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Added a test case for bug 3315503 to ensure that Mol2Writer is not th…
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…rowing an NPE when faced with an unknown atom type. Also added test data file.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@rajarshi @egonw
rajarshi authored and egonw committed Jun 20, 2011
1 parent 63619c2 commit aa35eae
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204 changes: 204 additions & 0 deletions src/test/data/mdl/ligand-1a0i.sdf
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@@ -0,0 +1,204 @@
1A0I_ATP_A_1
RCSB PDB04121112133D
Coordinates from PDB:1A0I:A:1 Model:1 without hydrogens
31 33 0 0 0 0 999 V2000
-1.4630 -18.5150 50.8220 P 0 0 0 0 0 0 0 0 0 0 0 0
-1.2090 -18.0430 49.4400 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.5300 -17.2750 51.6340 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8510 -19.0240 50.8640 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2750 -19.5630 52.8510 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.6560 -20.1450 53.8680 O 0 0 0 0 0 0 0 0 0 0 0 0
1.5190 -20.4000 52.9670 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.3050 -19.5070 51.3540 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9300 -17.4650 53.3890 P 0 0 0 0 0 0 0 0 0 0 0 0
2.5380 -17.6780 52.0570 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6500 -15.9920 53.4350 O 0 0 0 0 0 0 0 0 0 0 0 0
0.6260 -18.1970 53.3730 O 0 0 0 0 0 0 0 0 0 0 0 0
2.9180 -17.8830 54.5940 O 0 0 0 0 0 0 0 0 0 0 0 0
2.6240 -17.4710 55.9330 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1670 -18.7010 56.7120 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9630 -19.8680 56.4910 O 0 0 0 0 0 0 0 0 0 0 0 0
1.2670 -18.7570 57.9400 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0300 -18.1290 57.9260 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3200 -20.2340 58.3070 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0620 -20.8690 58.1950 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5980 -20.7080 57.6020 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6340 -21.5680 58.2300 N 0 0 0 0 0 0 0 0 0 0 0 0
3.9520 -22.9070 58.0310 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0160 -23.2570 58.8640 N 0 0 0 0 0 0 0 0 0 0 0 0
5.2750 -22.1220 59.5800 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2540 -22.1790 60.5260 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0510 -23.3780 60.8010 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4270 -21.0100 61.2320 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5890 -19.9570 60.8820 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6040 -19.9410 59.9160 N 0 0 0 0 0 0 0 0 0 0 0 0
4.4610 -21.1210 59.2230 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 8 1 0 0 0 0
5 6 2 0 0 0 0
5 7 1 0 0 0 0
5 8 1 0 0 0 0
5 12 1 0 0 0 0
9 10 2 0 0 0 0
9 11 1 0 0 0 0
9 12 1 0 0 0 0
9 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
15 17 1 0 0 0 0
16 21 1 0 0 0 0
17 18 1 0 0 0 0
17 19 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
21 22 1 0 0 0 0
22 23 1 0 0 0 0
22 31 1 0 0 0 0
23 24 2 0 0 0 0
24 25 1 0 0 0 0
25 26 1 0 0 0 0
25 31 2 0 0 0 0
26 27 1 0 0 0 0
26 28 2 0 0 0 0
28 29 1 0 0 0 0
29 30 2 0 0 0 0
30 31 1 0 0 0 0
A 1
PG
A 2
O1G
A 3
O2G
A 4
O3G
A 5
PB
A 6
O1B
A 7
O2B
A 8
O3B
A 9
PA
A 10
O1A
A 11
O2A
A 12
O3A
A 13
O5'
A 14
C5'
A 15
C4'
A 16
O4'
A 17
C3'
A 18
O3'
A 19
C2'
A 20
O2'
A 21
C1'
A 22
N9
A 23
C8
A 24
N7
A 25
C5
A 26
C6
A 27
N6
A 28
N1
A 29
C2
A 30
N3
A 31
C4
M END
> <InstanceId>
1A0I_ATP_A_1

> <ChemCompId>
ATP

> <PdbId>
1A0I

> <ChainId>
A

> <ResidueNumber>
1

> <InsertionCode>


> <Model>
1

> <AltIds>


> <MissingHeavyAtoms>
0

> <ObservedFormula>
C10 N5 O13 P3

> <Name>
ADENOSINE-5'-TRIPHOSPHATE

> <SystematicName>
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate

> <Synonyms>


> <Type>
NON-POLYMER

> <Formula>
C10 H16 N5 O13 P3

> <MolecularWeight>
507.181

> <ModifiedDate>
2008-10-14

> <Parent>


> <OneLetterCode>


> <SubcomponentList>


> <AmbiguousFlag>
N

> <InChI>
InChI=1/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1/f/h18-19,21,23H,11H2

> <InChIKey>
ZKHQWZAMYRWXGA-FJYXAIENDD

> <SMILES>
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N

$$$$
39 changes: 35 additions & 4 deletions src/test/org/openscience/cdk/io/Mol2WriterTest.java
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Expand Up @@ -24,22 +24,27 @@
*/
package org.openscience.cdk.io;

import java.io.IOException;
import java.io.StringWriter;

import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
import java.util.List;

/**
* TestCase for the writer MOL2 writer.
Expand Down Expand Up @@ -125,4 +130,30 @@ public void testWriterForAmide() throws Exception {
}


/**
* This test just ensures that Mol2Writer does not throw an NPE.
*
* It does not test whether the output is correct or not.
* @throws Exception
* @cdk.bug 3315503
*/
@Test
public void testMissingAtomType() throws Exception {
String filename = "data/mdl/ligand-1a0i.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
IChemFile fileContents = (IChemFile) reader.read(new ChemFile());
List<IAtomContainer> molecules = ChemFileManipulator.getAllAtomContainers(fileContents);
IAtomContainer mol = molecules.get(0);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);

StringWriter writer = new StringWriter();
Mol2Writer molwriter = new Mol2Writer(writer);
molwriter.write(mol);
molwriter.close();

String mol2file = writer.getBuffer().toString();
Assert.assertTrue(mol2file.indexOf("24 R24 -1.209 -18.043 49.44 X") > 0);
}
}

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