-
Notifications
You must be signed in to change notification settings - Fork 154
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Factored out the test for PDB atom customization; also fixed the test…
… to register the customizer (but there is more wrong) Change-Id: I02ada008ab0736a0137544266566ef96c21d4c56 Signed-off-by: John May <john.wilkinsonmay@gmail.com> Conflicts: build.xml src/test/org/openscience/cdk/io/cml/CML2Test.java
- Loading branch information
Showing
7 changed files
with
163 additions
and
68 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| cdk-annotation.jar | ||
| cdk-core.jar | ||
| cdk-data.jar | ||
| cdk-pdb.jar | ||
| cdk-standard.jar | ||
| cdk-interfaces.jar | ||
| cdk-libiocml.jar | ||
| cdk-pdbcml.jar | ||
| cdk-io.jar | ||
| cdk-test.jar | ||
| cdk-testdata.jar |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| junit-4.11.jar | ||
| hamcrest-core-1.3.jar | ||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| vecmath*.jar | ||
| xom*.jar | ||
| cmlxom-2.5-b1.jar | ||
| log4j*.jar | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
105 changes: 105 additions & 0 deletions
105
src/test/org/openscience/cdk/io/cml/PDBAtomCustomizerTest.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| /* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project | ||
| * 2013 Egon Willighagen <egonw@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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.io.cml; | ||
|
|
||
| import java.io.ByteArrayInputStream; | ||
| import java.io.InputStream; | ||
| import java.io.StringWriter; | ||
|
|
||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
| import org.openscience.cdk.CDKTestCase; | ||
| import org.openscience.cdk.ChemFile; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.interfaces.IBioPolymer; | ||
| import org.openscience.cdk.interfaces.IChemFile; | ||
| import org.openscience.cdk.interfaces.IChemModel; | ||
| import org.openscience.cdk.interfaces.IChemSequence; | ||
| import org.openscience.cdk.io.CMLReader; | ||
| import org.openscience.cdk.io.CMLWriter; | ||
| import org.openscience.cdk.io.ISimpleChemObjectReader; | ||
| import org.openscience.cdk.io.PDBReader; | ||
| import org.openscience.cdk.libio.cml.PDBAtomCustomizer; | ||
| import org.openscience.cdk.protein.data.PDBPolymer; | ||
|
|
||
| /** | ||
| * TestCase for the {@link PDBAtomCustomizer} class. | ||
| * | ||
| * @cdk.module test-pdbcml | ||
| */ | ||
| public class PDBAtomCustomizerTest extends CDKTestCase { | ||
|
|
||
| /** | ||
| * A roundtripping test to see of PDB atom customization works. | ||
| * | ||
| * @cdk.bug 1085912 | ||
| */ | ||
| @Test public void testSFBug1085912_1() throws Exception { | ||
| String filename_pdb = "data/pdb/1CKV.pdb"; | ||
| InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename_pdb); | ||
|
|
||
| ISimpleChemObjectReader reader = new PDBReader(ins1); | ||
| IChemFile chemFile1 = (IChemFile) reader.read(new ChemFile()); | ||
| IChemSequence seq1 = chemFile1.getChemSequence(0); | ||
| IChemModel model1 = seq1.getChemModel(0); | ||
| IAtomContainer container = model1.getMoleculeSet().getAtomContainer(0); | ||
| IBioPolymer polymer1 = (IBioPolymer)container; | ||
| int countchemFile1 = chemFile1.getChemSequenceCount(); | ||
| int countmodel1 = model1.getMoleculeSet().getAtomContainerCount(); | ||
| int countpolymer1 = polymer1.getAtomCount(); | ||
|
|
||
| StringWriter writer = new StringWriter(); | ||
| CMLWriter cmlWriter = new CMLWriter(writer); | ||
| cmlWriter.registerCustomizer(new PDBAtomCustomizer()); | ||
| cmlWriter.write(polymer1); | ||
| String cmlContent1 = writer.toString(); | ||
| System.out.println(cmlContent1.substring(0, 500)); | ||
|
|
||
| CMLReader reader2 = new CMLReader(new ByteArrayInputStream(cmlContent1.getBytes())); | ||
| IChemFile chemFil2 = (IChemFile)reader2.read(new ChemFile()); | ||
| IChemSequence seq2 = chemFil2.getChemSequence(0); | ||
| IChemModel model2 = seq2.getChemModel(0); | ||
| PDBPolymer polymer2 = (PDBPolymer) model2.getMoleculeSet().getAtomContainer(0); | ||
|
|
||
| int countchemFile2 = chemFil2.getChemSequenceCount(); | ||
| int countmodel2 = model2.getMoleculeSet().getAtomContainerCount(); | ||
| int countpolymer2 = polymer2.getAtomCount(); | ||
|
|
||
| Assert.assertEquals(countchemFile1, countchemFile2); | ||
| Assert.assertEquals(countmodel1,countmodel2); | ||
| Assert.assertEquals(countpolymer1,countpolymer2); | ||
|
|
||
| writer = new StringWriter(); | ||
| cmlWriter = new CMLWriter(writer); | ||
| cmlWriter.registerCustomizer(new PDBAtomCustomizer()); | ||
| cmlWriter.write(polymer2); | ||
| String cmlContent2 = writer.toString(); | ||
| System.out.println(cmlContent2.substring(0, 500)); | ||
|
|
||
| String conte1 = cmlContent1.substring(0, 1000); | ||
| String conte2 = cmlContent2.substring(0, 1000); | ||
| Assert.assertEquals(conte1,conte2); | ||
| } | ||
|
|
||
| } |
35 changes: 35 additions & 0 deletions
35
src/test/org/openscience/cdk/modulesuites/MpdbcmlTests.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| /* Copyright (C) 2013 Egon Willighagen <egonw@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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.modulesuites; | ||
|
|
||
| import org.junit.runner.RunWith; | ||
| import org.junit.runners.Suite; | ||
| import org.junit.runners.Suite.SuiteClasses; | ||
| import org.openscience.cdk.io.cml.PDBAtomCustomizerTest; | ||
|
|
||
| /** | ||
| * TestSuite that runs all the unit tests for the CDK module pdbcml. | ||
| * | ||
| * @cdk.module test-pdbcml | ||
| */ | ||
| @RunWith(value=Suite.class) | ||
| @SuiteClasses(value={ | ||
| PDBAtomCustomizerTest.class | ||
| }) | ||
| public class MpdbcmlTests {} |