Disable AuxInfo generation in InChIFactory by default. This can be as…

… much as 20% of the compute time and is largely ignored. If the AuxInfo is wanted it can be generated by explicitly passing in an empty set of options.
cdk · Aug 24, 2015 · d5afb4c · egonw · Aug 25, 2015 · johnmay
1 parent 7acf190
commit d5afb4c
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Showing 3 changed files with 18 additions and 10 deletions.
diff --git a/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java b/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java
@@ -23,6 +23,7 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Collections;
 
 import javax.vecmath.Point2d;
 import javax.vecmath.Point3d;
@@ -56,6 +57,8 @@
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
 import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
 
 /**
  * <p>This class generates the IUPAC International Chemical Identifier (InChI) for
@@ -99,10 +102,14 @@
  */
 public class InChIGenerator {
 
-    protected JniInchiInput  input;
+    protected JniInchiInput input;
 
     protected JniInchiOutput output;
 
+    private final boolean auxNone;
+
+    private static final ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(InChIGenerator.class);
+
     /**
      * AtomContainer instance refers to.
      */
@@ -120,12 +127,7 @@ public class InChIGenerator {
      * error during InChI generation
      */
     protected InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds) throws CDKException {
-        try {
-            input = new JniInchiInput("");
-            generateInchiFromCDKAtomContainer(atomContainer, ignoreAromaticBonds);
-        } catch (JniInchiException jie) {
-            throw new CDKException("InChI generation failed: " + jie.getMessage(), jie);
-        }
+        this(atomContainer, Collections.singletonList(INCHI_OPTION.AuxNone), ignoreAromaticBonds);
     }
 
     /**
@@ -146,6 +148,7 @@ protected InChIGenerator(IAtomContainer atomContainer, String options, boolean i
         try {
             input = new JniInchiInput(options);
             generateInchiFromCDKAtomContainer(atomContainer, ignoreAromaticBonds);
+            auxNone = input.getOptions() != null && input.getOptions().contains("AuxNone");
         } catch (JniInchiException jie) {
             throw new CDKException("InChI generation failed: " + jie.getMessage(), jie);
         }
@@ -167,6 +170,7 @@ protected InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> option
         try {
             input = new JniInchiInput(options);
             generateInchiFromCDKAtomContainer(atomContainer, ignoreAromaticBonds);
+            auxNone = input.getOptions() != null && input.getOptions().contains("AuxNone");
         } catch (JniInchiException jie) {
             throw new CDKException("InChI generation failed: " + jie.getMessage(), jie);
         }
@@ -551,6 +555,9 @@ public String getInchiKey() throws CDKException {
      * Gets auxillary information.
      */
     public String getAuxInfo() {
+        if (auxNone) {
+            LOGGER.warn("AuxInfo requested but AuxNone option is set (default).");
+        }
         return (output.getAuxInfo());
     }
 

diff --git a/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGeneratorFactory.java b/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGeneratorFactory.java
@@ -135,7 +135,9 @@ public boolean getIgnoreAromaticBonds() {
     }
 
     /**
-     * Gets an Standard InChI generator for a {@link IAtomContainer}.
+     * Gets an Standard InChI generator for a {@link IAtomContainer}. AuxInfo is not
+     * generated by this method, please use {@link #getInChIGenerator(IAtomContainer, List)}
+     * with no options specified if you would like to generate AuxInfo.
      *
      * @param container     AtomContainer to generate InChI for.
      * @return the InChI generator object

diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java
@@ -100,7 +100,7 @@ public void testGetAuxInfo() throws Exception {
         ac.addAtom(a1);
         ac.addAtom(a2);
         ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_SINGLE));
-        InChIGenerator gen = getFactory().getInChIGenerator(ac);
+        InChIGenerator gen = getFactory().getInChIGenerator(ac, "");
         Assert.assertNotNull(gen.getAuxInfo());
         Assert.assertTrue(gen.getAuxInfo().startsWith("AuxInfo="));
     }
@@ -712,7 +712,6 @@ public void testDoubleBondStereochemistry() throws Exception {
 
         InChIGenerator genE = getFactory().getInChIGenerator(acE);
         Assert.assertEquals(INCHI_RET.OKAY, genE.getReturnStatus());
-        System.out.println(genE.getMessage());
         Assert.assertEquals("InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+", genE.getInchi());
     }