bug fix if we read mol file containing a M ALS line with an AtomContainer

dkatzel-ncats · dkatzel-ncats · commit 57679c9d4c86 · 2020-09-21T16:15:24.000-04:00
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
@@ -520,17 +520,26 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
                 }
             }
 
-            // sanity check that we have a decent molecule, query bonds mean we
+            // sanity check that we have a decent molecule, query bonds or query atoms mean we
             // don't have a hydrogen count for atoms and stereo perception isn't
             // currently possible
             if (!(outputContainer instanceof IQueryAtomContainer) && !isQuery &&
                 addStereoElements.isSet() && hasX && hasY) {
-                if (hasZ) { // has 3D coordinates
-                    outputContainer.setStereoElements(StereoElementFactory.using3DCoordinates(outputContainer)
-                            .createAll());
-                } else if (!forceReadAs3DCoords.isSet()) { // has 2D coordinates (set as 2D coordinates)
-                    outputContainer.setStereoElements(StereoElementFactory.using2DCoordinates(outputContainer)
-                            .createAll());
+                //ALS property could have changed an atom into a QueryAtom
+                for(IAtom atom : outputContainer.atoms()){
+                    if (AtomRef.deref(atom) instanceof QueryAtom) {
+                        isQuery=true;
+                        break;
+                    }
+                }
+                if(!isQuery) {
+                    if (hasZ) { // has 3D coordinates
+                        outputContainer.setStereoElements(StereoElementFactory.using3DCoordinates(outputContainer)
+                                .createAll());
+                    } else if (!forceReadAs3DCoords.isSet()) { // has 2D coordinates (set as 2D coordinates)
+                        outputContainer.setStereoElements(StereoElementFactory.using2DCoordinates(outputContainer)
+                                .createAll());
+                    }
                 }
             }
 
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
@@ -1886,4 +1886,14 @@ public void checkFuseBondWithFewerBondsThanAtoms() throws IOException, CDKExcept
             assertThat(mol.getAtomCount(), is(108));
         }
     }
+    @Test
+    public void atomlistWithAtomContainer() throws Exception {
+        try (InputStream in = getClass().getResourceAsStream("query_notatomlist.mol");
+             MDLV2000Reader mdlr = new MDLV2000Reader(in)) {
+
+            IAtomContainer mol = mdlr.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
+            IAtom               deref     = AtomRef.deref(mol.getAtom(0));
+            assertThat(deref, CoreMatchers.<IAtom>instanceOf(QueryAtom.class));
+        }
+    }
 }

Original file line number	Diff line number	Diff line change
`@@ -1886,4 +1886,14 @@ public void checkFuseBondWithFewerBondsThanAtoms() throws IOException, CDKExcept`
`1886`	`1886`	`assertThat(mol.getAtomCount(), is(108));`
`1887`	`1887`	`}`
`1888`	`1888`	`}`
	`1889`	`+ @Test`
	`1890`	`+ public void atomlistWithAtomContainer() throws Exception {`
	`1891`	`+ try (InputStream in = getClass().getResourceAsStream("query_notatomlist.mol");`
	`1892`	`+ MDLV2000Reader mdlr = new MDLV2000Reader(in)) {`
	`1893`	`+`
	`1894`	`+ IAtomContainer mol = mdlr.read(SilentChemObjectBuilder.getInstance().newAtomContainer());`
	`1895`	`+ IAtom deref = AtomRef.deref(mol.getAtom(0));`
	`1896`	`+ assertThat(deref, CoreMatchers.<IAtom>instanceOf(QueryAtom.class));`
	`1897`	`+ }`
	`1898`	`+ }`
`1889`	`1899`	`}`