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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) {
// set args to all descriptors
if (args.length == 0) {
FeatureHelper helper = FeatureHelper.instance();
args = (String[]) helper.getNativeFeatures().toArray(new String[0]);
}
FeatureFactory factory = FeatureFactory.instance();
MoleculeFileIO loader = null;
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
String line = new String();
String sdf = new String();
try {
while ((line = br.readLine()) != null) { sdf += line + "\n"; }
br.close();
InputStream is = null;
is = new ByteArrayInputStream(sdf.getBytes("UTF-8"));
BasicIOType inType = BasicIOTypeHolder.instance().getIOType("SDF");
loader = MoleculeFileHelper.getMolReader(is, inType);
//BasicIOType outType = BasicIOTypeHolder.instance().getIOType("SMILES");
//JOEMol mol = new JOEMol(inType, inType);
BasicConformerMolecule mol = new BasicConformerMolecule(inType, inType);
while (true) {
try {
Boolean success = loader.read(mol);
if (!success) { break; }
//System.err.println( mol );
for (int i =0; i < args.length; i++) {
Feature feature = factory.getFeature(args[i]);
FeatureResult result = feature.calculate(mol);
if (i == 0) { System.out.print("- "); }
else { System.out.print(" "); }
System.out.print( args[i]+": " );
System.out.println( result.toString() );
}
}
catch (Exception e) {
System.err.println(e.toString());
e.printStackTrace();
//next;
}
}
}
catch (Exception e) {
e.printStackTrace();
//System.err.println(e.toString());
}
}
}
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