Skip to content

Commit

Permalink
Added type check for the atom-atom mapping property.
Browse files Browse the repository at this point in the history 
Change-Id: Iaa4fc3d4b89bb2314b162f9086471eb6cf17b135
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  • Loading branch information
@egonw
Stephan Beisken authored and egonw committed Dec 12, 2012
1 parent 856781e commit 962e33b
Show file tree
Hide file tree
Showing 2 changed files with 54 additions and 6 deletions.
17 changes: 15 additions & 2 deletions src/main/org/openscience/cdk/io/MDLV2000Writer.java
View file
Expand Up @@ -384,8 +384,21 @@ public void writeMolecule(IAtomContainer container) throws Exception {
line += " 0 0 0";

if (container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING) != null) {
int value = ((Integer)container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue();
line += formatMDLInt(value, 3);
Object atomAtomMapping = container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING);
if (atomAtomMapping instanceof String) {
try {
int value = Integer.parseInt((String) atomAtomMapping);
line += formatMDLInt(value, 3);
} catch (NumberFormatException exception) {
line += formatMDLInt(0, 3);
logger.warn("Skipping atom-atom mapping, invalid value: " + atomAtomMapping);
}
} else if (atomAtomMapping instanceof Integer) {
int value = (Integer) atomAtomMapping;
line += formatMDLInt(value, 3);
} else {
line += formatMDLInt(0, 3);
}
} else {
line += formatMDLInt(0, 3);
}
Expand Down
43 changes: 39 additions & 4 deletions src/test/org/openscience/cdk/io/MDLV2000WriterTest.java
View file
Expand Up @@ -27,6 +27,8 @@
import java.io.InputStream;
import java.io.StringWriter;
import java.util.Properties;
import java.util.regex.Pattern;
import java.util.regex.Matcher;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
Expand Down Expand Up @@ -90,7 +92,7 @@ public class MDLV2000WriterTest extends ChemObjectIOTest {
molecule.addAtom(new PseudoAtom("*"));
molecule.addAtom(new Atom("C"));
molecule.addAtom(new Atom("C"));

MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.write(molecule);
Assert.assertTrue(writer.toString().indexOf("M END") != -1);
Expand All @@ -105,14 +107,14 @@ public class MDLV2000WriterTest extends ChemObjectIOTest {
Atom atom = new Atom("C");
atom.setMassNumber(14);
molecule.addAtom(atom);

MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.write(molecule);
String output = writer.toString();
//logger.debug("MDL output for testBug1212219: " + output);
Assert.assertTrue(output.indexOf("M ISO 1 1 14") != -1);
}

@Test public void testWriteValence() throws Exception {
StringWriter writer = new StringWriter();
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
Expand All @@ -129,7 +131,7 @@ public class MDLV2000WriterTest extends ChemObjectIOTest {
Assert.assertTrue(output.indexOf("0 0 0 0 0 1 0 0 0 0 0 0") != -1);
Assert.assertTrue(output.indexOf("0 0 0 0 0 15 0 0 0 0 0 0") != -1);
}

@Test public void testWriteAtomAtomMapping() throws Exception {
StringWriter writer = new StringWriter();
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
Expand All @@ -141,6 +143,39 @@ public class MDLV2000WriterTest extends ChemObjectIOTest {
Assert.assertTrue(output.indexOf("0 0 0 0 0 0 0 0 0 1 0 0") != -1);
Assert.assertTrue(output.indexOf("0 0 0 0 0 0 0 0 0 15 0 0") != -1);
}

/**
* Tests if String atom atom mappings are parsed correctly
*/
@Test public void testWriteStringAtomAtomMapping() throws Exception {
StringWriter writer = new StringWriter();
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
molecule.getAtom(0).setProperty(CDKConstants.ATOM_ATOM_MAPPING,"1");
molecule.getAtom(1).setProperty(CDKConstants.ATOM_ATOM_MAPPING,"15");
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.write(molecule);
String output = writer.toString();
Assert.assertTrue(output.contains("0 0 0 0 0 0 0 0 0 1 0 0"));
Assert.assertTrue(output.contains("0 0 0 0 0 0 0 0 0 15 0 0"));
}

/**
* Tests if non-valid atom atom mappings are ignored by the reader.
*/
@Test public void testWriteInvalidAtomAtomMapping() throws Exception {
StringWriter writer = new StringWriter();
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
molecule.getAtom(0).setProperty(CDKConstants.ATOM_ATOM_MAPPING,"1a");
molecule.getAtom(1).setProperty(CDKConstants.ATOM_ATOM_MAPPING,"15");
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.write(molecule);
String output = writer.toString();
Pattern p = Pattern.compile(".*V2000.* 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 " +
"0 0.* 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 15 0 0.*",
Pattern.MULTILINE|Pattern.DOTALL);
Matcher m = p.matcher(output);
Assert.assertTrue(m.matches());
}

/**
* Test for bug #1778479 "MDLWriter writes empty PseudoAtom label string".
Expand Down

0 comments on commit 962e33b

Please sign in to comment.