Handle RXN files where the molecules end with $$$$ and not M END.

johnmay · johnmay · commit d6cad8b86d25 · 2019-09-25T21:45:58.000+01:00
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java
@@ -227,8 +227,10 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
         try {
             for (int i = 1; i <= reactantCount; i++) {
                 StringBuffer molFile = new StringBuffer();
-                input.readLine(); // announceMDLFileLine
                 String molFileLine = "";
+                while (!input.readLine().startsWith("$MOL")) {
+                    // skip
+                }
                 do {
                     molFileLine = input.readLine();
                     molFile.append(molFileLine);
@@ -256,7 +258,9 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
         try {
             for (int i = 1; i <= productCount; i++) {
                 StringBuffer molFile = new StringBuffer();
-                input.readLine(); // String announceMDLFileLine =
+                while (!input.readLine().startsWith("$MOL")) {
+                    // skip
+                }
                 String molFileLine = "";
                 do {
                     molFileLine = input.readLine();
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java
@@ -23,6 +23,7 @@
 package org.openscience.cdk.io;
 
 import java.io.InputStream;
+import java.io.StringReader;
 import java.util.Iterator;
 
 import org.junit.Assert;
@@ -32,9 +33,11 @@
 import org.openscience.cdk.ChemModel;
 import org.openscience.cdk.Reaction;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMapping;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
@@ -143,4 +146,36 @@ public void testAgentParts() throws Exception {
             assertThat(reaction.getAgents().getAtomContainerCount(), is(1));
         }
     }
+
+    @Test public void optionalSdfSeparator() throws Exception {
+        String dummyRecord = "ethanol\n" +
+                       "  Mrv1810 09251921392D          \n" +
+                       "\n" +
+                       "  3  2  0  0  0  0            999 V2000\n" +
+                       "    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                       "    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                       "    2.6664   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                       "  1  2  1  0  0  0  0\n" +
+                       "  1  3  1  0  0  0  0\n" +
+                       "M  END\n" +
+                       "$$$$\n";
+        StringBuilder sb = new StringBuilder();
+        sb.append("$RXN\n");
+        sb.append("Test\n\n\n  2  1\n");
+        sb.append("$MOL\n");
+        sb.append(dummyRecord);
+        sb.append("$MOL\n");
+        sb.append(dummyRecord);
+        sb.append("$MOL\n");
+        sb.append(dummyRecord);
+
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        try (MDLRXNV2000Reader reader = new MDLRXNV2000Reader(new StringReader(sb.toString()))) {
+            IReaction rxn = reader.read(bldr.newInstance(IReaction.class));
+            assertThat(rxn.getReactants().getAtomContainerCount(), is(2));
+            assertThat(rxn.getProducts().getAtomContainerCount(), is(1));
+            assertThat(rxn.getReactants().getAtomContainer(0).getAtomCount(), is(3));
+            assertThat(rxn.getReactants().getAtomContainer(1).getAtomCount(), is(3));
+        }
+    }
 }
