Watch out for strange valences

johnmay · egonw · commit 692239286849 · 2021-05-09T10:02:58.000+02:00
diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java b/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
@@ -527,7 +527,8 @@ private Type supportedType(int i, int v, int d, int h, int x) {
                 if (x == 4 && h == 0 && (q == 0 && v == 5 || q == 1 && v == 4))
                     return verifyTerminalHCount(i) ? Type.Tetracoordinate : Type.None;
                 // note: bridgehead not allowed by InChI but makes sense
-                return x == 3 && h == 0 && (isBridgeHead(i) || inThreeMemberRing(i)) ? Type.Tetracoordinate : Type.None;
+                return x == 3 && h == 0 && v == 3 && q == 0 &&
+                        (isBridgeHead(i) || inThreeMemberRing(i)) ? Type.Tetracoordinate : Type.None;
 
             case 14: // silicon
                 if (v != 4 || q != 0) return Type.None;
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java b/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java
@@ -212,6 +212,7 @@ public void nitrogen_v4_cation_reject_h() throws Exception {
         none("[NH4+]");
     }
 
+
     /**
      * An atom or positive ion N, P, As, S, or Se is not treated as stereogenic
      * if it has - (b) At least two terminal neighbors, XHm and XHn, (n+m>0)
@@ -789,6 +790,8 @@ public void bridgehead_nitrogens() throws Exception {
         none("N1(CCCC2)CCCC12");
         // adjacent to fused (but not fused)
         tetrahedral("N1(c(cccc3)c32)CC2CC1");
+
+        none("[N]2([Mn+]1)=CC=CC3=C2C2=[N]1C=CC=C2C=C3");
     }
 
     // assert the first atom of the SMILES is accepted as a tetrahedral center

Original file line number	Diff line number	Diff line change
`@@ -212,6 +212,7 @@ public void nitrogen_v4_cation_reject_h() throws Exception {`
`212`	`212`	`none("[NH4+]");`
`213`	`213`	`}`
`214`	`214`
	`215`	`+`
`215`	`216`	`/**`
`216`	`217`	`* An atom or positive ion N, P, As, S, or Se is not treated as stereogenic`
`217`	`218`	`* if it has - (b) At least two terminal neighbors, XHm and XHn, (n+m>0)`
`@@ -789,6 +790,8 @@ public void bridgehead_nitrogens() throws Exception {`
`789`	`790`	`none("N1(CCCC2)CCCC12");`
`790`	`791`	`// adjacent to fused (but not fused)`
`791`	`792`	`tetrahedral("N1(c(cccc3)c32)CC2CC1");`
	`793`	`+`
	`794`	`+ none("[N]2([Mn+]1)=CC=CC3=C2C2=[N]1C=CC=C2C=C3");`
`792`	`795`	`}`
`793`	`796`
`794`	`797`	`// assert the first atom of the SMILES is accepted as a tetrahedral center`