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[Cdk-commits] SF.net SVN: cdk: [11004] cdk/branches/miguelrojasch-IP/src
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From: <mig...@us...> - 2008-05-15 13:28:35
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Revision: 11004
http://cdk.svn.sourceforge.net/cdk/?rev=11004&view=rev
Author: miguelrojasch
Date: 2008-05-15 06:27:25 -0700 (Thu, 15 May 2008)
Log Message:
-----------
added method to extract the container which the atom belongs and furthermore it is in resonance. Tests
Modified Paths:
--------------
cdk/branches/miguelrojasch-IP/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
cdk/branches/miguelrojasch-IP/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
Modified: cdk/branches/miguelrojasch-IP/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
===================================================================
--- cdk/branches/miguelrojasch-IP/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java 2008-05-15 00:11:47 UTC (rev 11003)
+++ cdk/branches/miguelrojasch-IP/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java 2008-05-15 13:27:25 UTC (rev 11004)
@@ -278,7 +278,7 @@
IMoleculeSet setOfMol = getStructures(molecule);
if(setOfMol.getMoleculeCount() == 0)
return setOfCont;
-
+
/*extraction of all bonds which has been produced a changes of order*/
List<IBond> bondList = new ArrayList<IBond>();
for(int i = 1 ; i < setOfMol.getMoleculeCount() ; i++){
@@ -321,7 +321,7 @@
for(int i = 0 ; i < maxGroup ; i ++){
IAtomContainer container = molecule.getBuilder().newAtomContainer();
for(int j = 0 ; j < bondList.size(); j++){
- if(flagBelonging[j] != maxGroup)
+ if(flagBelonging[j] != i+1)
continue;
IBond bond = bondList.get(j);
IAtom atomA1 = bond.getAtom(0);
@@ -336,6 +336,27 @@
}
return setOfCont;
}
+ /**
+ * <p>Get the container which the atom is found on resonance from a IMolecule.
+ * It is based on looking if the order of the bond changes. Return null
+ * is any is found.</p>
+ *
+ * @param molecule The IMolecule to analyze
+ * @param molecule The IAtom
+ * @return The different containers
+ */
+ @TestMethod("testGetContainer_IMolecule_IAtom")
+ public IAtomContainer getContainer(IMolecule molecule, IAtom atom) {
+ IAtomContainerSet setOfCont = getContainers(molecule);
+
+ for(Iterator<IAtomContainer> it = setOfCont.atomContainers(); it.hasNext();){
+ IAtomContainer container = it.next();
+ if(container.contains(atom))
+ return container;
+ }
+
+ return null;
+ }
/**
* Search if the setOfAtomContainer contains the atomContainer
*
@@ -345,9 +366,10 @@
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
-
for(int i = 0 ; i < atomContainer.getAtomCount(); i++)
- atomContainer.getAtom(i).setID(""+atomContainer.getAtomNumber(atomContainer.getAtom(i)));
+// if(atomContainer.getAtom(i).getID() == null)
+ atomContainer.getAtom(i).setID(""+atomContainer.getAtomNumber(atomContainer.getAtom(i)));
+
if(lookingSymmetry){
try {
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
@@ -359,7 +381,9 @@
for(int i = 0 ; i < set.getAtomContainerCount(); i++){
IAtomContainer ss = set.getAtomContainer(i);
for(int j = 0 ; j < ss.getAtomCount(); j++)
- ss.getAtom(j).setID(""+ss.getAtomNumber(ss.getAtom(j)));
+// if(ss.getAtom(j).getID() == null)
+ ss.getAtom(j).setID(""+ss.getAtomNumber(ss.getAtom(j)));
+
try {
if(!lookingSymmetry ){
Modified: cdk/branches/miguelrojasch-IP/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
===================================================================
--- cdk/branches/miguelrojasch-IP/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java 2008-05-15 00:11:47 UTC (rev 11003)
+++ cdk/branches/miguelrojasch-IP/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java 2008-05-15 13:27:25 UTC (rev 11004)
@@ -34,6 +34,7 @@
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
@@ -1103,7 +1104,8 @@
molecule.addBond(6, 7, IBond.Order.SINGLE);
molecule.getAtom(7).setFormalCharge(+1);
addExplicitHydrogens(molecule);
-
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ lpcheck.saturate(molecule);
StructureResonanceGenerator sRG = new StructureResonanceGenerator();
IAtomContainerSet setOfContainers = sRG.getContainers(molecule);
@@ -1116,6 +1118,107 @@
}
}
/**
+ * A unit test suite for JUnit: Resonance C-C=C-[C+]-C-C=C-[C+] <=> C-[C+]-C=C-C-C=C-[C+]
+ *
+ * @return The test suite
+ */
+ @Test public void testGetContainer_IMolecule_IAtom() throws Exception {
+ IMolecule molecule = builder.newMolecule();
+ IAtom atom1 = builder.newAtom("C");
+ atom1.setID("atom1");
+ molecule.addAtom(atom1);
+ IAtom atom2 = builder.newAtom("C");
+ atom2.setID("atom2");
+ molecule.addAtom(atom2);
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ IAtom atom3 = builder.newAtom("C");
+ atom3.setID("atom3");
+ molecule.addAtom(atom3);
+ molecule.addBond(1, 2, IBond.Order.DOUBLE);
+ IAtom atom4 = builder.newAtom("C");
+ atom4.setID("atom4");
+ molecule.addAtom(atom4);
+ atom4.setFormalCharge(+1);
+ molecule.addBond(2, 3, IBond.Order.SINGLE);
+ molecule.addAtom(new Atom("C"));
+ molecule.addBond(3, 4, IBond.Order.SINGLE);
+ molecule.addAtom(new Atom("C"));
+ molecule.addBond(4, 5, IBond.Order.SINGLE);
+ molecule.addAtom(new Atom("C"));
+ molecule.addBond(5, 6, IBond.Order.DOUBLE);
+ molecule.addAtom(new Atom("C"));
+ molecule.getAtom(7).setFormalCharge(+1);
+ molecule.addBond(6, 7, IBond.Order.SINGLE);
+ addExplicitHydrogens(molecule);
+
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ lpcheck.saturate(molecule);
+
+ StructureResonanceGenerator sRG = new StructureResonanceGenerator();
+ IAtomContainer container = sRG.getContainer(molecule,atom4);
+
+ Assert.assertEquals(3, container.getAtomCount());
+ Assert.assertEquals(2, container.getBondCount());
+ Assert.assertTrue(container.contains(atom4));
+
+ }
+
+ /**
+ * A unit test suite for JUnit: Resonance C-C=C-[C+]-C-C=C-[C+] <=> C-[C+]-C=C-C-C=C-[C+]
+ *
+ * @return The test suite
+ */
+ @Test public void testGetID() throws Exception {
+ IMolecule molecule = builder.newMolecule();
+ IAtom atom1 = builder.newAtom("C");
+ atom1.setID("atom1");
+ molecule.addAtom(atom1);
+ IAtom atom2 = builder.newAtom("C");
+ atom2.setID("atom2");
+ molecule.addAtom(atom2);
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ IAtom atom3 = builder.newAtom("C");
+ atom3.setID("atom3");
+ molecule.addAtom(atom3);
+ molecule.addBond(1, 2, IBond.Order.DOUBLE);
+ IAtom atom4 = builder.newAtom("C");
+ atom4.setID("atom4");
+ molecule.addAtom(atom4);
+ atom4.setFormalCharge(+1);
+ molecule.addBond(2, 3, IBond.Order.SINGLE);
+ IAtom atom5 = builder.newAtom("C");
+ atom5.setID("atom5");
+ molecule.addAtom(atom5);
+ molecule.addBond(3, 4, IBond.Order.SINGLE);
+ IAtom atom6 = builder.newAtom("C");
+ atom6.setID("atom6");
+ molecule.addAtom(atom6);
+ molecule.addBond(4, 5, IBond.Order.SINGLE);
+ IAtom atom7 = builder.newAtom("C");
+ atom7.setID("atom7");
+ molecule.addAtom(atom7);
+ molecule.addBond(5, 6, IBond.Order.DOUBLE);
+ IAtom atom8 = builder.newAtom("C");
+ atom8.setID("atom8");
+ molecule.addAtom(atom8);
+ atom8.setFormalCharge(+1);
+ molecule.addBond(6, 7, IBond.Order.SINGLE);
+ addExplicitHydrogens(molecule);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ lpcheck.saturate(molecule);
+
+ StructureResonanceGenerator sRG = new StructureResonanceGenerator();
+ IAtomContainer container = sRG.getContainer(molecule,atom4);
+
+ Assert.assertNotNull(atom2.getID());
+ Assert.assertNotNull(atom3.getID());
+ Assert.assertNotNull(atom4.getID());
+ Assert.assertEquals(atom2.getID(), container.getAtom(0).getID());
+ Assert.assertEquals(atom3.getID(), container.getAtom(1).getID());
+ Assert.assertEquals(atom4.getID(), container.getAtom(2).getID());
+
+ }
+ /**
* A unit test suite for JUnit: Resonance 1-fluoro-2-methylbenzene Fc1ccccc1C <=> Fc1ccccc1
*
* @cdk.inchi InChI=1/C7H7F/c1-6-4-2-3-5-7(6)8/h2-5H,1H3
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