Anonymise should copy coordinates from the input.

cdk · Jun 26, 2018 · 9966e60 · 9966e60
1 parent 60b2bcc
commit 9966e60
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -71,6 +71,9 @@
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
 import org.openscience.cdk.stereo.TetrahedralChirality;
 
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+
 /**
  * Class with convenience methods that provide methods to manipulate
  * AtomContainer's. For example:
@@ -1491,7 +1494,15 @@ public static IAtomContainer anonymise(IAtomContainer src) {
         IBond[] bonds = new IBond[src.getBondCount()];
 
         for (int i = 0; i < atoms.length; i++) {
-            atoms[i] = builder.newInstance(IAtom.class, "C");
+            atoms[i] = builder.newAtom();
+            atoms[i].setAtomicNumber(6);
+            atoms[i].setSymbol("C");
+            atoms[i].setImplicitHydrogenCount(0);
+            IAtom srcAtom = src.getAtom(i);
+            if (srcAtom.getPoint2d() != null)
+                atoms[i].setPoint2d(new Point2d(srcAtom.getPoint2d()));
+            if (srcAtom.getPoint3d() != null)
+                atoms[i].setPoint3d(new Point3d(srcAtom.getPoint3d()));
         }
         for (int i = 0; i < bonds.length; i++) {
             IBond bond = src.getBond(i);

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java
@@ -360,7 +360,6 @@ public static TemplateHandler createFromSubstructure(Pattern ptrn, IAtomContaine
     IdentityTemplateLibrary toIdentityTemplateLibrary() {
         IdentityTemplateLibrary lib = IdentityTemplateLibrary.empty();
         for (IAtomContainer mol : templates) {
-            lib.add(mol);
             lib.add(AtomContainerManipulator.anonymise(mol));
         }
         return lib;