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johnmayegonw
johnmay
authored and
egonw
committed
Some collatoral damage - there is a "defeat device" that tries to slurp up all MDL files and run them though the atom typer. Probably will just replace with SMILES or at best an SDFfile. For now let's keep it working as we expect.
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‎base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java

Lines changed: 3 additions & 1 deletion
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@@ -96,6 +96,8 @@ public void testASNfiles() throws Exception {
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Assert.assertEquals("Could not match all atom types!", tested, (tested - failed));
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}
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// this test is a bit of a "defeat device" for modularising testdata, hey ho, let's just dupe
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// them all locally for now and perhaps replace with an SDF
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@Test
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public void testMDLMolfiles() throws Exception {
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final String DIRNAME = "data/mdl/";
@@ -106,7 +108,7 @@ public void testMDLMolfiles() throws Exception {
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"bug716259.mol", "bug771485-1.mol", "bug771485-2.mol", "bug853254-1.mol", "bug853254-2.mol",
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"bug931608-1.mol", "bug931608-2.mol", "bug934819-1.mol", "bug934819-2.mol", "Butane-TestFF.mol",
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"Butane-TestFF-output.mol", "butanoic_acid.mol", "C12308.mol", "carbocations.mol", "choloylcoa.mol",
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"clorobenzene.mol", "cyclooctadien.mol", "cyclooctan.mol", "cycloocten.mol", "cyclopropane.mol",
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"chlorobenzene.mol", "cyclooctadien.mol", "cyclooctan.mol", "cycloocten.mol", "cyclopropane.mol",
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"d-ala.mol", "decalin.mol", "D+-glucose.mol", "D-mannose.mol", "Ethane-TestFF.mol",
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"Ethane-TestFF-output.mol", "figueras-test-buried.mol", "figueras-test-inring.mol",
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"figueras-test-sep3D.mol", "four-ring-5x10.mol", "heptane_almost_cyclic.mol",

‎base/test-core/src/test/resources/data/mdl/allmol231.mol

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‎base/test-core/src/test/resources/data/mdl/allmol232.mol

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‎base/test-core/src/test/resources/data/mdl/bug1772609.mol

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$$$$

‎base/test-core/src/test/resources/data/mdl/bug771485-1.mol

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‎base/test-core/src/test/resources/data/mdl/bug771485-2.mol

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‎base/test-core/src/test/resources/data/mdl/bug853254-1.mol

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‎base/test-core/src/test/resources/data/mdl/bug853254-2.mol

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‎base/test-core/src/test/resources/data/mdl/bug931608-2.mol

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1.4584 -2.0551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10+
1.4584 -1.2301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11+
0.7366 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12+
0.7366 -3.1747 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
13+
0.0000 -3.5798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14+
1.3258 -3.6829 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
15+
1 2 2 0 0 0 0
16+
1 6 1 0 0 0 0
17+
1 7 1 0 0 0 0
18+
2 3 1 0 0 0 0
19+
3 4 2 0 0 0 0
20+
4 5 1 0 0 0 0
21+
4 8 1 0 0 0 0
22+
5 6 2 0 0 0 0
23+
8 9 1 0 0 0 0
24+
8 10 2 0 0 0 0
25+
M CHG 1 8 1
26+
M CHG 1 9 -1
27+
M END

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