test_class.declarator: logger = LoggingToolFactory.createLoggingTool(MDMoleculeTest.class)
test_class.modifier: private
test_class.original_string: private ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDMoleculeTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/libiomd/src/test/java/org/openscience/cdk/libio/md/MDMoleculeTest.java
test_class.identifier: MDMoleculeTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testMDMolecule() {
  
          MDMolecule mol = new MDMolecule();
          mol.addAtom(new Atom("C")); // 0
          mol.addAtom(new Atom("C")); // 1
          mol.addAtom(new Atom("C")); // 2
          mol.addAtom(new Atom("C")); // 3
          mol.addAtom(new Atom("C")); // 4
          mol.addAtom(new Atom("C")); // 5
  
          mol.addBond(0, 1, IBond.Order.SINGLE); // 1
          mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
          mol.addBond(2, 3, IBond.Order.SINGLE); // 3
          mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
          mol.addBond(4, 5, IBond.Order.SINGLE); // 5
          mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
  
          //Create 2 residues
          AtomContainer ac = new AtomContainer();
          ac.addAtom(mol.getAtom(0));
          ac.addAtom(mol.getAtom(1));
          ac.addAtom(mol.getAtom(2));
          Residue res1 = new Residue(ac, 0, mol);
          res1.setName("myResidue1");
          mol.addResidue(res1);
  
          AtomContainer ac2 = new AtomContainer();
          ac2.addAtom(mol.getAtom(3));
          ac2.addAtom(mol.getAtom(4));
          ac2.addAtom(mol.getAtom(5));
          Residue res2 = new Residue(ac2, 1, mol);
          res2.setName("myResidue2");
          mol.addResidue(res2);
  
          //Test residue creation
          Assert.assertEquals(res1.getParentMolecule(), mol);
          Assert.assertEquals(res2.getParentMolecule(), mol);
          Assert.assertEquals(res1.getAtomCount(), 3);
          Assert.assertEquals(res2.getAtomCount(), 3);
          Assert.assertEquals(res1.getName(), "myResidue1");
          Assert.assertEquals(res2.getName(), "myResidue2");
          Assert.assertNotNull(mol.getResidues());
          Assert.assertEquals(mol.getResidues().size(), 2);
          Assert.assertEquals(mol.getResidues().get(0), res1);
          Assert.assertEquals(mol.getResidues().get(1), res2);
  
          //Create 2 chargegroups
          AtomContainer ac3 = new AtomContainer();
          ac3.addAtom(mol.getAtom(0));
          ac3.addAtom(mol.getAtom(1));
          ChargeGroup chg1 = new ChargeGroup(ac3, 0, mol);
          mol.addChargeGroup(chg1);
  
          AtomContainer ac4 = new AtomContainer();
          ac4.addAtom(mol.getAtom(2));
          ac4.addAtom(mol.getAtom(3));
          ac4.addAtom(mol.getAtom(4));
          ac4.addAtom(mol.getAtom(5));
          ChargeGroup chg2 = new ChargeGroup(ac4, 1, mol);
          mol.addChargeGroup(chg2);
  
          //Test chargegroup creation
          Assert.assertEquals(chg1.getParentMolecule(), mol);
          Assert.assertEquals(chg2.getParentMolecule(), mol);
          Assert.assertEquals(chg1.getAtomCount(), 2);
          Assert.assertEquals(chg2.getAtomCount(), 4);
  
          Assert.assertNotNull(mol.getChargeGroups());
          Assert.assertEquals(mol.getChargeGroups().size(), 2);
          Assert.assertEquals(mol.getChargeGroups().get(0), chg1);
          Assert.assertEquals(mol.getChargeGroups().get(1), chg2);
  
      }
test_case.class_method_signature: MDMoleculeTest.testMDMolecule()
test_case.full_signature: @Test public void testMDMolecule()
test_case.identifier: testMDMolecule
test_case.invocations: addAtom addAtom addAtom addAtom addAtom addAtom addBond addBond addBond addBond addBond addBond addAtom getAtom addAtom getAtom addAtom getAtom setName addResidue addAtom getAtom addAtom getAtom addAtom getAtom setName addResidue assertEquals getParentMolecule assertEquals getParentMolecule assertEquals getAtomCount assertEquals getAtomCount assertEquals getName assertEquals getName assertNotNull getResidues assertEquals size getResidues assertEquals get getResidues assertEquals get getResidues addAtom getAtom addAtom getAtom addChargeGroup addAtom getAtom addAtom getAtom addAtom getAtom addAtom getAtom addChargeGroup assertEquals getParentMolecule assertEquals getParentMolecule assertEquals getAtomCount assertEquals getAtomCount assertNotNull getChargeGroups assertEquals size getChargeGroups assertEquals get getChargeGroups assertEquals get getChargeGroups
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testMDMolecule()
focal_class.declarator: serialVersionUID = -3129626782945020908L
focal_class.modifier: private static final
focal_class.original_string: private static final long serialVersionUID = -3129626782945020908L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: residues
focal_class.modifier: private
focal_class.original_string: private List<Residue>              residues;
focal_class.type: List<Residue>
focal_class.var_name: residues
focal_class.declarator: chargeGroups
focal_class.modifier: private
focal_class.original_string: private List<ChargeGroup>          chargeGroups;
focal_class.type: List<ChargeGroup>
focal_class.var_name: chargeGroups
focal_class.file: storage/libiomd/src/main/java/org/openscience/cdk/libio/md/MDMolecule.java
focal_class.identifier: MDMolecule
focal_class.class_method_signature: MDMolecule.MDMolecule()
focal_class.full_signature: public  MDMolecule()
focal_class.identifier: MDMolecule
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDMolecule()
focal_class.class_method_signature: MDMolecule.MDMolecule(IAtomContainer container)
focal_class.full_signature: public  MDMolecule(IAtomContainer container)
focal_class.identifier: MDMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.signature:  MDMolecule(IAtomContainer container)
focal_class.class_method_signature: MDMolecule.getResidues()
focal_class.full_signature: public List<Residue> getResidues()
focal_class.identifier: getResidues
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Residue>
focal_class.signature: List<Residue> getResidues()
focal_class.class_method_signature: MDMolecule.setResidues(List<Residue> residues)
focal_class.full_signature: public void setResidues(List<Residue> residues)
focal_class.identifier: setResidues
focal_class.modifiers: public
focal_class.parameters: (List<Residue> residues)
focal_class.return: void
focal_class.signature: void setResidues(List<Residue> residues)
focal_class.class_method_signature: MDMolecule.addResidue(Residue residue)
focal_class.full_signature: public void addResidue(Residue residue)
focal_class.identifier: addResidue
focal_class.modifiers: public
focal_class.parameters: (Residue residue)
focal_class.return: void
focal_class.signature: void addResidue(Residue residue)
focal_class.class_method_signature: MDMolecule.getChargeGroups()
focal_class.full_signature: public List<ChargeGroup> getChargeGroups()
focal_class.identifier: getChargeGroups
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<ChargeGroup>
focal_class.signature: List<ChargeGroup> getChargeGroups()
focal_class.class_method_signature: MDMolecule.setChargeGroups(List<ChargeGroup> chargeGroups)
focal_class.full_signature: public void setChargeGroups(List<ChargeGroup> chargeGroups)
focal_class.identifier: setChargeGroups
focal_class.modifiers: public
focal_class.parameters: (List<ChargeGroup> chargeGroups)
focal_class.return: void
focal_class.signature: void setChargeGroups(List<ChargeGroup> chargeGroups)
focal_class.class_method_signature: MDMolecule.addChargeGroup(ChargeGroup chargeGroup)
focal_class.full_signature: public void addChargeGroup(ChargeGroup chargeGroup)
focal_class.identifier: addChargeGroup
focal_class.modifiers: public
focal_class.parameters: (ChargeGroup chargeGroup)
focal_class.return: void
focal_class.signature: void addChargeGroup(ChargeGroup chargeGroup)
focal_class.superclass: extends AtomContainer
focal_method.body: public MDMolecule() {
          super();
      }
focal_method.class_method_signature: MDMolecule.MDMolecule()
focal_method.full_signature: public  MDMolecule()
focal_method.identifier: MDMolecule
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  MDMolecule()