1 files changed, 0 insertions, 141 deletions
diff --git a/java/CdkDescriptors.java b/java/CdkDescriptors.java
deleted file mode 100644
index b5f8672..0000000
--- a/java/CdkDescriptors.java
+++ /dev/null
@@ -1,141 +0,0 @@
-import java.util.*;
-import java.io.*;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.IImplementationSpecification;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.io.iterator.IteratingSDFReader;
-import org.openscience.cdk.qsar.*;
-import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.exception.NoSuchAtomTypeException;
-
-class CdkDescriptors {
-  public static void main(String[] args) {
-
-    if (args==null || args.length<2) {
-	System.err.println("required params: <sd-file> <descriptor1> <descriptor2(optional)> <descriptor3(optional)> ...");
-	System.exit(1);
-    }
-    if (! new File(args[0]).exists()){
-      System.err.println("file not found "+args[0]);
-      System.exit(1);
-    }
-
-    // command line descriptor params can be either "descriptorName" or "descriptorValueName"
-    // terminology:
-    // A descriptor can calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
-    // "descriptorName" ALOGP
-    // "valueName" AMR
-    // "descriptorValueName" ALOGP.AMR
-    DescriptorEngine engine;
-    Set<String> classNames = new LinkedHashSet<String>(); // descriptors to be computed
-    Set<String> descriptorNames = new LinkedHashSet<String>(); // all values of this descriptor will be printed
-    Set<String> descriptorValueNames = new LinkedHashSet<String>(); // only these values of a descriptor will be printed
-    for (int i =1; i < args.length; i++) {
-      String descriptorName;
-      if (args[i].indexOf(".")!=-1) {
-        descriptorValueNames.add(args[i]);
-        descriptorName = args[i].substring(0,args[i].indexOf("."));
-      }
-      else {
-        descriptorNames.add(args[i]);
-        descriptorName = args[i];
-      }
-      classNames.add(getDescriptorClassName(descriptorName));
-    }
-
-    engine = new DescriptorEngine(new ArrayList<String>(classNames),null);
-    List<IDescriptor> instances =  engine.instantiateDescriptors(new ArrayList<String>(classNames));
-    List<IImplementationSpecification> specs = engine.initializeSpecifications(instances);
-    engine.setDescriptorInstances(instances);
-    engine.setDescriptorSpecifications(specs);
-
-    try {
-      BufferedReader br = new BufferedReader(new FileReader(args[0]));
-      PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"cdk.yaml"));
-      // parse 3d sdf from file and calculate descriptors
-      IteratingSDFReader reader = new IteratingSDFReader( br, DefaultChemObjectBuilder.getInstance());
-      int c = 0;
-      while (reader.hasNext()) {
-        try {
-          System.out.println("computing "+(args.length-1)+" descriptors for compound "+(++c));
-          IAtomContainer molecule = (IAtomContainer)reader.next();
-          molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
-          try {
-            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-          }
-	      catch (NoSuchAtomTypeException e) {
-            e.printStackTrace();
-          }
-          CDKHueckelAromaticityDetector.detectAromaticity(molecule);
-
-          engine.process(molecule);
-          Map<Object,Object> properties = molecule.getProperties();
-          Boolean first = true;
-          for (Map.Entry<Object, Object> entry : properties.entrySet()) {
-            try {
-              if ((entry.getKey() instanceof DescriptorSpecification) && (entry.getValue() instanceof DescriptorValue)) {
-                DescriptorSpecification property = (DescriptorSpecification)entry.getKey();
-                DescriptorValue value = (DescriptorValue)entry.getValue();
-                String[] values = value.getValue().toString().split(",");
-                for (int i = 0; i < values.length; i++) {
-                  String cdk_class = property.getImplementationTitle();
-                  String descriptorName = cdk_class.substring(cdk_class.lastIndexOf(".")+1).replace("Descriptor","");
-                  String descriptorValueName = descriptorName + "." + value.getNames()[i];
-		  if (descriptorNames.contains(descriptorName) || descriptorValueNames.contains(descriptorValueName)) {
-		      if (first) { yaml.print("- "); first = false; }
-		      else { yaml.print("  "); }
-                      yaml.println("Cdk." + descriptorValueName  + ": " + values[i]);
-		  }
-                }
-              }
-            }
-            catch (ClassCastException e) { } // sdf properties are stored as molecules properties (strings), ignore them
-            catch (Exception e) { e.printStackTrace(); } // output nothing to yaml
-          }
-        }
-        catch (Exception e) {
-          yaml.println("- {}");
-          e.printStackTrace();
-          continue;
-        }
-      }
-      yaml.close();
-    }
-    catch (Exception e) { e.printStackTrace(); }
-  }
-    
-
-    /** HACK to find the class for a descriptor
-     * problem: Descriptor is not always at the end of the class (APolDescriptor), but may be in the middle (AutocorrelationDescriptorPolarizability)
-     * this method makes a class-lookup using trial and error */
-    static String getDescriptorClassName(String descriptorName) {
-      String split = splitCamelCase(descriptorName)+" "; // space mark possible positions for 'Descriptor'
-      for(int i = split.length()-1; i>0; i--) {
-        if (split.charAt(i)==' ') { // iterate over all spaces, starting with the trailing one
-          String test = split.substring(0,i)+"Descriptor"+split.substring(i+1,split.length()); // replace current space with 'Descriptor' ..
-          test = test.replaceAll("\\s",""); // .. and remove other spaces
-          String className = "org.openscience.cdk.qsar.descriptors.molecular." + test;
-          try {
-              Class.forName(className);
-              return className;
-          } catch (ClassNotFoundException e) {}
-        }
-      }
-      System.err.println("Descriptor not found: "+descriptorName);
-      System.exit(1);
-      return null;
-    }
-
-    /** inserts space in between camel words */
-  static String splitCamelCase(String s) {
-   return s.replaceAll(
-      String.format("%s|%s|%s",
-         "(?<=[A-Z])(?=[A-Z][a-z])",
-         "(?<=[^A-Z])(?=[A-Z])",
-         "(?<=[A-Za-z])(?=[^A-Za-z])"
-      ),
-      " "
-   );
-  }
-}