Merge pull request #354 from cdk/patch/22Aug17

Looks good.
cdk · Aug 23, 2017 · 4de578c · 4de578c
2 parents ac6a353 + 9caea10
commit 4de578c
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Showing 15 changed files with 289 additions and 37 deletions.
diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java b/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
@@ -681,9 +681,11 @@ private boolean ensure2dLayout(IAtomContainer container) throws CDKException {
      * @throws CDKException coordinates could not be generated
      */
     private void ensure2dLayout(IReaction rxn) throws CDKException {
-        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
-        sdg.setAlignMappedReaction(alignMappedReactions);
-        sdg.generateCoordinates(rxn);
+        if (!GeometryUtil.has2DCoordinates(rxn)) {
+            StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+            sdg.setAlignMappedReaction(alignMappedReactions);
+            sdg.generateCoordinates(rxn);
+        }
     }
 
     /**

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java b/base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
@@ -715,7 +715,17 @@ public IChemObjectBuilder getBuilder() {
                                                                  public void stateChanged(IChemObjectChangeEvent event) {
 
                                                                  }
-                                                             };
+
+                                                                 @Override
+                                                                 public String getTitle() {
+                                                                    return null;
+                                                                 }
+
+                                                                 @Override
+                                                                 public void setTitle(String title) {
+
+                                                                 }
+    };
 
     /**
      * pseudo shortest-paths - when an invalid atom is given. this will always

diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java
@@ -1479,6 +1479,23 @@ public boolean isEmpty() {
         return atomCount == 0;
     }
 
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public String getTitle() {
+        return getProperty(CDKConstants.TITLE);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void setTitle(String title) {
+        setProperty(CDKConstants.TITLE, title);
+    }
+
     /**
      * The inner AtomIterator class.
      */

diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java
@@ -752,6 +752,20 @@ public interface IAtomContainer extends IChemObject, IChemObjectListener {
      */
     boolean isEmpty();
 
+    /**
+     * Access the title of the record.
+     *
+     * @return the title
+     */
+    String getTitle();
+
+    /**
+     * Modify the title of the record.
+     *
+     * @param title the title
+     */
+    void setTitle(String title);
+
     /**
      * {@inheritDoc}
      */

diff --git a/...somorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java b/...somorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
@@ -24,6 +24,7 @@
 import java.util.List;
 import java.util.Map;
 
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -1615,6 +1616,22 @@ public boolean isEmpty() {
         return atomCount == 0;
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public String getTitle() {
+        return getProperty(CDKConstants.TITLE);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void setTitle(String title) {
+        setProperty(CDKConstants.TITLE, title);
+    }
+
     @Override
     public void setStereoElements(List<IStereoElement> elements) {
         this.stereoElements.clear();

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
@@ -1413,6 +1413,22 @@ public boolean isEmpty() {
         return atomCount == 0;
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public String getTitle() {
+        return getProperty(CDKConstants.TITLE);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void setTitle(String title) {
+        setProperty(CDKConstants.TITLE, title);
+    }
+
     /**
      * The inner AtomIterator class.
      */

diff --git a/base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java b/base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java
@@ -967,6 +967,25 @@ public static boolean has2DCoordinates(IAtomContainer container) {
 
     }
 
+    /**
+     * Determine if all parts of a reaction have coodinates
+     *
+     * @param reaction a reaction
+     * @return the reaction has coordinates
+     */
+    public static boolean has2DCoordinates(IReaction reaction) {
+        for (IAtomContainer mol : reaction.getReactants().atomContainers())
+            if (!has2DCoordinates(mol))
+                return false;
+        for (IAtomContainer mol : reaction.getProducts().atomContainers())
+            if (!has2DCoordinates(mol))
+                return false;
+        for (IAtomContainer mol : reaction.getAgents().atomContainers())
+            if (!has2DCoordinates(mol))
+                return false;
+        return true;
+    }
+
     /**
      * Determines the coverage of this {@link org.openscience.cdk.interfaces.IAtomContainer}'s 2D
      * coordinates. If all atoms are non-null and have 2D coordinates this method will return {@link

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
@@ -200,15 +200,23 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
 
         int reactantCount = 0;
         int productCount = 0;
+        int agentCount = 0;
         try {
             String countsLine = input.readLine();
             /*
              * this line contains the number of reactants and products
              */
             StringTokenizer tokenizer = new StringTokenizer(countsLine);
-            reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
+            reactantCount = Integer.valueOf(tokenizer.nextToken());
             logger.info("Expecting " + reactantCount + " reactants in file");
-            productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
+            productCount = Integer.valueOf(tokenizer.nextToken());
+            if (tokenizer.hasMoreTokens()) {
+                agentCount = Integer.valueOf(tokenizer.nextToken());
+                // ChemAxon extension, technically BIOVIA now support this but
+                // not documented yet
+                if (mode == Mode.STRICT && agentCount > 0)
+                    throw new CDKException("RXN files uses agent count extension");
+            }
             logger.info("Expecting " + productCount + " products in file");
         } catch (IOException | NumberFormatException exception) {
             logger.debug(exception);
@@ -272,6 +280,34 @@ private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
             throw new CDKException("Error while reading products", exception);
         }
 
+        // now read the products
+        try {
+            for (int i = 1; i <= agentCount; i++) {
+                StringBuffer molFile = new StringBuffer();
+                input.readLine(); // String announceMDLFileLine =
+                String molFileLine = "";
+                do {
+                    molFileLine = input.readLine();
+                    molFile.append(molFileLine);
+                    molFile.append(System.getProperty("line.separator"));
+                } while (!molFileLine.equals("M  END"));
+
+                // read MDL molfile content
+                MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.toString()));
+                IAtomContainer product = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
+                reader.close();
+
+                // add reactant
+                reaction.addAgent(product);
+            }
+        } catch (CDKException exception) {
+            // rethrow exception from MDLReader
+            throw exception;
+        } catch (IOException | IllegalArgumentException exception) {
+            logger.debug(exception);
+            throw new CDKException("Error while reading products", exception);
+        }
+
         // now try to map things, if wanted
         logger.info("Reading atom-atom mapping from file");
         // distribute all atoms over two AtomContainer's

diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -703,9 +703,13 @@ IAtom readAtomFast(String line, IChemObjectBuilder builder, Map<IAtom,Integer> p
             parities.put(atom, parity);
 
         // if there was a mass difference, set the mass number
-        if (massDiff != 0 && atom.getAtomicNumber() > 0)
-            atom.setMassNumber(Isotopes.getInstance().getMajorIsotope(atom.getAtomicNumber()).getMassNumber()
-                    + massDiff);
+        if (massDiff != 0 && atom.getAtomicNumber() > 0) {
+            IIsotope majorIsotope = Isotopes.getInstance().getMajorIsotope(atom.getAtomicNumber());
+            if (majorIsotope == null)
+                atom.setMassNumber(-1); // checked after M ISO is processed
+            else
+                atom.setMassNumber(majorIsotope.getMassNumber() + massDiff);
+        }
 
         if (valence > 0 && valence < 16) atom.setValency(valence == 15 ? 0 : valence);
 
@@ -1188,6 +1192,12 @@ void readPropertiesFast(final BufferedReader input, final IAtomContainer contain
             }
         }
 
+        // check of ill specified atomic mass
+        for (IAtom atom : container.atoms()) {
+            if (atom.getMassNumber() != null && atom.getMassNumber() < 0)
+                throw new CDKException("Unstable use of mass delta on " + atom.getSymbol() + " please use M  ISO");
+        }
+
 
         if (!sgroups.isEmpty()) {
             // load Sgroups into molecule, first we downcast

diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
@@ -360,22 +360,25 @@ public void writeMolecule(IAtomContainer container) throws Exception {
         writer.write(comment);
         writer.newLine();
 
-        // write Counts line
-        line += formatMDLInt(container.getAtomCount(), 3);
-        line += formatMDLInt(container.getBondCount(), 3);
-        line += "  0  0  0  0  0  0  0  0999 V2000";
-        writer.write(line);
-        writer.newLine();
-
         // index stereo elements for setting atom parity values
         Map<IAtom,ITetrahedralChirality> atomstereo = new HashMap<>();
         Map<IAtom,Integer> atomindex = new HashMap<>();
         for (IStereoElement element : container.stereoElements())
-                if (element instanceof ITetrahedralChirality)
-                    atomstereo.put(((ITetrahedralChirality) element).getChiralAtom(), (ITetrahedralChirality) element);
+            if (element instanceof ITetrahedralChirality)
+                atomstereo.put(((ITetrahedralChirality) element).getChiralAtom(), (ITetrahedralChirality) element);
         for (IAtom atom : container.atoms())
             atomindex.put(atom, atomindex.size());
 
+        // write Counts line
+        line += formatMDLInt(container.getAtomCount(), 3);
+        line += formatMDLInt(container.getBondCount(), 3);
+        line += "  0  0";
+        // we mark all stereochemistry to absolute for now
+        line += atomstereo.isEmpty() ? "  0" : "  1";
+        line += "  0  0  0  0  0999 V2000";
+        writer.write(line);
+        writer.newLine();
+
         // write Atom block
         for (int f = 0; f < container.getAtomCount(); f++) {
             IAtom atom = container.getAtom(f);

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
@@ -38,6 +38,9 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
+import static org.hamcrest.CoreMatchers.is;
+import static org.junit.Assert.assertThat;
+
 /**
  * TestCase for the reading MDL RXN files using one test file.
  *
@@ -131,4 +134,13 @@ public void testReadMapping() throws Exception {
         maps.next();
         Assert.assertTrue(maps.hasNext());
     }
+
+    @Test
+    public void testAgentParts() throws Exception {
+        try (InputStream in = this.getClass().getResourceAsStream("ethylesterification.mol");
+             MDLRXNV2000Reader rdr = new MDLRXNV2000Reader(in);) {
+            IReaction reaction = rdr.read(new Reaction());
+            assertThat(reaction.getAgents().getAtomContainerCount(), is(1));
+        }
+    }
 }