Merge pull request #410 from cdk/patch/acceptLpInCxSmiles

Looks good to me.
cdk · Jan 10, 2018 · a32c59f · a32c59f
2 parents 29a0a9b + 2b9e401
commit a32c59f
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Showing 2 changed files with 27 additions and 3 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java
@@ -428,7 +428,7 @@ static int processCx(final String str, final CxSmilesState state) {
                     if (!processCoords(iter, state))
                         return -1;
                     break;
-                case 'c': // Skip cis/trans/unspec
+                case 'c': // cis/trans/unspec ignored
                 case 't':
                     // c/t:
                     if (iter.nextIf(':')) {
@@ -441,12 +441,18 @@ else if (iter.nextIf("tu:")) {
                             return -1;
                     }
                     break;
-                case 'r': // Skip relative stereochemistry
+                case 'r': // relative stereochemistry ignored
                     if (!iter.nextIf(':'))
                         return -1;
                     if (!skipIntList(iter, COMMA_SEPARATOR))
                         return -1;
                     break;
+                case 'l': // lone pairs ignored
+                    if (!iter.nextIf("p:"))
+                        return -1;
+                    if (!skipIntMap(iter))
+                        return -1;
+                    break;
                 case 'f': // fragment grouping
                     if (!iter.nextIf(':'))
                         return -1;
@@ -477,7 +483,7 @@ else if (iter.nextIf("gD:")) {
                         return -1;
                     break;
                 case 'C':
-                case 'H': // skip coordination and hydrogen bonding
+                case 'H': // coordination and hydrogen bonding ignored
                     if (!iter.nextIf(':'))
                         return -1;
                     while (iter.hasNext() && isDigit(iter.curr())) {
@@ -514,6 +520,18 @@ private static boolean skipIntList(CharIter iter, char sep) {
         return false;
     }
 
+    private static boolean skipIntMap(CharIter iter) {
+        while (iter.hasNext()) {
+            char c = iter.curr();
+            if (isDigit(c) || c == ',' || c == ':')
+                iter.next();
+            else
+                return true;
+        }
+        // ran of end
+        return false;
+    }
+
     private static int processUnsignedInt(CharIter iter) {
         if (!iter.hasNext())
             return -1;

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesParserTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesParserTest.java
@@ -112,6 +112,12 @@ public void skipCisTransUnspec() {
         assertThat(CxSmilesParser.processCx("|c:2,6,8,ctu:10,t:1,4,5|", state), is(not(-1)));
     }
 
+    @Test
+    public void skipLonePairDefinitions() {
+        CxSmilesState state = new CxSmilesState();
+        assertThat(CxSmilesParser.processCx("|c:6,8,t:4,lp:2:2,4:1,11:1,m:1:8.9|", state), is(not(-1)));
+    }
+
     @Test
     public void fragmentGrouping() {
         CxSmilesState state = new CxSmilesState();