Read dimension field - there was actually already a test file that pr…

…eviously required setting a flag.
shekfeh · Sep 25, 2017 · a37ba2f · a37ba2f
1 parent 77ce652
commit a37ba2f
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Showing 2 changed files with 24 additions and 2 deletions.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -314,6 +314,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
 
  int linecount = 0;
  String title = null;
+ String program = null;
  String remark = null;
  String line = "";
 
@@ -333,6 +334,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
  }
  line = input.readLine();
  linecount++;
+ program = line;
  line = input.readLine();
  linecount++;
  if (line.length() > 0) {
@@ -406,8 +408,10 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
  }
  }
  } else if (!hasZ) {
-
- if (!forceReadAs3DCoords.isSet()) {
+ //' CDK 09251712073D'
+ // 0123456789012345678901
+ if (!(program.length() >= 22 && program.substring(20, 22).equals("3D"))
+ && !forceReadAs3DCoords.isSet()) {
  for (IAtom atomToUpdate : atoms) {
  Point3d p3d = atomToUpdate.getPoint3d();
  if (p3d != null) {

diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -561,6 +561,24 @@ public void testZeroZCoordinates() throws Exception {
  assertTrue(has3d);
  }
 
+ /**
+ * @cdk.bug 1732307
+ */
+ @Test
+ public void testZeroZCoordinates3DMarked() throws Exception {
+ String filename = "data/mdl/nozcoord.sdf";
+ logger.info("Testing: " + filename);
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ IAtomContainer mol = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
+ reader.close();
+ Assert.assertNotNull(mol);
+ Assert.assertEquals(5, mol.getAtomCount());
+
+ boolean has3d = GeometryUtil.has3DCoordinates(mol);
+ assertTrue(has3d);
+ }
+
  /**
  * @cdk.bug 1826577
  */