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Deprecate MM2/MMFF94 atom type matchers. MMFF94 matcher is now much b…
…etter covered by the Mmff class.
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johnmay committed Sep 15, 2015
1 parent 46ec90b commit a431bd1
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Showing 5 changed files with 26 additions and 4 deletions.
9 changes: 8 additions & 1 deletion legacy/pom.xml
Expand Up @@ -48,13 +48,20 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-testdata</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-test-core</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-interfaces</artifactId>
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Expand Up @@ -41,7 +41,9 @@
* @cdk.created 2005-18-07
* @cdk.module extra
* @cdk.githash
* @deprecated Incomplete and error prone - use at your own risk.
*/
@Deprecated
public class MM2AtomTypeMatcher implements IAtomTypeMatcher {

private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MM2AtomTypeMatcher.class);
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Expand Up @@ -24,8 +24,11 @@

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.openscience.cdk.Atom;
import org.openscience.cdk.SlowTest;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
Expand All @@ -40,13 +43,18 @@
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;

import java.io.InputStream;
import java.util.HashMap;
import java.util.Map;

/**
* Checks the functionality of the AtomType-MMFF2AtomTypeMatcher.
*
* @cdk.module test-extra
*
* @see org.openscience.cdk.atomtype.MM2AtomTypeMatcher
* @see MM2AtomTypeMatcher
*/
@Category(SlowTest.class)
public class MM2AtomTypeMatcherTest extends AbstractAtomTypeTest {

private static ILoggingTool logger = LoggingToolFactory
Expand Down Expand Up @@ -153,7 +161,7 @@ public void testNsp2() {
* in the source. Ugly, but @AfterClass does not work because that
* method cannot Assert.assert anything.
*/
@Test
@Ignore("Atom type matcher is incomplete")
public void countTestedAtomTypes() {
AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/mm2_atomtypes.xml",
SilentChemObjectBuilder.getInstance());
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Expand Up @@ -45,12 +45,17 @@
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;

import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;

/**
* Checks the functionality of the AtomType-MMFF94AtomTypeMatcher.
*
* @cdk.module test-extra
*
* @see org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
* @see MMFF94AtomTypeMatcher
*/
public class MMFF94AtomTypeMatcherTest extends AbstractAtomTypeTest {

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