1 files changed, 29 insertions, 22 deletions

diff --git a/java/CdkDescriptors.java b/java/CdkDescriptors.java
index 5635507..69c27a8 100644
--- a/java/CdkDescriptors.java
+++ b/java/CdkDescriptors.java
@@ -9,13 +9,13 @@ import org.openscience.cdk.qsar.DescriptorValue;
 class CdkDescriptors {
   public static void main(String[] args) {
 
-    // parse command line arguments (descriptors)
+    // parse command line arguments > 1 (descriptors)
     DescriptorEngine engine;
-    if (args.length > 0) {
-      for (int i =0; i < args.length; i++) {
-        args[i] = "org.openscience.cdk.qsar.descriptors.molecular." + args[i] + "Descriptor";
+    if (args.length > 1) {
+      List<String> classNames = new ArrayList<String>();
+      for (int i =1; i < args.length; i++) {
+        classNames.add("org.openscience.cdk.qsar.descriptors.molecular." + args[i] + "Descriptor");
       }
-      List<String> classNames = Arrays.asList(args);
       engine = new DescriptorEngine(classNames);
       List<IDescriptor> instances =  engine.instantiateDescriptors(classNames);
       List<DescriptorSpecification> specs = engine.initializeSpecifications(instances);
@@ -25,13 +25,21 @@ class CdkDescriptors {
       engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
     }
 
-    // parse 3d sdf from stdin and calculate descriptors
-    BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
-    IteratingMDLReader reader = new IteratingMDLReader( br, DefaultChemObjectBuilder.getInstance());
-    while (reader.hasNext()) {
-      IMolecule molecule = (IMolecule)reader.next();
-      try {
-        engine.process(molecule);
+    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());
+      while (reader.hasNext()) {
+        try {
+          IMolecule molecule = (IMolecule)reader.next();
+          engine.process(molecule);
+        }
+        catch (Exception e) {
+          yaml.println("- {}");
+          e.printStackTrace();
+          continue;
+        }
         Iterator it = molecule.getProperties().values().iterator(); 
         Boolean first = true;
         while (it.hasNext()) {
@@ -39,28 +47,27 @@ class CdkDescriptors {
             DescriptorValue value = (DescriptorValue)it.next();
             int size = value.getValue().length();
             if (size == 1) {
-              if (first) { System.out.print("- "); }
-              else { System.out.print("  "); }
-              System.out.println(":"+value.getNames()[0].toString() + ": " + value.getValue());
+              if (first) { yaml.print("- "); }
+              else { yaml.print("  "); }
+              yaml.println(":"+value.getNames()[0].toString() + ": " + value.getValue());
               first = false;
             }
             else {
               String[] values = value.getValue().toString().split(",");
               for (int i = 0; i < size; i++) {
-                if (first) { System.out.print("- "); }
-                else { System.out.print("  "); }
-                System.out.println(":"+value.getNames()[i].toString() + ": "  + values[i]);
+                if (first) { yaml.print("- "); }
+                else { yaml.print("  "); }
+                yaml.println(":"+value.getNames()[i].toString() + ": "  + values[i]);
                 first = false;
               }
             }
           }
           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) {
-        System.out.println("- {}");
-        System.err.println(e.toString());
-      }
+      yaml.close();
     }
+    catch (Exception e) { e.printStackTrace(); }
   }
 }