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

Looks good.

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);
+ }
  }
 
  /**

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

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.
  */

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}
  */

base/isomorphism/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();

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.
  */

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

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

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

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);

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));
+ }
+ }
 }