-
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.
Moved all tests with smiles from cdk-test-io to cdk-test-smiles
Conflicts: src/META-INF/test-io.devellibdepends Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
- Loading branch information
Showing
11 changed files
with
164 additions
and
36 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
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 |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| junit-4.11.jar | ||
| hamcrest-core-1.3.jar | ||
| mockito-all-1.9.5.jar | ||
| groovy.jar | ||
| asm-3.2.jar | ||
| antlr.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 |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| cdk-annotation.jar | ||
| cdk-interfaces.jar | ||
| cdk-atomtype.jar | ||
| cdk-core.jar | ||
| cdk-standard.jar | ||
| cdk-data.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
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
112 changes: 112 additions & 0 deletions
112
src/test/org/openscience/cdk/io/SMILES2Mol2WriterTest.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 +1,112 @@ | ||
| /* | ||
| * Copyright (c) 2013. John May <jwmay@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 U | ||
| */ | ||
| package org.openscience.cdk.io; | ||
|
|
||
| import org.junit.Assert; | ||
| import org.junit.BeforeClass; | ||
| import org.junit.Test; | ||
| import org.openscience.cdk.ChemFile; | ||
| import org.openscience.cdk.DefaultChemObjectBuilder; | ||
| import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.interfaces.IChemFile; | ||
| import org.openscience.cdk.interfaces.IChemObjectBuilder; | ||
| import org.openscience.cdk.silent.AtomContainer; | ||
| import org.openscience.cdk.silent.SilentChemObjectBuilder; | ||
| import org.openscience.cdk.smiles.SmilesParser; | ||
| import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; | ||
| import org.openscience.cdk.tools.manipulator.ChemFileManipulator; | ||
|
|
||
| import java.io.InputStream; | ||
| import java.io.StringWriter; | ||
| import java.util.List; | ||
|
|
||
| /** | ||
| * TestCase for the writer MOL2 writer from smiles. | ||
| * | ||
| * @cdk.module test-smiles | ||
| * @see org.openscience.cdk.io.Mol2Writer | ||
| */ | ||
| public class SMILES2Mol2WriterTest { | ||
|
|
||
| private static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance(); | ||
|
|
||
| /** | ||
| * @throws org.openscience.cdk.exception.CDKException | ||
| * @throws java.io.IOException | ||
| * @cdk.bug 2675188 | ||
| */ | ||
| @Test | ||
| public void testWriter1() throws Exception { | ||
| SmilesParser sp = new SmilesParser(builder); | ||
| IAtomContainer molecule = sp.parseSmiles("C([H])([H])([H])([H])"); | ||
|
|
||
| StringWriter swriter = new StringWriter(); | ||
| Mol2Writer writer = new Mol2Writer(swriter); | ||
| writer.write(molecule); | ||
| writer.close(); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("1 C1 0.000 0.000 0.000 C.3") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("1 2 1 1") > 0); | ||
| } | ||
|
|
||
| @Test | ||
| public void testWriter2() throws Exception { | ||
| SmilesParser sp = new SmilesParser(builder); | ||
| IAtomContainer molecule = sp.parseSmiles("c1ccccc1C=O"); | ||
| CDKHueckelAromaticityDetector.detectAromaticity(molecule); | ||
|
|
||
| StringWriter swriter = new StringWriter(); | ||
| Mol2Writer writer = new Mol2Writer(swriter); | ||
| writer.write(molecule); | ||
| writer.close(); | ||
|
|
||
| Assert.assertTrue("Aromatic atom not properly reported", | ||
| swriter.getBuffer().toString().indexOf("1 C1 0.000 0.000 0.000 C.ar") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("8 O8 0.000 0.000 0.000 O.2") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("7 C7 0.000 0.000 0.000 C.2") > 0); | ||
| Assert.assertTrue("Aromatic bond not properly reported", | ||
| swriter.getBuffer().toString().indexOf("1 2 1 ar") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("8 8 7 2") > 0); | ||
| } | ||
|
|
||
| @Test | ||
| public void testWriterForAmide() throws Exception { | ||
| SmilesParser sp = new SmilesParser(builder); | ||
| IAtomContainer molecule = sp.parseSmiles("CC(=O)NC"); | ||
| CDKHueckelAromaticityDetector.detectAromaticity(molecule); | ||
|
|
||
| StringWriter swriter = new StringWriter(); | ||
| Mol2Writer writer = new Mol2Writer(swriter); | ||
| writer.write(molecule); | ||
| writer.close(); | ||
|
|
||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("1 C1 0.000 0.000 0.000 C.3") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("3 O3 0.000 0.000 0.000 O.") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("4 N4 0.000 0.000 0.000 N.a") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("1 2 1 1") > 0); | ||
| Assert.assertTrue("Amide bond not properly reported", | ||
| swriter.getBuffer().toString().indexOf("3 4 2 am") > 0); | ||
| Assert.assertTrue(swriter.getBuffer().toString().indexOf("4 5 4 1") > 0); | ||
| } | ||
| } |
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
Oops, something went wrong.