new master branch

1 files changed, 60 insertions, 0 deletions

diff --git a/java/JoelibDescriptors.java b/java/JoelibDescriptors.java
new file mode 100644
index 0000000..e90e35f
--- /dev/null
+++ b/java/JoelibDescriptors.java
@@ -0,0 +1,60 @@
+import java.util.*;
+import java.io.*;
+import joelib2.feature.Feature;
+import joelib2.feature.FeatureHelper;
+import joelib2.feature.FeatureFactory;
+import joelib2.feature.FeatureResult;
+import joelib2.io.BasicIOType;
+import joelib2.io.BasicIOTypeHolder;
+import joelib2.io.BasicReader;
+import joelib2.io.MoleculeFileHelper;
+import joelib2.io.MoleculeFileIO;
+import joelib2.io.MoleculeIOException;
+import joelib2.molecule.BasicConformerMolecule;
+
+class JoelibDescriptors {
+  public static void main(String[] args) {
+
+    String[] features = null;
+    features = new String[args.length-1];
+    System.arraycopy(args,1,features,0,args.length-1);
+
+    FeatureFactory factory = FeatureFactory.instance();
+    MoleculeFileIO loader = null;
+    String line = new String();
+    String sdf = new String();
+    try {
+      // parse 3d sdf from file and calculate descriptors
+      InputStream is = new FileInputStream(args[0]);
+      PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"joelib.yaml"));
+      BasicIOType inType = BasicIOTypeHolder.instance().getIOType("SDF");
+      loader = MoleculeFileHelper.getMolReader(is, inType);
+      BasicConformerMolecule mol = new BasicConformerMolecule(inType, inType);
+      while (true) {
+        try {
+          Boolean success = loader.read(mol);
+          if (!success) { break; } // last molecule
+          for (int i =0; i < features.length; i++) {
+            String name = "joelib2.feature.types." + features[i];
+            Feature feature = factory.getFeature(name);
+            FeatureResult result = feature.calculate(mol);
+            if (i == 0) { yaml.print("- "); }
+            else { yaml.print("  "); }
+            yaml.print( "Joelib."+features[i]+": " );
+            yaml.println( result.toString() );
+          }
+
+        }
+        catch (Exception e) { 
+          System.err.println(e.toString());
+          e.printStackTrace();
+        }
+      }
+      yaml.close();
+    }
+    catch (Exception e) {
+      System.err.println(e.toString());
+      e.printStackTrace();
+    }
+  }
+}