From 49ce3d0184bc6dbab634ab11b1c3d4877c077589 Mon Sep 17 00:00:00 2001
From: John Mayfield <john@nextmovesoftware.com>
Date: Wed, 23 Aug 2023 15:20:42 +0100
Subject: [PATCH 1/4] Fix - avoid placing a wedge on the right-angled bond when
 a centre is D3 and two neighbours are co-linear.

---
 .../cdk/stereo/StereoElementFactory.java      |  2 +-
 .../cdk/layout/NonplanarBonds.java            | 39 ++++++++++++++-----
 .../cdk/layout/NonPlanarBondsTest.java        | 35 ++++++++++++-----
 3 files changed, 56 insertions(+), 20 deletions(-)

diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java b/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
index 85a28f5dfe0..5b0989cbebd 100644
--- a/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
+++ b/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
@@ -699,7 +699,7 @@ else if (delta < -threshold) {
                     Vector2d v1 = toUnitVector(focus, bonds.get(0).getOther(focus));
                     Vector2d v2 = toUnitVector(focus, bonds.get(1).getOther(focus));
                     Vector2d v3 = toUnitVector(focus, bonds.get(2).getOther(focus));
-                    String ambiuousStereoMesg = "Ambiguous stereochemistry - 3 neighbours and two";
+                    String ambiuousStereoMesg = "Ambiguous stereochemistry - 3 neighbours and two bonds are co-linear";
                     if (Math.abs(signedAngle(v1,v2) - Math.PI) < threshold) {
                         if (elevationOf(focus, bonds.get(0)) == 0 &&
                             elevationOf(focus, bonds.get(1)) == 0 &&
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
index c80b4a59328..fb185cba5a9 100644
--- a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
+++ b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -40,6 +40,7 @@
 import org.openscience.cdk.stereo.Octahedral;
 import org.openscience.cdk.stereo.SquarePlanar;
 import org.openscience.cdk.stereo.TrigonalBipyramidal;
+import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
 import javax.vecmath.Point2d;
@@ -637,6 +638,15 @@ private <T> void swap(List<T> l, int i, int j) {
          l.set(j, tmp);
     }
 
+    private IBond.Stereo invert(IBond.Stereo disp) {
+        switch (disp) {
+            case UP: return DOWN;
+            case DOWN: return UP;
+            default: return disp;
+        }
+    }
+
+
     private IBond.Stereo flip(IBond.Stereo disp) {
         switch (disp) {
             case UP: return UP_INVERTED;
@@ -894,7 +904,10 @@ private void label(final ITetrahedralChirality element) {
         // hydrogen is opposite all three neighbors. The central label needs to
         // be inverted, atoms could be laid out like this automatically, consider
         // CC1C[C@H]2CC[C@@H]1C2
+        // Like wise if the other two bonds are co-linear we should not place a
+        // wedge on the one off to the side (avoid is set).
         int invert = -1;
+        int avoid  = -1;
         if (n == 3) {
             // find a triangle of non-sequential neighbors (sorted clockwise)
             // which has anti-clockwise winding
@@ -903,22 +916,26 @@ private void label(final ITetrahedralChirality element) {
                 Point2d b = focus.getPoint2d();
                 Point2d c = atoms[rank[(i + 2) % n]].getPoint2d();
                 double det = (a.x - c.x) * (b.y - c.y) - (a.y - c.y) * (b.x - c.x);
-                if (det > 0) {
-                    invert = rank[(i + 1) % n];
-                    break;
-                }
+                if (Math.abs(det) <= 0.05)
+                    avoid = rank[(i + 1) % n]; // i,i+2 are co-linear, i+1=no wedge
+                else if (det > 0.05 && invert == -1)
+                    invert = rank[(i + 1) % n]; // acute angle, invert wedge
             }
         }
-
+        
         // assign all up/down labels to an auxiliary array
         IBond.Stereo[] labels = new IBond.Stereo[n];
+        IBond.Stereo refWedge = p > 0 ? UP : DOWN;
         for (int i = 0; i < n; i++) {
             int v = rank[i];
-
-            // 4 neighbors (invert every other one)
-            if (n == 4) p *= -1;
-
-            labels[v] = invert == v ? p > 0 ? DOWN : UP : p > 0 ? UP : DOWN;
+            // no wedge here (would be ambiguous)
+            if (avoid == v)
+                labels[v] = NONE;
+            // invert (if D3 acute, or odd index of D4)
+            else if (invert == v || (n == 4 && i % 2 == 0))
+                labels[v] = invert(refWedge);
+            else
+                labels[v] = refWedge;
         }
 
         // set the label for the highest priority and available bond
@@ -928,6 +945,8 @@ private void label(final ITetrahedralChirality element) {
             IBond bond = bonds[v];
             if (bond.getStereo() != NONE || bond.getOrder() != SINGLE)
                 continue;
+            if (labels[v] == NONE)
+                continue;
             // first label
             if (firstlabel == null) {
                 bond.setAtoms(new IAtom[]{focus, atoms[v]}); // avoids UP_INVERTED/DOWN_INVERTED
diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
index 997d9e261fa..07301e466a7 100644
--- a/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
+++ b/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
@@ -34,6 +34,8 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.io.MDLV2000Writer;
 import org.openscience.cdk.silent.Atom;
 import org.openscience.cdk.silent.AtomContainer;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
@@ -41,10 +43,15 @@
 import org.openscience.cdk.stereo.Atropisomeric;
 import org.openscience.cdk.stereo.DoubleBondStereochemistry;
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
+import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.stereo.TetrahedralChirality;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
 
 import javax.vecmath.Point2d;
 
+import java.io.StringReader;
+import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -322,8 +329,8 @@ void clockwiseSortShouldHandleExactlyOppositeAtoms() throws Exception {
         NonplanarBonds.assign(m);
         assertThat(m.getBond(2).getStereo(), is(IBond.Stereo.UP));
     }
-    
-    
+
+
     // ethene is left alone and not marked as crossed
     @Test
     void dontCrossEtheneDoubleBond() {
@@ -411,8 +418,8 @@ void useCrossedBondIfNeeded() {
     }
 
     /**
-     * @cdk.inchi InChI=1S/C6H14S/c1-5-7(4)6(2)3/h5H2,1-4H3/t7-/m0/s1 
-     */                                                                  
+     * @cdk.inchi InChI=1S/C6H14S/c1-5-7(4)6(2)3/h5H2,1-4H3/t7-/m0/s1
+     */
     @Test
     void dontMarkTetrahedralCentresWithDoubleBondsAsUnspecified() {
         IAtomContainer m = new AtomContainer();
@@ -436,7 +443,7 @@ void dontMarkTetrahedralCentresWithDoubleBondsAsUnspecified() {
         assertThat(m.getBond(2).getStereo(), is(not(IBond.Stereo.UP_OR_DOWN)));
         assertThat(m.getBond(3).getStereo(), is(not(IBond.Stereo.UP_OR_DOWN)));
     }
-    
+
     @Test
     void dontMarkRingBondsInBezeneAsUnspecified() {
         IAtomContainer m = new AtomContainer();
@@ -454,7 +461,7 @@ void dontMarkRingBondsInBezeneAsUnspecified() {
         m.addBond(0, 5, IBond.Order.SINGLE);
         NonplanarBonds.assign(m);
         for (IBond bond : m.bonds()) {
-            assertThat(bond.getStereo(), is(IBond.Stereo.NONE));   
+            assertThat(bond.getStereo(), is(IBond.Stereo.NONE));
         }
     }
 
@@ -644,8 +651,8 @@ void atropisomerWedgeBonds() throws CDKException {
         SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
         IAtomContainer mol = smipar.parseSmiles("OC1=CC=C2C=CC=CC2=C1C1=C(O)C=CC2=C1C=CC=C2");
 
-        IBond       focus    = mol.getBond(mol.getAtom(10),
-                                           mol.getAtom(11));
+        IBond focus = mol.getBond(mol.getAtom(10),
+                                  mol.getAtom(11));
         List<IAtom> carriers = new ArrayList<>();
         carriers.addAll(mol.getConnectedAtomsList(focus.getBegin()));
         carriers.addAll(mol.getConnectedAtomsList(focus.getEnd()));
@@ -664,7 +671,7 @@ void atropisomerWedgeBonds() throws CDKException {
         assertThat(bond2.getOrder(), is(IBond.Order.SINGLE));
 
         Assertions.assertTrue(bond1.getStereo() == IBond.Stereo.DOWN ||
-        bond2.getStereo() == IBond.Stereo.DOWN, "One of the single bonds should have been wedged");
+                                      bond2.getStereo() == IBond.Stereo.DOWN, "One of the single bonds should have been wedged");
 
     }
 
@@ -775,4 +782,14 @@ static IAtom atom(String symbol, int hCount, double x, double y) {
         return a;
     }
 
+    @Test
+    void testColinearD3bonds() throws CDKException {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("[C@@H]12[C@@H]([C@H]([C@@H]([C@@H](CO1)O2)O)O)O |(1.3,0.1,;1.3,-1.4,;0.01,-2.15,;-1.29,-1.4,;-1.29,0.1,;-1.29,1.95,;1.26,1.93,;0.01,0.85,;-2.59,-2.15,;0.01,-3.65,;2.6,-2.15,)|");
+        NonplanarBonds.assign(mol);
+        // there are 4
+        Assertions.assertEquals(5,
+                                StereoElementFactory.using2DCoordinates(mol).withStrictMode().createAll().size());
+    }
+
 }

From 250bcf1e0d117774ffbf947a3f79f874c104154d Mon Sep 17 00:00:00 2001
From: John Mayfield <john@nextmovesoftware.com>
Date: Wed, 23 Aug 2023 15:26:42 +0100
Subject: [PATCH 2/4] Update this template to avoid ambiguous stereo
 assignment.

---
 .../org/openscience/cdk/layout/chebi-ring-templates.smi         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi b/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
index ee727ed3817..a961c98c667 100644
--- a/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
+++ b/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
@@ -440,7 +440,7 @@ N1NCCN1 |(.0,1.28,;1.21,.39,;.75,-1.03,;-.75,-1.03,;-1.21,.39,)|
 OC1CC(O)CC(C)C1 |(-.0,3.0,;-.0,1.5,;-1.3,.75,;-1.3,-.75,;-2.6,-1.5,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,)|
 OC1NC(N)NC(C)C1 |(-2.6,-1.5,;-1.3,-.75,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,;.0,1.5,;.0,3.0,;-1.3,.75,)|
 NC1CC(N)C(C)C(N)C1 |(.0,-3.3,;.0,-1.8,;1.3,-1.05,;1.3,.45,;2.6,1.2,;.0,1.2,;.0,2.7,;-1.3,.45,;-2.6,1.2,;-1.3,-1.05,)|
-O1CC2OC1CCC2 |(1.26,1.93,;-1.29,1.95,;-1.29,.1,;.01,.85,;1.3,.1,;1.3,-1.4,;.01,-2.15,;-1.29,-1.4,)|
+O1CC2OC1CCC2 |(1.64,0.75,;1.64,-0.75,;0.47,-1.69,;-0.5,,;0.47,1.69,;-0.99,1.35,;-1.64,,;-0.99,-1.35,)|
 OC1CC2N(C)C(CC2)C1 |(3.06,.0,;1.6,.0,;.86,-1.27,;-.6,-1.6,;-1.33,.0,;.17,.0,;-.6,1.6,;-2.01,.89,;-2.01,-.89,;.86,1.27,)|
 N1CC2CN3CCCCC3C(C1)C2 |(-2.92,.73,;-2.92,-.77,;-1.85,-1.83,;-.35,-1.83,;.71,-.77,;2.01,-1.51,;3.31,-.77,;3.31,.73,;2.01,1.49,;.71,.73,;-.35,1.79,;-1.85,1.79,;-1.79,.18,)|
 SC1CCCCC1 |(2.23,1.29,;.93,.54,;.93,-.96,;-.37,-1.71,;-1.67,-.96,;-1.67,.54,;-.37,1.29,)|

From 41fff70a3c0553391d67e302dc892a81e4990aec Mon Sep 17 00:00:00 2001
From: John Mayfield <john@nextmovesoftware.com>
Date: Wed, 23 Aug 2023 15:29:26 +0100
Subject: [PATCH 3/4] Better template orrientation.

---
 .../org/openscience/cdk/layout/chebi-ring-templates.smi         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi b/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
index a961c98c667..1c2854b3128 100644
--- a/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
+++ b/tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
@@ -440,7 +440,7 @@ N1NCCN1 |(.0,1.28,;1.21,.39,;.75,-1.03,;-.75,-1.03,;-1.21,.39,)|
 OC1CC(O)CC(C)C1 |(-.0,3.0,;-.0,1.5,;-1.3,.75,;-1.3,-.75,;-2.6,-1.5,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,)|
 OC1NC(N)NC(C)C1 |(-2.6,-1.5,;-1.3,-.75,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,;.0,1.5,;.0,3.0,;-1.3,.75,)|
 NC1CC(N)C(C)C(N)C1 |(.0,-3.3,;.0,-1.8,;1.3,-1.05,;1.3,.45,;2.6,1.2,;.0,1.2,;.0,2.7,;-1.3,.45,;-2.6,1.2,;-1.3,-1.05,)|
-O1CC2OC1CCC2 |(1.64,0.75,;1.64,-0.75,;0.47,-1.69,;-0.5,,;0.47,1.69,;-0.99,1.35,;-1.64,,;-0.99,-1.35,)|
+O1CC2OC1CCC2 |(-0.75,1.64,;0.75,1.64,;1.69,0.47,;,-0.5,;-1.69,0.47,;-1.35,-0.99,;,-1.64,;1.35,-0.99,)|
 OC1CC2N(C)C(CC2)C1 |(3.06,.0,;1.6,.0,;.86,-1.27,;-.6,-1.6,;-1.33,.0,;.17,.0,;-.6,1.6,;-2.01,.89,;-2.01,-.89,;.86,1.27,)|
 N1CC2CN3CCCCC3C(C1)C2 |(-2.92,.73,;-2.92,-.77,;-1.85,-1.83,;-.35,-1.83,;.71,-.77,;2.01,-1.51,;3.31,-.77,;3.31,.73,;2.01,1.49,;.71,.73,;-.35,1.79,;-1.85,1.79,;-1.79,.18,)|
 SC1CCCCC1 |(2.23,1.29,;.93,.54,;.93,-.96,;-.37,-1.71,;-1.67,-.96,;-1.67,.54,;-.37,1.29,)|

From 44d3df0740cc29f91d7423d70a7492db9ae163da Mon Sep 17 00:00:00 2001
From: John Mayfield <john@nextmovesoftware.com>
Date: Wed, 23 Aug 2023 15:37:14 +0100
Subject: [PATCH 4/4] Unused import

---
 .../src/main/java/org/openscience/cdk/layout/NonplanarBonds.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
index fb185cba5a9..104f415f9bf 100644
--- a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
+++ b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -40,7 +40,6 @@
 import org.openscience.cdk.stereo.Octahedral;
 import org.openscience.cdk.stereo.SquarePlanar;
 import org.openscience.cdk.stereo.TrigonalBipyramidal;
-import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
 import javax.vecmath.Point2d;