Bug enhanced stereo should not be emitted for exclusively "Isomeric" SMILES flavour.

johnmay · egonw · commit 223f7cdf0d69 · 2021-11-20T07:37:55.000+01:00
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java
@@ -192,7 +192,7 @@ public int compare(List<Integer> a, List<Integer> b) {
             sb.append('$');
         }
 
-        if (SmiFlavor.isSet(opts, SmiFlavor.CxEnhancedStereo)) {
+        if (SmiFlavor.isFullySet(opts, SmiFlavor.CxEnhancedStereo)) {
             if (state.racemic) {
                 if (sb.length() > 2)
                     sb.append(',');
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.java
@@ -241,7 +241,13 @@ private SmiFlavor() {
      */
     public static final int UniversalSmiles     = InChILabelling | Isomeric;
 
+    // test if a single bit flag is set
     static boolean isSet(int opts, int opt) {
         return (opts & opt) != 0;
     }
+
+    // test if the flag is fully set with all bits
+    static boolean isFullySet(int opts, int opt) {
+        return (opts & opt) == opt;
+    }
 }
diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java
@@ -189,4 +189,11 @@ public void radicalCanon() throws Exception {
         SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.CxEnhancedStereo);
         assertThat(smigen.create(mol), is("C[C@H](O)[C@H](O)C1CCCCC1 |a:1,&1:3|"));
     }
+
+    @Test public void noEnhancedStereoInIsomeric() throws Exception {
+        SmilesParser    smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer  mol    = smipar.parseSmiles("C[C@H](O)[C@H](O)C1CCCCC1 |r|");
+        SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Isomeric);
+        assertThat(smigen.create(mol), is("C[C@H](O)[C@H](O)C1CCCCC1"));
+    }
 }

Original file line number	Diff line number	Diff line change
`@@ -192,7 +192,7 @@ public int compare(List<Integer> a, List<Integer> b) {`
`192`	`192`	`sb.append('$');`
`193`	`193`	`}`
`194`	`194`
`195`		`- if (SmiFlavor.isSet(opts, SmiFlavor.CxEnhancedStereo)) {`
	`195`	`+ if (SmiFlavor.isFullySet(opts, SmiFlavor.CxEnhancedStereo)) {`
`196`	`196`	`if (state.racemic) {`
`197`	`197`	`if (sb.length() > 2)`
`198`	`198`	`sb.append(',');`
Original file line number	Diff line number	Diff line change
`@@ -241,7 +241,13 @@ private SmiFlavor() {`
`241`	`241`	`*/`
`242`	`242`	`public static final int UniversalSmiles = InChILabelling \| Isomeric;`
`243`	`243`
	`244`	`+ // test if a single bit flag is set`
`244`	`245`	`static boolean isSet(int opts, int opt) {`
`245`	`246`	`return (opts & opt) != 0;`
`246`	`247`	`}`
	`248`	`+`
	`249`	`+ // test if the flag is fully set with all bits`
	`250`	`+ static boolean isFullySet(int opts, int opt) {`
	`251`	`+ return (opts & opt) == opt;`
	`252`	`+ }`
`247`	`253`	`}`
Original file line number	Diff line number	Diff line change
`@@ -189,4 +189,11 @@ public void radicalCanon() throws Exception {`
`189`	`189`	`SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.CxEnhancedStereo);`
`190`	`190`	`assertThat(smigen.create(mol), is("C[C@H](O)[C@H](O)C1CCCCC1 \|a:1,&1:3\|"));`
`191`	`191`	`}`
	`192`	`+`
	`193`	`+ @Test public void noEnhancedStereoInIsomeric() throws Exception {`
	`194`	`+ SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());`
	`195`	`+ IAtomContainer mol = smipar.parseSmiles("C[C@H](O)[C@H](O)C1CCCCC1 \|r\|");`
	`196`	`+ SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Isomeric);`
	`197`	`+ assertThat(smigen.create(mol), is("C[C@H](O)[C@H](O)C1CCCCC1"));`
	`198`	`+ }`
`192`	`199`	`}`