import java.util.*;
import java.io.*;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.qsar.*;
import org.openscience.cdk.qsar.DescriptorValue;

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];
      }
      String className = "org.openscience.cdk.qsar.descriptors.molecular." + descriptorName + "Descriptor";
      try {
	  Class.forName(className);
      } catch (ClassNotFoundException e) {
	  System.err.println("Descriptor not found: "+args[i]);
	  System.exit(1);
      }
      classNames.add(className);
    }

    engine = new DescriptorEngine(new ArrayList<String>(classNames));
    List<IDescriptor> instances =  engine.instantiateDescriptors(new ArrayList<String>(classNames));
    List<DescriptorSpecification> 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
      IteratingMDLReader reader = new IteratingMDLReader( br, DefaultChemObjectBuilder.getInstance());
      int c = 0;
      while (reader.hasNext()) {
        try {
          System.out.println("computing "+(args.length-1)+" descriptors for compound "+(++c));
          IMolecule molecule = (IMolecule)reader.next();
          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(); }
  }
}