From 4895adacde3283fdf1401f9e8612ee2a68f69bd8 Mon Sep 17 00:00:00 2001 From: Rajarshi Guha Date: Thu, 11 Feb 2016 10:45:57 -0500 Subject: [PATCH] Ensure that we reset visited flag each time we start path search from new atom Added test cases --- .../molecular/LargestChainDescriptor.java | 6 ++-- .../molecular/LargestChainDescriptorTest.java | 36 ++++++++++++++++++++++ 2 files changed, 38 insertions(+), 4 deletions(-) diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java index be991c6..ccdeb00 100644 --- a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java +++ b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java @@ -210,13 +210,11 @@ public class LargestChainDescriptor extends AbstractMolecularDescriptor implemen //IAtom[] atoms = container.getAtoms(); ArrayList startSphere; ArrayList path; - //Set all VisitedFlags to False - for (int i = 0; i < container.getAtomCount(); i++) { - container.getAtom(i).setFlag(CDKConstants.VISITED, false); - } //logger.debug("Set all atoms to Visited False"); for (int i = 0; i < container.getAtomCount(); i++) { + for (IAtom a : container.atoms()) a.setFlag(CDKConstants.VISITED, false); + IAtom atomi = container.getAtom(i); // chain sp3 //logger.debug("atom:"+i+" maxBondOrder:"+container.getMaximumBondOrder(atoms[i])+" Aromatic:"+atoms[i].getFlag(CDKConstants.ISAROMATIC)+" Ring:"+atoms[i].getFlag(CDKConstants.ISINRING)+" FormalCharge:"+atoms[i].getFormalCharge()+" Charge:"+atoms[i].getCharge()+" Flag:"+atoms[i].getFlag(CDKConstants.VISITED)); diff --git a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java index 8fc77e4..15352b8 100644 --- a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java +++ b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java @@ -115,4 +115,40 @@ public class LargestChainDescriptorTest extends MolecularDescriptorTest { Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue()); } + @Test + public void test8LargestChainDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception { + Object[] params = {new Boolean(true), new Boolean(true)}; + descriptor.setParameters(params); + SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); + IAtomContainer mol = sp.parseSmiles("Cc1nn(c(c1)N)c1nc2c(s1)cccc2"); + Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue()); + } + + @Test + public void test9LargestChainDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception { + Object[] params = {new Boolean(true), new Boolean(true)}; + descriptor.setParameters(params); + SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); + IAtomContainer mol = sp.parseSmiles("Nc1c(cn[nH]1)C#N"); + Assert.assertEquals(2, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue()); + } + + @Test + public void test10LargestChainDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception { + Object[] params = {new Boolean(true), new Boolean(true)}; + descriptor.setParameters(params); + SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); + IAtomContainer mol = sp.parseSmiles("OCc1ccccc1CN"); + Assert.assertEquals(2, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue()); + } + + @Test + public void test11LargestChainDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception { + Object[] params = {new Boolean(true), new Boolean(true)}; + descriptor.setParameters(params); + SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); + IAtomContainer mol = sp.parseSmiles("COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C"); + Assert.assertEquals(2, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue()); + } + } -- 1.9.3 (Apple Git-50)