Don't allow 'Z' in loose SMARTS. RDKit now match CACTVS so 2:1.

cdk · Oct 25, 2018 · 23b39d3 · 23b39d3
1 parent 3ce35ed
commit 23b39d3
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Showing 2 changed files with 7 additions and 5 deletions.
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
@@ -864,7 +864,7 @@ else if (isFlavor(FLAVOR_OECHEM))
                             default:  // Z=None
                                 unget();
                                 num = nextUnsignedInt();
-                                if (isFlavor(FLAVOR_LOOSE | FLAVOR_DAYLIGHT)) {
+                                if (isFlavor(FLAVOR_DAYLIGHT)) {
                                     if (num < 0)
                                         expr = new Expr(IS_IN_RING);
                                     else if (num == 0)

diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsExprReadTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsExprReadTest.java
@@ -430,7 +430,7 @@ public void hetero() {
     @Test
     public void ringSize() {
         IAtomContainer mol = new AtomContainer();
-        assertTrue(Smarts.parse(mol, "[Z8]", Smarts.FLAVOR_LOOSE));
+        assertTrue(Smarts.parse(mol, "[Z8]", Smarts.FLAVOR_DAYLIGHT));
         Expr actual   = getAtomExpr(mol.getAtom(0));
         Expr expected = expr(RING_SIZE, 8);
         assertThat(actual, is(expected));
@@ -439,7 +439,7 @@ public void ringSize() {
     @Test
     public void ringSize0() {
         IAtomContainer mol = new AtomContainer();
-        assertTrue(Smarts.parse(mol, "[Z0]", Smarts.FLAVOR_LOOSE));
+        assertTrue(Smarts.parse(mol, "[Z0]", Smarts.FLAVOR_DAYLIGHT));
         Expr actual   = getAtomExpr(mol.getAtom(0));
         Expr expected = expr(IS_IN_CHAIN);
         assertThat(actual, is(expected));
@@ -448,7 +448,7 @@ public void ringSize0() {
     @Test
     public void ringSizeDefault() {
         IAtomContainer mol = new AtomContainer();
-        assertTrue(Smarts.parse(mol, "[Z]", Smarts.FLAVOR_LOOSE));
+        assertTrue(Smarts.parse(mol, "[Z]", Smarts.FLAVOR_DAYLIGHT));
         Expr actual   = getAtomExpr(mol.getAtom(0));
         Expr expected = expr(IS_IN_RING);
         assertThat(actual, is(expected));
@@ -697,7 +697,9 @@ public void atomStereoLeftOrUnspec() {
     @Test
     public void atomStereoSimpleLeft() {
         Expr actual   = getAtomExpr("[C@H]");
-        System.out.println(actual);
+        assertThat(actual, is(new Expr(ALIPHATIC_ELEMENT, 6)
+                                      .and(new Expr(STEREOCHEMISTRY, 1))
+                                      .and(new Expr(TOTAL_H_COUNT, 1))));
     }
 
     @Test