Critical patch: SMARTS ring closures must use '%' for rnum >= 10.

johnmay · johnmay · commit 9cad0c5fd505 · 2020-09-23T21:49:13.000+01:00
diff --git a/tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java b/tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java
@@ -3116,6 +3116,8 @@ private void writePart(StringBuilder sb, IAtom atom, IBond prev) {
                 if (isRingClose(bond)) {
                     Integer rnum = rnums.get(bond);
                     sb.append(generate(bond.getOther(atom), ((QueryBond) BondRef.deref(bond))));
+                    if (rnum >= 10)
+                        sb.append('%');
                     sb.append(rnum);
                     rvisit[rnum] = false;
                     rnums.remove(bond);
@@ -3124,6 +3126,8 @@ private void writePart(StringBuilder sb, IAtom atom, IBond prev) {
                 // ring open
                 else if (isRingOpen(bond)) {
                     int rnum = nextRingNum();
+                    if (rnum >= 10)
+                        sb.append('%');
                     sb.append(rnum);
                     rnums.put(bond, rnum);
                     rbonds.remove(bond);
diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsExprWriteTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsExprWriteTest.java
@@ -487,4 +487,11 @@ private static void swap(Object[] a, int i, int j) {
         Smarts.parse(mol, "O1.[S@]=1(C)CC");
         assertThat(Smarts.generate(mol), is("O=[S@@](C)CC"));
     }
+
+    @Test public void ringClosures() {
+        String sma = "C12=C3C4=C5C1=C1C6=C7C2=C2C8=C3C3=C9C4=C4C%10=C5C5=C1C1=C6C6=C%11C7=C2C2=C7C8=C3C3=C8C9=C4C4=C9C%10=C5C5=C1C1=C6C6=C%11C2=C2C7=C3C3=C8C4=C4C9=C5C1=C1C6=C2C3=C41";
+        QueryAtomContainer mol = new QueryAtomContainer(null);
+        Smarts.parse(mol, sma);
+        assertThat(Smarts.generate(mol), is("C12C3C4=C5C=2C2=C6C7=C1C1=C8C=3C3=C9C4=C4C%10=C5C5=C2C2=C6C6=C%11C7=C1C1=C7C8=C3C3=C8C9=C4C4=C9C%10=C5C5=C2C2=C6C6=C%11C1=C1C7=C3C3C8=C4C4=C9C5=C2C2C6=C1C=3C4=2"));
+    }
 }

Original file line number	Diff line number	Diff line change
`@@ -487,4 +487,11 @@ private static void swap(Object[] a, int i, int j) {`
`487`	`487`	`Smarts.parse(mol, "O1.[S@]=1(C)CC");`
`488`	`488`	`assertThat(Smarts.generate(mol), is("O=[S@@](C)CC"));`
`489`	`489`	`}`
	`490`	`+`
	`491`	`+ @Test public void ringClosures() {`
	`492`	`+ String sma = "C12=C3C4=C5C1=C1C6=C7C2=C2C8=C3C3=C9C4=C4C%10=C5C5=C1C1=C6C6=C%11C7=C2C2=C7C8=C3C3=C8C9=C4C4=C9C%10=C5C5=C1C1=C6C6=C%11C2=C2C7=C3C3=C8C4=C4C9=C5C1=C1C6=C2C3=C41";`
	`493`	`+ QueryAtomContainer mol = new QueryAtomContainer(null);`
	`494`	`+ Smarts.parse(mol, sma);`
	`495`	`+ assertThat(Smarts.generate(mol), is("C12C3C4=C5C=2C2=C6C7=C1C1=C8C=3C3=C9C4=C4C%10=C5C5=C2C2=C6C6=C%11C7=C1C1=C7C8=C3C3=C8C9=C4C4=C9C%10=C5C5=C2C2=C6C6=C%11C1=C1C7=C3C3C8=C4C4=C9C5=C2C2C6=C1C=3C4=2"));`
	`496`	`+ }`
`490`	`497`	`}`