switch

yoink-core-molecule/src/main/java/org/wallerlab/yoink/molecule/data/JaxbFileReader.java

@@ -45,11 +45,15 @@ public class JaxbFileReader extends AbstractJaxbReader {
 	 */
 	public JAXBElement<Cml> read(String input, Object jaxbObject) {
 		this.input = new File(input);
+		System.out.println("input is" + input);
 		JAXBElement<Cml> marshalled = init(jaxbObject);
+		System.out.println("Marshalled" + marshalled);
+
 		return marshalled;
 	}
 
 	protected JAXBElement<Cml> unmarshal(Object jaxbObject) throws JAXBException{
+		System.out.println("input is " + input);
 		JAXBElement<Cml> marshalled = (JAXBElement<Cml>) jaxbUnmarshaller.unmarshal(input);
 		return marshalled;
 	}

yoink-core-molecule/src/test/groovy/org/wallerlab/yoink/molecule/data/JaxbFileReaderSpec.groovy

@@ -13,11 +13,11 @@ class JaxbFileReaderSpec extends Specification{
 	def "test method read()"(){
 		when:"jaxb reader reads a given file"
 			def reader= new JaxbFileReader()
-			JAXBElement<Cml> msr= reader.read("./src/test/resources/lih.xml",new Cml())
-			JAXBElement mlJAXB =((((JAXBElement)msr.getValue().getAnyCmlOrAnyOrAny().get(0))))
-		MoleculeList ml= mlJAXB.getValue()
+			    JAXBElement<Cml> msr= reader.read("./src/test/resources/1D.xml",new Cml())
+			    JAXBElement mlJAXB =((((JAXBElement)msr.getValue().getAnyCmlOrAnyOrAny().get(0))))
+		         MoleculeList ml= mlJAXB.getValue()
 			then:"assert the content in the given file"
-			msr.getValue().getAnyCmlOrAnyOrAny().size()==2
-			ml.getAnyCmlOrAnyOrAny().size()==2
+			    msr.getValue().getAnyCmlOrAnyOrAny().size()==2
+			    ml.getAnyCmlOrAnyOrAny().size()==2
 	}
 }

yoink-core-region/src/main/java/org/wallerlab/yoink/region/service/partitioners/NumberPartitioner.java

@@ -73,23 +73,14 @@ else if (job.getParameter(PARTITIONER).equals(SIZE)){
 			int    qmNumberSize 	 =  Integer.parseInt(  job.getParameter(NUMBER_QM).toString()) * 2 / 3;
 			double distance_s_qm_in  =  Double.parseDouble(job.getParameter(DISTANCE_S_QM_IN).toString());
 			double distance_t_qm_out =  Double.parseDouble(job.getParameter(DISTANCE_T_QM_OUT).toString());
-
-			System.out.println("com" + centerOfMass);
-			System.out.println("com" + sortedMolecules.get(0).getAtoms());
-			System.out.println("distance is " + distanceCalculator.closest(centerOfMass,sortedMolecules.get(0)) );
-
 			//find first molecule that is outside of limit.
 		    MolecularSystem.Molecule moleculeAtT_Qm_Out =
 		       sortedMolecules.stream()
 		                      .filter(molecule ->
 		                               distanceCalculator.closest(centerOfMass, molecule) > distance_t_qm_out)
 				              .findFirst()
 				              .get();
-			System.out.println("qmNumberSize is " + qmNumberSize);
 			qmAdaptiveMolecules = new HashSet<>(sortedMolecules.subList(0, qmNumberSize));
-
-			System.out.println("index " + sortedMolecules.indexOf(moleculeAtT_Qm_Out));
-
 			bufferMolecules = new HashSet<>(sortedMolecules.subList(numberOfQm,
 								    	  	  sortedMolecules.indexOf(moleculeAtT_Qm_Out) + 1));
 		}

yoink-core-region/src/test/groovy/org/wallerlab/yoink/region/service/partitioners/NumberPartitionerSpec.groovy

@@ -134,4 +134,11 @@ class  NumberPartitionerSpec extends Specification{
 		qmAdaptiveAndBuffer.get(BUFFER).size()==1
 	}
 
+	private MolecularSystem.Molecule createMolecule() {
+		def atom = Mock(MolecularSystem.Molecule.Atom)
+		def molecule = Mock(MolecularSystem.Molecule)
+		molecule.getAtoms() >> [atom]
+		molecule
+	}
+
 }