Merged cdk-1.4.x

cdk · Oct 2, 2011 · 3a8307c · 3a8307c
2 parents c72d442 + a7cbe48
commit 3a8307c
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Showing 23 changed files with 1,012 additions and 230 deletions.
diff --git a/src/META-INF/test-data.cdkdepends b/src/META-INF/test-data.cdkdepends
@@ -1,6 +1,7 @@
 cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
+cdk-standard.jar
 cdk-data.jar
 cdk-nonotify.jar
 cdk-test.jar

diff --git a/src/META-INF/test-datadebug.cdkdepends b/src/META-INF/test-datadebug.cdkdepends
@@ -1,6 +1,7 @@
 cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
+cdk-standard.jar
 cdk-data.jar
 cdk-datadebug.jar
 cdk-test.jar

diff --git a/src/META-INF/test-nonotify.cdkdepends b/src/META-INF/test-nonotify.cdkdepends
@@ -1,6 +1,7 @@
 cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
+cdk-standard.jar
 cdk-data.jar
 cdk-nonotify.jar
 cdk-test.jar

diff --git a/src/META-INF/test-silent.cdkdepends b/src/META-INF/test-silent.cdkdepends
@@ -2,6 +2,7 @@ cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
 cdk-silent.jar
+cdk-standard.jar
 cdk-test.jar
 cdk-test-interfaces.jar
 cdk-diff.jar
diff --git a/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java b/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java
@@ -214,7 +214,7 @@ public String[] getModuleAndSet(File file) {
 					index = line.indexOf("@cdk.set");
 					String set = "";
 					if (index != -1) {
-						index += 11;
+						index += 8;
 						// skip the first chars
 						while (Character.isWhitespace(line.charAt(index))) index++;
 						while (index < line.length() && 

diff --git a/src/main/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java b/src/main/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java
@@ -1,6 +1,4 @@
-/* $Revision: 6707 $ $Author: egonw $ $Date: 2006-07-30 16:38:18 -0400 (Sun, 30 Jul 2006) $
- * 
- * Copyright (C) 2007  Egon Willighagen <egonw@users.sf.net>
+/* Copyright (C) 2007,2011  Egon Willighagen <egonw@users.sf.net>
  * 
  * Contact: cdk-devel@lists.sourceforge.net
  * 
@@ -65,16 +63,40 @@ public String toHTML() {
 				getString(article, "pages", "?-?")
 			);
 		}
-		// b:article
-		results = entry.query("./b:misc", context);
+		// b:thesis
+		results = entry.query("./b:phdthesis", context);
 		for (int i=0; i<results.size(); i++) {
-			Element misc = (Element)results.get(i);
+			Element thesis = (Element)results.get(i);
 			// the obligatory fields
-			return formatMisc(
-				getString(misc, "author", "?Authors?"),
-				getString(misc, "title", "?Title?")
+			return formatThesis(
+				getString(thesis, "author", "?Authors?"),
+				getString(thesis, "title", "?Title?"),
+                getString(thesis, "year", "19??"),
+                getString(thesis, "adress", "?Institute?")
 			);
 		}
+        // b:phdthesis
+        results = entry.query("./b:book", context);
+        for (int i=0; i<results.size(); i++) {
+            Element book = (Element)results.get(i);
+            // the obligatory fields
+            return formatBook(
+                getString(book, "author", "?Authors?"),
+                getString(book, "title", "?Title?"),
+                getString(book, "year", "19??"),
+                getString(book, "publisher", "?Publisher?")
+            );
+        }
+        // b:misc
+        results = entry.query("./b:misc", context);
+        for (int i=0; i<results.size(); i++) {
+            Element misc = (Element)results.get(i);
+            // the obligatory fields
+            return formatMisc(
+                getString(misc, "author", "?Authors?"),
+                getString(misc, "title", "?Title?")
+            );
+        }
 		return "Unknown BibTeXML type: " + ((Element)entry).getAttributeValue("id");
 	}
 
@@ -92,6 +114,22 @@ protected String formatMisc(String authors, String title) {
 		return buffer.toString();
 	}
 
+    protected String formatThesis(String authors, String title, String year, String institute) {
+        StringBuffer buffer = new StringBuffer();
+        buffer.append(authors).append(", <i>").append(title).append("</i>, ");
+        buffer.append("<b>").append(year).append("</b>, ");
+        buffer.append(institute);
+        return buffer.toString();
+    }
+
+    protected String formatBook(String authors, String title, String year, String publisher) {
+        StringBuffer buffer = new StringBuffer();
+        buffer.append(authors).append(", <i>").append(title).append("</i>, ");
+        buffer.append("<b>").append(year).append("</b>, ");
+        buffer.append(publisher);
+        return buffer.toString();
+    }
+
 	/**
 	 * @param node         Parent for the child.
 	 * @param childElement Localname of the child element.

diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -155,6 +155,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             type = perceiveGadolinum(atomContainer, atom);
         } else if ("Ge".equals(atom.getSymbol())) {
             type = perceiveGermanium(atomContainer, atom);
+        } else if ("Co".equals(atom.getSymbol())) {
+            type = perceiveCobalt(atomContainer, atom);
         } else if ("Br".equals(atom.getSymbol())) {
             type = perceiveBromine(atomContainer, atom);
         } else if ("V".equals(atom.getSymbol())) {
@@ -2370,6 +2372,63 @@ private IAtomType perceiveBromine(IAtomContainer atomContainer, IAtom atom) thro
     private int countAttachedDoubleBonds(IAtomContainer container, IAtom atom, String symbol) {
         return countAttachedBonds(container, atom, IBond.Order.DOUBLE, symbol);
     }
+
+    private IAtomType perceiveCobalt(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            // no idea how to deal with this yet
+            return null;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+                atom.getFormalCharge() == +2)) {
+            IAtomType type = getAtomType("Co.2plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+                atom.getFormalCharge() == +3)) {
+            IAtomType type = getAtomType("Co.3plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if ((atom.getFormalCharge() == CDKConstants.UNSET ||
+                atom.getFormalCharge() == 0)) {
+            int neighbors = atomContainer.getConnectedAtomsCount(atom);
+            if (neighbors == 2) {
+                IAtomType type = getAtomType("Co.2");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 4) {
+                IAtomType type = getAtomType("Co.4");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 6) {
+                IAtomType type = getAtomType("Co.6");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 1) {
+                IAtomType type = getAtomType("Co.1");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else {
+                IAtomType type = getAtomType("Co.metallic");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
+        } else if ((atom.getFormalCharge() != null
+                && atom.getFormalCharge() == +1)) {
+            int neighbors = atomContainer.getConnectedAtomsCount(atom);
+            if (neighbors == 2) {
+                IAtomType type = getAtomType("Co.plus.2");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 4) {
+                IAtomType type = getAtomType("Co.plus.4");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 1) {
+                IAtomType type = getAtomType("Co.plus.1");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 6) {
+                IAtomType type = getAtomType("Co.plus.6");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 5) {
+                IAtomType type = getAtomType("Co.plus.5");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else {
+                IAtomType type = getAtomType("Co.plus");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
+        }
+        return null;
+    }
 
     private int countAttachedDoubleBonds(IAtomContainer container, IAtom atom) {
     	return countAttachedBonds(container, atom, IBond.Order.DOUBLE, null);

diff --git a/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl b/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
@@ -1494,7 +1494,7 @@
     <at:formalNeighbourCount>0</at:formalNeighbourCount>
     <at:piBondCount>0</at:piBondCount>
   </at:AtomType>
-
+ 
   <at:AtomType rdf:ID="Co.3plus">
     <at:formalCharge>3</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Co"/>
@@ -1508,6 +1508,69 @@
     <at:formalNeighbourCount>0</at:formalNeighbourCount>
     <at:piBondCount>0</at:piBondCount>
   </at:AtomType>
+
+    <at:AtomType rdf:ID="Co.plus.6">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>6</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.plus.2">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>2</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType> 
+
+    <at:AtomType rdf:ID="Co.2">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>2</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.6">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>6</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.plus.4">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+     <at:AtomType rdf:ID="Co.4">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.plus.5">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>5</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.plus.1">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Co.1">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Co"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>
 
   <at:AtomType rdf:ID="Cu.plus">
     <at:formalCharge>1</at:formalCharge>

diff --git a/src/main/org/openscience/cdk/io/CMLWriter.java b/src/main/org/openscience/cdk/io/CMLWriter.java
@@ -109,7 +109,7 @@
  *
  * @cdk.keyword file format, CML
  */
-@TestClass("org.openscience.cdk.io.CMLWriterTest")
+@TestClass("org.openscience.cdk.io.CML2WriterTest")
 public class CMLWriter extends DefaultChemObjectWriter {
 
     private OutputStream output;

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -747,11 +747,11 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
                         int charge = Integer.parseInt(token.trim());
                         outputContainer.getAtom(atomNumber - 1).setFormalCharge(charge);
                     }
-                }  else if (line.matches("^A    \\d+")) {
+                }  else if (line.matches("A\\s{1,4}\\d+")) {
             		// Reads the pseudo atom property from the mol file
 
                 	// The atom number of the to replaced atom
-            		int aliasAtomNumber = Integer.parseInt(line.replaceFirst("^A    ", "")) - RGroupCounter;
+            		int aliasAtomNumber = Integer.parseInt(line.replaceFirst("A\\s{1,4}", "")) - RGroupCounter;
             		line = input.readLine(); linecount++;
 					String[] aliasArray = line.split("\\\\");
 					// name of the alias atom like R1 odr R2 etc. 

diff --git a/src/main/org/openscience/cdk/qsar/DescriptorEngine.java b/src/main/org/openscience/cdk/qsar/DescriptorEngine.java
@@ -645,6 +645,7 @@ public static List<String> getDescriptorClassNameByPackage(String packageName, S
         String[] jars;
         if (jarFileNames == null) {
             String classPath = System.getProperty("java.class.path");
+            logger.debug("Dictionary classpath: ", classPath);
             jars = classPath.split(File.pathSeparator);
         } else {
             jars = jarFileNames;

diff --git a/src/main/org/openscience/cdk/tools/LoggingTool.java b/src/main/org/openscience/cdk/tools/LoggingTool.java
@@ -264,7 +264,11 @@ public void debug(Object object, Object... objects) {
             StringBuilder result = new StringBuilder();
             result.append(object.toString());
             for (Object obj : objects) {
-                result.append(obj.toString());
+                if (obj == null) {
+                    result.append("null");
+                } else {
+                    result.append(obj.toString());
+                }
             }
             debugString(result.toString());
         }

diff --git a/src/main/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java b/src/main/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java
@@ -93,9 +93,9 @@ public int compare(IAtomContainer o1, IAtomContainer o2) {
     if (o1 == null && o2 == null)
       return 0;
     if (o1 == null)
-      return -1;
-    if (o2 == null)
       return 1;
+    if (o2 == null)
+      return -1;
 
     // Check for correct instances
     if (!(o1 instanceof IAtomContainer) && !(o2 instanceof IAtomContainer))