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Added test data and setUp method for manager tests
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/0037.cml
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<cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110444"><atomArray><atom id="a1" elementType="C" x2="2.89" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="2.89" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="2.17" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="1.44" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="1.44" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="0.72" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.61" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="2.17" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="2.89" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="1.44" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-4.58" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="C" x2="0.72" y2="-5.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="C" x2="0.0" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="C" x2="2.89" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="C" x2="3.61" y2="-4.17" formalCharge="0" hydrogenCount="0" /><atom id="a16" elementType="C" x2="4.33" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a17" elementType="C" x2="4.33" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a18" elementType="C" x2="3.61" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a19" elementType="O" x2="1.44" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a20" elementType="N" x2="2.17" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a21" elementType="N" x2="0.0" y2="-2.08" formalCharge="0" hydrogenCount="0" /><atom id="a22" elementType="Si" x2="0.72" y2="-4.17" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a20" order="S" /><bond id="b2" atomRefs2="a1 a2" order="S" /><bond id="b3" atomRefs2="a1 a7" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a3 a4" order="S" /><bond id="b6" atomRefs2="a4 a5" order="S" /><bond id="b7" atomRefs2="a5 a20" order="S" /><bond id="b8" atomRefs2="a5 a6" order="S" /><bond id="b9" atomRefs2="a6 a21" order="T" /><bond id="b10" atomRefs2="a8 a20" order="S" /><bond id="b11" atomRefs2="a8 a9" order="S" /><bond id="b12" atomRefs2="a8 a10" order="S" /><bond id="b13" atomRefs2="a9 a14" order="D" /><bond id="b14" atomRefs2="a9 a18" order="S" /><bond id="b15" atomRefs2="a10 a19" order="S" /><bond id="b16" atomRefs2="a11 a22" order="S" /><bond id="b17" atomRefs2="a12 a22" order="S" /><bond id="b18" atomRefs2="a13 a22" order="S" /><bond id="b19" atomRefs2="a14 a15" order="S" /><bond id="b20" atomRefs2="a15 a16" order="D" /><bond id="b21" atomRefs2="a16 a17" order="S" /><bond id="b22" atomRefs2="a17 a18" order="D" /><bond id="b23" atomRefs2="a19 a22" order="S" /></bondArray></molecule></cml> |
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/0106.cml
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<cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110098"><atomArray><atom id="a1" elementType="C" x2="1.73" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="1.73" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="0.87" y2="-1.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="2.6" y2="-1.0" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="2.6" y2="-3.0" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="3.46" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.46" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="5.0" y2="-2.0" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="4.41" y2="-1.19" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="0.87" y2="-3.0" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="O" x2="2.6" y2="-4.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="O" x2="2.6" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="N" x2="0.0" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="N" x2="4.41" y2="-2.81" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="D" /><bond id="b2" atomRefs2="a1 a5" order="S" /><bond id="b3" atomRefs2="a1 a10" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a2 a4" order="S" /><bond id="b6" atomRefs2="a3 a14" order="D" /><bond id="b7" atomRefs2="a4 a7" order="S" /><bond id="b8" atomRefs2="a4 a13" order="D" /><bond id="b9" atomRefs2="a5 a6" order="S" /><bond id="b10" atomRefs2="a5 a12" order="D" /><bond id="b11" atomRefs2="a6 a7" order="D" /><bond id="b12" atomRefs2="a6 a15" order="S" /><bond id="b13" atomRefs2="a7 a9" order="S" /><bond id="b14" atomRefs2="a8 a9" order="D" /><bond id="b15" atomRefs2="a8 a15" order="S" /><bond id="b16" atomRefs2="a10 a11" order="D" /><bond id="b17" atomRefs2="a11 a14" order="S" /></bondArray></molecule></cml> |
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/TestData.java
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/******************************************************************************* | |||
* Copyright (c) 2007-2008 Bioclipse Project | |||
* All rights reserved. This program and the accompanying materials | |||
* are made available under the terms of the Eclipse Public License v1.0 | |||
* which accompanies this distribution, and is available at | |||
* http://www.eclipse.org/legal/epl-v10.html | |||
* | |||
* Contributors: | |||
* | |||
*******************************************************************************/ | |||
package testData; | |||
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import java.io.File; | |||
import java.io.InputStream; | |||
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import org.openscience.cdk.AtomContainer; | |||
import org.openscience.cdk.ChemObject; | |||
import org.openscience.cdk.Molecule; | |||
import org.openscience.cdk.exception.CDKException; | |||
import org.openscience.cdk.io.MDLReader; | |||
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/** | |||
* Instatiates some testdata from files in the testdata package | |||
* | |||
* @author jonalv | |||
* | |||
*/ | |||
public abstract class TestData { | |||
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private TestData() { | |||
} | |||
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public static AtomContainer getCycloPropane() throws CDKException { | |||
return readFromFile( "testData/cyclopropane.mol" ); | |||
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} | |||
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public static AtomContainer getCycloOctan() throws CDKException { | |||
return readFromFile( "testData/cyclooctan.mol" ); | |||
} | |||
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public static AtomContainer readFromFile(String path) throws CDKException { | |||
InputStream ins = TestData.class.getClassLoader().getResourceAsStream(path); | |||
MDLReader reader = new MDLReader(ins); | |||
return (AtomContainer) reader.read( (ChemObject)new Molecule() ); | |||
} | |||
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public static String getTestSDFFilePath() { | |||
return TestData.class | |||
.getClassLoader() | |||
.getResource("testData/sdfTestFile.sdf") | |||
.getPath(); | |||
} | |||
} |
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/atp.mol
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Marvin 07140515482D | |||
|
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31 33 0 0 0 0 999 V2000 | |||
0.4239 -4.2648 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
0.4239 -3.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.1384 -3.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.1384 -2.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
0.4239 -1.7898 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-0.2906 -2.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-1.0752 -1.9474 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-1.5601 -2.6148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-1.0752 -3.2823 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-0.2906 -3.0273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-1.3301 -1.1628 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 | |||
-0.8452 -0.4953 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-1.3301 0.1721 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 | |||
-1.0752 0.9567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-0.2682 1.1283 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-0.0133 1.9129 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 | |||
-0.7979 2.1678 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
0.7713 1.6579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
0.2417 2.6975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.0486 2.8690 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 | |||
0.8771 3.6760 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.2202 2.0621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.8556 3.0406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
2.4076 2.4275 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 | |||
3.0207 2.9795 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.7945 1.8754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
2.9597 1.8144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-2.1147 -0.0828 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 | |||
-2.7822 0.4021 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
-2.1147 -0.9078 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 | |||
-2.7822 -1.3927 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1 2 1 0 0 0 0 | |||
2 3 4 0 0 0 0 | |||
3 4 4 0 0 0 0 | |||
4 5 4 0 0 0 0 | |||
5 6 4 0 0 0 0 | |||
6 7 4 0 0 0 0 | |||
7 8 4 0 0 0 0 | |||
8 9 4 0 0 0 0 | |||
9 10 4 0 0 0 0 | |||
2 10 4 0 0 0 0 | |||
6 10 4 0 0 0 0 | |||
7 11 1 0 0 0 0 | |||
11 12 1 0 0 0 0 | |||
12 13 1 0 0 0 0 | |||
13 14 1 0 0 0 0 | |||
14 15 1 0 0 0 0 | |||
15 16 1 0 0 0 0 | |||
16 17 1 0 0 0 0 | |||
16 18 2 0 0 0 0 | |||
16 19 1 0 0 0 0 | |||
19 20 1 0 0 0 0 | |||
20 21 1 0 0 0 0 | |||
20 22 2 0 0 0 0 | |||
20 23 1 0 0 0 0 | |||
23 24 1 0 0 0 0 | |||
24 25 1 0 0 0 0 | |||
24 26 1 0 0 0 0 | |||
24 27 2 0 0 0 0 | |||
13 28 1 0 0 0 0 | |||
28 29 1 0 0 0 0 | |||
28 30 1 0 0 0 0 | |||
11 30 1 0 0 0 0 | |||
30 31 1 0 0 0 0 | |||
M END |
22 changes: 22 additions & 0 deletions
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/cyclooctan.mol
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|
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CDK | |||
|
|||
8 8 0 0 0 0 0 0 0 0999 V2000 | |||
258.0000 1001.9637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
224.7403 1015.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
291.2597 1015.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
210.9637 1049.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
305.0363 1049.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
224.7403 1082.2596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
291.2597 1082.2596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
258.0000 1096.0363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1 2 2 0 0 0 0 | |||
3 1 1 0 0 0 0 | |||
2 4 1 0 0 0 0 | |||
5 3 1 0 0 0 0 | |||
4 6 1 0 0 0 0 | |||
7 5 1 0 0 0 0 | |||
6 8 1 0 0 0 0 | |||
8 7 1 0 0 0 0 | |||
M END | |||
$$$$ |
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/cyclopropane.mol
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cyclopropane.mol | |||
|
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|
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9 9 0 0 0 1 V2000 | |||
-0.0073 -0.5272 0.9655 C 0 0 0 0 0 | |||
-0.6776 -0.7930 -0.3498 C 0 0 0 0 0 | |||
0.2103 0.4053 -0.1891 C 0 0 0 0 0 | |||
0.8019 -1.1711 1.2970 H 0 0 0 0 0 | |||
-0.6000 -0.2021 1.8155 H 0 0 0 0 0 | |||
-1.7511 -0.6586 -0.4435 H 0 0 0 0 0 | |||
-0.3492 -1.6277 -0.9620 H 0 0 0 0 0 | |||
1.1755 0.4303 -0.6860 H 0 0 0 0 0 | |||
-0.2264 1.3994 -0.1675 H 0 0 0 0 0 | |||
1 2 1 6 0 0 | |||
1 3 1 6 0 0 | |||
1 4 1 0 0 0 | |||
1 5 1 1 0 0 | |||
2 3 1 0 0 0 | |||
2 6 1 0 0 0 | |||
2 7 1 6 0 0 | |||
3 8 1 6 0 0 | |||
3 9 1 0 0 0 | |||
M END |
29 changes: 29 additions & 0 deletions
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plugins/net.bioclipse.structuredb.rdf.tests/src/testData/sdfTestFile.sdf
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@@ -0,0 +1,29 @@ | |||
|
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MassFron052fd10709212D | |||
|
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4 4 0 0 0 0 0 0 0 0 2 V2000 | |||
1.8966 -3.2759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.8966 -4.0345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
2.2759 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1.5172 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1 2 2 0 0 0 0 | |||
2 3 1 0 0 0 0 | |||
2 4 1 0 0 0 0 | |||
3 4 1 0 0 0 0 | |||
M CHG 1 3 1 | |||
M END | |||
$$$$ | |||
|
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MassFron052poiiiiiiii10709212D | |||
|
|||
4 3 0 0 0 0 0 0 0 0 2 V2000 | |||
4.5172 2.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
4.5172 3.5517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |||
5.1724 3.9310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
5.1724 4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |||
1 2 3 0 0 0 0 | |||
2 3 1 0 0 0 0 | |||
3 4 2 0 0 0 0 | |||
M CHG 1 2 1 | |||
M END | |||
$$$$ |