preserve atom coords from ALS atom

dkatzel-ncats · dkatzel-ncats · commit e62804a86000 · 2020-09-21T20:47:28.000-04:00
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
@@ -979,7 +979,11 @@ void readPropertiesFast(final BufferedReader input, final IAtomContainer contain
                             QueryAtom ref = (QueryAtom)AtomRef.deref(atom);
                             ref.setExpression(expr);
                         } else {
-                            container.setAtom(index, new QueryAtom(expr));
+                            QueryAtom queryAtom = new QueryAtom(expr);
+                            //keep coordinates from old atom
+                            queryAtom.setPoint2d(atom.getPoint2d());
+                            queryAtom.setPoint3d(atom.getPoint3d());
+                            container.setAtom(index, queryAtom);
                         }
                     }
                     break;

Original file line number	Diff line number	Diff line change
`@@ -979,7 +979,11 @@ void readPropertiesFast(final BufferedReader input, final IAtomContainer contain`
`979`	`979`	`QueryAtom ref = (QueryAtom)AtomRef.deref(atom);`
`980`	`980`	`ref.setExpression(expr);`
`981`	`981`	`} else {`
`982`		`- container.setAtom(index, new QueryAtom(expr));`
	`982`	`+ QueryAtom queryAtom = new QueryAtom(expr);`
	`983`	`+ //keep coordinates from old atom`
	`984`	`+ queryAtom.setPoint2d(atom.getPoint2d());`
	`985`	`+ queryAtom.setPoint3d(atom.getPoint3d());`
	`986`	`+ container.setAtom(index, queryAtom);`
`983`	`987`	`}`
`984`	`988`	`}`
`985`	`989`	`break;`