), true));
- Assert.assertNotNull(new MFAnalyser(new org.openscience.cdk.AtomContainer(), false));
- }
-
- @Test public void testGetMolecularFormula() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer());
- IAtomContainer ac = mfa.getAtomContainer();
- MFAnalyser mfa2 = new MFAnalyser(ac);
- String mf = mfa2.getMolecularFormula();
- Assert.assertEquals("C10H16", mf);
- }
-
- @Test public void testGetElements() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new NNAtomContainer());
- Assert.assertEquals(2, mfa.getElements().size());
- mfa = new MFAnalyser("C10H19N", new NNAtomContainer());
- Assert.assertEquals(3, mfa.getElements().size());
- }
-
- @Test public void testGetDBE() throws Exception{
- MFAnalyser mfa = new MFAnalyser("C10H22", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(0, (int)mfa.getDBE());
-
- mfa = new MFAnalyser("C10H16", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(3, (int)mfa.getDBE());
-
- mfa = new MFAnalyser("C10H16O", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(3, (int)mfa.getDBE());
-
- mfa = new MFAnalyser("C10H19N", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(2, (int)mfa.getDBE());
- }
-
- @Test public void testGenerateElementFormula_IMolecule_arrayString() {
- MFAnalyser mfa = new MFAnalyser("C10H19N", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals("C10N1H19", MFAnalyser.generateElementFormula(
- new Molecule(mfa.getAtomContainer()), new String[] { "C", "N", "H" })
- );
- Assert.assertEquals("C10H19N1", MFAnalyser.generateElementFormula(
- new Molecule(mfa.getAtomContainer()), new String[] { "C", "H", "N" })
- );
- Assert.assertEquals("N1H19C10", MFAnalyser.generateElementFormula(
- new Molecule(mfa.getAtomContainer()), new String[] { "N", "H", "C" })
- );
- }
-
- @Test public void testAnalyseAtomContainer_IAtomContainer() {
- MFAnalyser mfa = new MFAnalyser("C10H19N", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals("C10H19N", mfa.analyseAtomContainer(
- new Molecule(mfa.getAtomContainer()))
- );
- }
-
- @Test public void testElements() throws Exception{
- MFAnalyser mfa = new MFAnalyser("C10H22", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(2, (int)mfa.getElements().size());
-
- mfa = new MFAnalyser("C10H16O", DefaultChemObjectBuilder.getInstance().newAtomContainer());
- Assert.assertEquals(3, (int)mfa.getElements().size());
- }
-
- @Test public void testGetAtomContainer() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer());
- IAtomContainer ac = mfa.getAtomContainer();
- Assert.assertEquals(26, ac.getAtomCount());
- }
-
- @Test public void testGetElementCount() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(2, mfa.getElementCount());
- }
-
- @Test public void testGetElementCount2() {
- MFAnalyser mfa = new MFAnalyser("CH3OH", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(3, mfa.getElementCount());
- }
-
- @Test public void testGetAtomCount_String() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(10, mfa.getAtomCount("C"));
- Assert.assertEquals(16, mfa.getAtomCount("H"));
- }
-
- @Test public void testGetAtomCount_String2() {
- MFAnalyser mfa = new MFAnalyser("CH3OH", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(1, mfa.getAtomCount("C"));
- Assert.assertEquals(1, mfa.getAtomCount("O"));
- Assert.assertEquals(4, mfa.getAtomCount("H"));
- }
-
- @Test public void testGetHeavyAtoms() {
- MFAnalyser mfa = new MFAnalyser("C10H16", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(10, mfa.getHeavyAtoms().size());
- }
-
- @Test public void testGetHeavyAtoms2() {
- MFAnalyser mfa = new MFAnalyser("CH3OH", new org.openscience.cdk.AtomContainer());
- Assert.assertEquals(2, mfa.getHeavyAtoms().size());
- }
-
- /**
- * Test removeHydrogensPreserveMultiplyBonded for B2H6, which contains two multiply bonded H.
- *
- * @throws IOException
- * @throws ClassNotFoundException
- * @throws CDKException
- */
- @Test public void testRemoveHydrogensPreserveMultiplyBonded() throws IOException, ClassNotFoundException, CDKException
- {...
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