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Removes instanceof and .class usage of Molecule

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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rajarshi authored and egonw committed Dec 11, 2011
1 parent 5da1d1b commit 436dba589d018e50b7164fa74d15d57c468a5ee2
@@ -20,29 +20,27 @@
*/
package org.openscience.cdk.atomtype;

import java.io.InputStream;
import java.util.List;

import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
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.ISimpleChemObjectReader;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.PDBReader;
import org.openscience.cdk.silent.AtomContainer;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

import java.io.InputStream;
import java.util.List;

/**
* This class tests the matching of atom types defined in the
* cdk atom type list, using the test files in <code>src/test/data</code>.
@@ -228,11 +226,11 @@ private TestResults testFile(String dir, String filename, ISimpleChemObjectReade
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(dir+filename);
reader.setReader(ins);
IAtomContainer mol = null;
if (reader.accepts(Molecule.class)) {
mol = (IMolecule)reader.read(new AtomContainer());
if (reader.accepts(AtomContainer.class)) {
mol = reader.read(new AtomContainer());
} else if (reader.accepts(ChemFile.class)) {
IChemFile cf = (IChemFile)reader.read(new ChemFile());
mol = new AtomContainer();
IChemFile cf = reader.read(new ChemFile());
mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cf);
for (IAtomContainer container : containers) mol.add(container);
}
@@ -22,13 +22,10 @@
*/
package org.openscience.cdk.fingerprint;

import java.io.IOException;
import java.io.StringReader;
import java.util.BitSet;

import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.ISimpleChemObjectReader;
@@ -39,6 +36,10 @@
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.IOException;
import java.io.StringReader;
import java.util.BitSet;

/**
* @cdk.module test-standard
*/
@@ -81,15 +82,14 @@ public void testFingerprint() throws Exception {
* @throws Exception
*
* @cdk.bug 1626894
*
* @see testExtendedFingerPrint()
*
*/
@Test
public void testFingerPrint() throws Exception {
IFingerprinter printer = new GraphOnlyFingerprinter();

Molecule mol1 = createMolecule(molecule_test_2);
Molecule mol2 = createMolecule(ethanolamine);
IAtomContainer mol1 = createMolecule(molecule_test_2);
IAtomContainer mol2 = createMolecule(ethanolamine);
Assert.assertTrue("SubGraph does NOT match", UniversalIsomorphismTester.isSubgraph(mol1, mol2));

BitSet bs1 = printer.getFingerprint((IAtomContainer) mol1.clone());
@@ -101,13 +101,13 @@ public void testFingerPrint() throws Exception {
logger.debug("Subset (with fingerprint) does match");
}

private static Molecule createMolecule(String molecule) throws IOException, CDKException {
Molecule structure = null;
private static IAtomContainer createMolecule(String molecule) throws IOException, CDKException {
IAtomContainer structure = null;
if (molecule != null) {
ISimpleChemObjectReader reader = new MDLV2000Reader(new StringReader(molecule));
Assert.assertNotNull("Could not create reader", reader);
if (reader.accepts(Molecule.class)) {
structure = (Molecule) reader.read(new Molecule());
if (reader.accepts(AtomContainer.class)) {
structure = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
}
}
return structure;
@@ -24,16 +24,15 @@
package org.openscience.cdk.io;

import groovy.lang.GroovyShell;

import java.io.StringWriter;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.Molecule;

import java.io.StringWriter;

/**
* TestCase for the writer CDK source code files using one test file.
*
@@ -48,7 +47,6 @@
}

@Test public void testAccepts() throws Exception {
Assert.assertTrue(chemObjectIO.accepts(Molecule.class));
Assert.assertTrue(chemObjectIO.accepts(AtomContainer.class));
}

@@ -28,15 +28,12 @@
*/
package org.openscience.cdk.io;

import java.io.InputStream;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Reaction;
import org.openscience.cdk.ReactionSet;
import org.openscience.cdk.exception.CDKException;
@@ -46,9 +43,12 @@
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.silent.AtomContainer;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.InputStream;

/**
* TestCase for the reading MDL RXN files using one test file.
*
@@ -72,7 +72,7 @@
Assert.assertTrue(reader.accepts(Reaction.class));
Assert.assertTrue(reader.accepts(ReactionSet.class));
Assert.assertFalse(reader.accepts(AtomContainerSet.class));
Assert.assertFalse(reader.accepts(Molecule.class));
Assert.assertFalse(reader.accepts(AtomContainer.class));
}

@Test public void testReadReactions1() throws Exception {
@@ -24,10 +24,6 @@
* */
package org.openscience.cdk.io;

import java.io.InputStream;
import java.io.StringReader;
import java.util.List;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -48,6 +44,10 @@
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

import java.io.InputStream;
import java.io.StringReader;
import java.util.List;

/**
* TestCase for the reading MDL mol files using one test file.
* A test case for SDF files is available as separate Class.
@@ -71,7 +71,7 @@
reader.setReaderMode(Mode.STRICT);
Assert.assertTrue(reader.accepts(ChemFile.class));
Assert.assertTrue(reader.accepts(ChemModel.class));
Assert.assertTrue(reader.accepts(Molecule.class));
Assert.assertTrue(reader.accepts(AtomContainer.class));
}

@Test public void testReadFromStringReader() throws Exception {
@@ -24,14 +24,6 @@
* */
package org.openscience.cdk.io;

import java.io.InputStream;
import java.io.StringReader;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -58,6 +50,14 @@
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

import java.io.InputStream;
import java.io.StringReader;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;


/**
* TestCase for the reading MDL mol files using one test file.
@@ -81,7 +81,6 @@
MDLV2000Reader reader = new MDLV2000Reader();
Assert.assertTrue(reader.accepts(ChemFile.class));
Assert.assertTrue(reader.accepts(ChemModel.class));
Assert.assertTrue(reader.accepts(Molecule.class));
Assert.assertTrue(reader.accepts(AtomContainer.class));
}

@@ -23,12 +23,6 @@
*/
package org.openscience.cdk.io;

import java.io.StringWriter;
import java.util.Properties;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -56,6 +50,11 @@
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import java.io.StringWriter;
import java.util.Properties;


/**
* TestCase for the writer MDL mol files using one test file.
@@ -77,7 +76,6 @@
MDLV2000Writer reader = new MDLV2000Writer();
Assert.assertTrue(reader.accepts(ChemFile.class));
Assert.assertTrue(reader.accepts(ChemModel.class));
Assert.assertTrue(reader.accepts(Molecule.class));
Assert.assertTrue(reader.accepts(AtomContainer.class));
}

@@ -24,20 +24,19 @@
* */
package org.openscience.cdk.io;

import java.io.InputStream;
import java.io.StringReader;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
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.silent.AtomContainer;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.InputStream;
import java.io.StringReader;

/**
* TestCase for the reading MDL V3000 mol files using one test file.
*
@@ -57,7 +56,7 @@

@Test public void testAccepts() {
MDLV3000Reader reader = new MDLV3000Reader();
Assert.assertTrue(reader.accepts(Molecule.class));
Assert.assertTrue(reader.accepts(AtomContainer.class));
}

/**
@@ -27,14 +27,6 @@
* */
package org.openscience.cdk.io;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.util.Iterator;
import java.util.List;
import java.util.zip.GZIPInputStream;

import org.junit.Assert;
import org.junit.Assume;
import org.junit.BeforeClass;
@@ -49,12 +41,21 @@
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.silent.AtomContainer;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.util.Iterator;
import java.util.List;
import java.util.zip.GZIPInputStream;

/**
* TestCase for the reading SYBYL mol2 files using a test file.
*
@@ -75,7 +76,7 @@
Mol2Reader reader = new Mol2Reader();
Assert.assertTrue(reader.accepts(ChemFile.class));
Assert.assertTrue(reader.accepts(ChemModel.class));
Assert.assertTrue(reader.accepts(Molecule.class));
Assert.assertTrue(reader.accepts(AtomContainer.class));
}

/**

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