test_class.file: base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java
test_class.identifier: PDBPolymerTest
test_class.superclass: extends AbstractPDBPolymerTest
test_case.body: @Test
      public void testPDBPolymer() {
          IPDBPolymer pdbPolymer = new PDBPolymer();
          Assert.assertNotNull(pdbPolymer);
          Assert.assertEquals(pdbPolymer.getMonomerCount(), 0);
  
          IStrand oStrand1 = pdbPolymer.getBuilder().newInstance(IStrand.class);
          oStrand1.setStrandName("A");
          IStrand oStrand2 = pdbPolymer.getBuilder().newInstance(IStrand.class);
          oStrand2.setStrandName("B");
          IMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
          oMono1.setMonomerName(new String("TRP279"));
          IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
          oMono2.setMonomerName(new String("HOH"));
          IMonomer oMono3 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
          oMono3.setMonomerName(new String("GLYA16"));
          IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C");
          IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C");
          IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C");
          IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C");
          IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C");
  
          pdbPolymer.addAtom(oPDBAtom1);
          pdbPolymer.addAtom(oPDBAtom2, oStrand1);
          pdbPolymer.addAtom(oPDBAtom3, oMono1, oStrand1);
          pdbPolymer.addAtom(oPDBAtom4, oMono2, oStrand2);
          pdbPolymer.addAtom(oPDBAtom5, oMono3, oStrand2);
          Assert.assertNotNull(pdbPolymer.getAtom(0));
          Assert.assertNotNull(pdbPolymer.getAtom(1));
          Assert.assertNotNull(pdbPolymer.getAtom(2));
          Assert.assertNotNull(pdbPolymer.getAtom(3));
          Assert.assertNotNull(pdbPolymer.getAtom(4));
          Assert.assertEquals(oPDBAtom1, pdbPolymer.getAtom(0));
          Assert.assertEquals(oPDBAtom2, pdbPolymer.getAtom(1));
          Assert.assertEquals(oPDBAtom3, pdbPolymer.getAtom(2));
          Assert.assertEquals(oPDBAtom4, pdbPolymer.getAtom(3));
          Assert.assertEquals(oPDBAtom5, pdbPolymer.getAtom(4));
  
          Assert.assertNull(pdbPolymer.getMonomer("0815", "A"));
          Assert.assertNull(pdbPolymer.getMonomer("0815", "B"));
          Assert.assertNull(pdbPolymer.getMonomer("0815", ""));
          Assert.assertNull(pdbPolymer.getStrand(""));
          Assert.assertNotNull(pdbPolymer.getMonomer("TRP279", "A"));
          Assert.assertEquals(oMono1, pdbPolymer.getMonomer("TRP279", "A"));
          Assert.assertEquals(pdbPolymer.getMonomer("TRP279", "A").getAtomCount(), 1);
          Assert.assertNotNull(pdbPolymer.getMonomer("HOH", "B"));
          Assert.assertEquals(oMono2, pdbPolymer.getMonomer("HOH", "B"));
          Assert.assertEquals(pdbPolymer.getMonomer("HOH", "B").getAtomCount(), 1);
          Assert.assertEquals(pdbPolymer.getStrand("B").getAtomCount(), 2);
          Assert.assertEquals(pdbPolymer.getStrand("B").getMonomerCount(), 2);
          Assert.assertNull(pdbPolymer.getStrand("C"));
          Assert.assertNotNull(pdbPolymer.getStrand("B"));
      }
test_case.class_method_signature: PDBPolymerTest.testPDBPolymer()
test_case.full_signature: @Test public void testPDBPolymer()
test_case.identifier: testPDBPolymer
test_case.invocations: assertNotNull assertEquals getMonomerCount newInstance getBuilder setStrandName newInstance getBuilder setStrandName newInstance getBuilder setMonomerName newInstance getBuilder setMonomerName newInstance getBuilder setMonomerName newInstance getBuilder newInstance getBuilder newInstance getBuilder newInstance getBuilder newInstance getBuilder addAtom addAtom addAtom addAtom addAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertNotNull getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertEquals getAtom assertNull getMonomer assertNull getMonomer assertNull getMonomer assertNull getStrand assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertNotNull getMonomer assertEquals getMonomer assertEquals getAtomCount getMonomer assertEquals getAtomCount getStrand assertEquals getMonomerCount getStrand assertNull getStrand assertNotNull getStrand
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testPDBPolymer()
focal_class.declarator: serialVersionUID = 4173552834313952358L
focal_class.modifier: private static final
focal_class.original_string: private static final long serialVersionUID = 4173552834313952358L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: sequentialListOfMonomers
focal_class.original_string: List<String>              sequentialListOfMonomers;
focal_class.type: List<String>
focal_class.var_name: sequentialListOfMonomers
focal_class.declarator: secondaryStructures
focal_class.original_string: List<IPDBStructure>       secondaryStructures;
focal_class.type: List<IPDBStructure>
focal_class.var_name: secondaryStructures
focal_class.file: base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java
focal_class.identifier: PDBPolymer
focal_class.interfaces: implements Cloneable, IPDBPolymer
focal_class.class_method_signature: PDBPolymer.PDBPolymer()
focal_class.full_signature: public  PDBPolymer()
focal_class.identifier: PDBPolymer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  PDBPolymer()
focal_class.class_method_signature: PDBPolymer.addStructure(IPDBStructure structure)
focal_class.full_signature: @Override public void addStructure(IPDBStructure structure)
focal_class.identifier: addStructure
focal_class.modifiers: @Override public
focal_class.parameters: (IPDBStructure structure)
focal_class.return: void
focal_class.signature: void addStructure(IPDBStructure structure)
focal_class.class_method_signature: PDBPolymer.getStructures()
focal_class.full_signature: @Override public Collection<IPDBStructure> getStructures()
focal_class.identifier: getStructures
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Collection<IPDBStructure>
focal_class.signature: Collection<IPDBStructure> getStructures()
focal_class.class_method_signature: PDBPolymer.addAtom(IPDBAtom oAtom)
focal_class.full_signature: @Override public void addAtom(IPDBAtom oAtom)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IPDBAtom oAtom)
focal_class.return: void
focal_class.signature: void addAtom(IPDBAtom oAtom)
focal_class.class_method_signature: PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer)
focal_class.full_signature: public void addAtom(IPDBAtom oAtom, IMonomer oMonomer)
focal_class.identifier: addAtom
focal_class.modifiers: public
focal_class.parameters: (IPDBAtom oAtom, IMonomer oMonomer)
focal_class.return: void
focal_class.signature: void addAtom(IPDBAtom oAtom, IMonomer oMonomer)
focal_class.class_method_signature: PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.full_signature: @Override public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.return: void
focal_class.signature: void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
focal_class.class_method_signature: PDBPolymer.getMonomerNamesInSequentialOrder()
focal_class.full_signature: public Collection<String> getMonomerNamesInSequentialOrder()
focal_class.identifier: getMonomerNamesInSequentialOrder
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Collection<String>
focal_class.signature: Collection<String> getMonomerNamesInSequentialOrder()
focal_class.class_method_signature: PDBPolymer.clone()
focal_class.full_signature: @Override public IPDBPolymer clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IPDBPolymer
focal_class.signature: IPDBPolymer clone()
focal_class.class_method_signature: PDBPolymer.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.superclass: extends BioPolymer
focal_method.body: public PDBPolymer() {
          super();
          sequentialListOfMonomers = new ArrayList<String>();
          secondaryStructures = new ArrayList<IPDBStructure>();
      }
focal_method.class_method_signature: PDBPolymer.PDBPolymer()
focal_method.full_signature: public  PDBPolymer()
focal_method.identifier: PDBPolymer
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  PDBPolymer()