test_class.declarator: standAlone = false
test_class.original_string: boolean standAlone = false;
test_class.type: boolean
test_class.var_name: standAlone
test_class.file: tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java
test_class.identifier: AtomPlacer3DTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetPlacedHeavyAtom_IAtomContainer_IAtom() {
          IAtomContainer ac = makeAlphaPinene();
          IAtom acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0));
          Assert.assertNull(acplaced);
          ac.getAtom(1).setFlag(CDKConstants.ISPLACED, true);
          acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0));
          Assert.assertEquals(ac.getAtom(1), acplaced);
      }
test_case.class_method_signature: AtomPlacer3DTest.testGetPlacedHeavyAtom_IAtomContainer_IAtom()
test_case.full_signature: @Test public void testGetPlacedHeavyAtom_IAtomContainer_IAtom()
test_case.identifier: testGetPlacedHeavyAtom_IAtomContainer_IAtom
test_case.invocations: makeAlphaPinene getPlacedHeavyAtom getAtom assertNull setFlag getAtom getPlacedHeavyAtom getAtom assertEquals getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetPlacedHeavyAtom_IAtomContainer_IAtom()
focal_class.declarator: pSet                    = null
focal_class.modifier: private
focal_class.original_string: private Map<Object, List>   pSet                    = null;
focal_class.type: Map<Object, List>
focal_class.var_name: pSet
focal_class.declarator: distances
focal_class.modifier: private
focal_class.original_string: private double[]            distances;
focal_class.type: double[]
focal_class.var_name: distances
focal_class.declarator: firstAtoms              = null
focal_class.modifier: private
focal_class.original_string: private int[]               firstAtoms              = null;
focal_class.type: int[]
focal_class.var_name: firstAtoms
focal_class.declarator: angles                  = null
focal_class.modifier: private
focal_class.original_string: private double[]            angles                  = null;
focal_class.type: double[]
focal_class.var_name: angles
focal_class.declarator: secondAtoms             = null
focal_class.modifier: private
focal_class.original_string: private int[]               secondAtoms             = null;
focal_class.type: int[]
focal_class.var_name: secondAtoms
focal_class.declarator: dihedrals               = null
focal_class.modifier: private
focal_class.original_string: private double[]            dihedrals               = null;
focal_class.type: double[]
focal_class.var_name: dihedrals
focal_class.declarator: thirdAtoms              = null
focal_class.modifier: private
focal_class.original_string: private int[]               thirdAtoms              = null;
focal_class.type: int[]
focal_class.var_name: thirdAtoms
focal_class.declarator: DIHEDRAL_EXTENDED_CHAIN = (180.0 / 180) * Math.PI
focal_class.modifier: private final static
focal_class.original_string: private final static double DIHEDRAL_EXTENDED_CHAIN = (180.0 / 180) * Math.PI;
focal_class.type: double
focal_class.var_name: DIHEDRAL_EXTENDED_CHAIN
focal_class.declarator: DIHEDRAL_BRANCHED_CHAIN = 0.0
focal_class.modifier: private final static
focal_class.original_string: private final static double DIHEDRAL_BRANCHED_CHAIN = 0.0;
focal_class.type: double
focal_class.var_name: DIHEDRAL_BRANCHED_CHAIN
focal_class.declarator: DEFAULT_BOND_LENGTH     = 1.5
focal_class.modifier: private final static
focal_class.original_string: private final static double DEFAULT_BOND_LENGTH     = 1.5;
focal_class.type: double
focal_class.var_name: DEFAULT_BOND_LENGTH
focal_class.declarator: DEFAULT_SP3_ANGLE       = 109.471
focal_class.modifier: private final static
focal_class.original_string: private final static double DEFAULT_SP3_ANGLE       = 109.471;
focal_class.type: double
focal_class.var_name: DEFAULT_SP3_ANGLE
focal_class.declarator: DEFAULT_SP2_ANGLE       = 120.000
focal_class.modifier: private final static
focal_class.original_string: private final static double DEFAULT_SP2_ANGLE       = 120.000;
focal_class.type: double
focal_class.var_name: DEFAULT_SP2_ANGLE
focal_class.declarator: DEFAULT_SP_ANGLE        = 180.000
focal_class.modifier: private final static
focal_class.original_string: private final static double DEFAULT_SP_ANGLE        = 180.000;
focal_class.type: double
focal_class.var_name: DEFAULT_SP_ANGLE
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(AtomPlacer3D.class)
focal_class.modifier: private final
focal_class.original_string: private final ILoggingTool logger = LoggingToolFactory.createLoggingTool(AtomPlacer3D.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
focal_class.identifier: AtomPlacer3D
focal_class.class_method_signature: AtomPlacer3D.AtomPlacer3D()
focal_class.full_signature:   AtomPlacer3D()
focal_class.identifier: AtomPlacer3D
focal_class.parameters: ()
focal_class.signature:  AtomPlacer3D()
focal_class.class_method_signature: AtomPlacer3D.initilize(Map parameterSet)
focal_class.full_signature: public void initilize(Map parameterSet)
focal_class.identifier: initilize
focal_class.modifiers: public
focal_class.parameters: (Map parameterSet)
focal_class.return: void
focal_class.signature: void initilize(Map parameterSet)
focal_class.class_method_signature: AtomPlacer3D.findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.full_signature: public int[] findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.identifier: findHeavyAtomsInChain
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtomContainer chain)
focal_class.return: int[]
focal_class.signature: int[] findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.class_method_signature: AtomPlacer3D.markPlaced(IAtomContainer ac)
focal_class.full_signature: public IAtomContainer markPlaced(IAtomContainer ac)
focal_class.identifier: markPlaced
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer markPlaced(IAtomContainer ac)
focal_class.class_method_signature: AtomPlacer3D.placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.full_signature: public void placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.identifier: placeAliphaticHeavyChain
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtomContainer chain)
focal_class.return: void
focal_class.signature: void placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain)
focal_class.class_method_signature: AtomPlacer3D.zmatrixChainToCartesian(IAtomContainer molecule, boolean flagBranched)
focal_class.full_signature: public void zmatrixChainToCartesian(IAtomContainer molecule, boolean flagBranched)
focal_class.identifier: zmatrixChainToCartesian
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, boolean flagBranched)
focal_class.return: void
focal_class.signature: void zmatrixChainToCartesian(IAtomContainer molecule, boolean flagBranched)
focal_class.class_method_signature: AtomPlacer3D.getHybridisationState(IAtom atom1)
focal_class.full_signature: private int getHybridisationState(IAtom atom1)
focal_class.identifier: getHybridisationState
focal_class.modifiers: private
focal_class.parameters: (IAtom atom1)
focal_class.return: int
focal_class.signature: int getHybridisationState(IAtom atom1)
focal_class.class_method_signature: AtomPlacer3D.getDoubleBondConfiguration2D(IBond bond, Point2d a, Point2d b, Point2d c, Point2d d)
focal_class.full_signature: private int getDoubleBondConfiguration2D(IBond bond, Point2d a, Point2d b, Point2d c, Point2d d)
focal_class.identifier: getDoubleBondConfiguration2D
focal_class.modifiers: private
focal_class.parameters: (IBond bond, Point2d a, Point2d b, Point2d c, Point2d d)
focal_class.return: int
focal_class.signature: int getDoubleBondConfiguration2D(IBond bond, Point2d a, Point2d b, Point2d c, Point2d d)
focal_class.class_method_signature: AtomPlacer3D.getBondLengthValue(String id1, String id2)
focal_class.full_signature: public double getBondLengthValue(String id1, String id2)
focal_class.identifier: getBondLengthValue
focal_class.modifiers: public
focal_class.parameters: (String id1, String id2)
focal_class.return: double
focal_class.signature: double getBondLengthValue(String id1, String id2)
focal_class.class_method_signature: AtomPlacer3D.getAngleValue(String id1, String id2, String id3)
focal_class.full_signature: public double getAngleValue(String id1, String id2, String id3)
focal_class.identifier: getAngleValue
focal_class.modifiers: public
focal_class.parameters: (String id1, String id2, String id3)
focal_class.return: double
focal_class.signature: double getAngleValue(String id1, String id2, String id3)
focal_class.class_method_signature: AtomPlacer3D.getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
focal_class.full_signature: public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
focal_class.identifier: getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtom
focal_class.signature: IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.getUnplacedHeavyAtom(IAtomContainer molecule)
focal_class.full_signature:  IAtom getUnplacedHeavyAtom(IAtomContainer molecule)
focal_class.identifier: getUnplacedHeavyAtom
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtom
focal_class.signature: IAtom getUnplacedHeavyAtom(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
focal_class.full_signature: public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
focal_class.identifier: getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtom
focal_class.signature: IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
focal_class.full_signature: public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
focal_class.identifier: getNextPlacedHeavyAtomWithUnplacedRingNeighbour
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtom
focal_class.signature: IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.getFarthestAtom(Point3d refAtomPoint, IAtomContainer ac)
focal_class.full_signature: public IAtom getFarthestAtom(Point3d refAtomPoint, IAtomContainer ac)
focal_class.identifier: getFarthestAtom
focal_class.modifiers: public
focal_class.parameters: (Point3d refAtomPoint, IAtomContainer ac)
focal_class.return: IAtom
focal_class.signature: IAtom getFarthestAtom(Point3d refAtomPoint, IAtomContainer ac)
focal_class.class_method_signature: AtomPlacer3D.getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.full_signature: public IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.identifier: getUnplacedRingHeavyAtom
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtom atom)
focal_class.return: IAtom
focal_class.signature: IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.geometricCenterAllPlacedAtoms(IAtomContainer molecule)
focal_class.full_signature: public Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule)
focal_class.identifier: geometricCenterAllPlacedAtoms
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: Point3d
focal_class.signature: Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.full_signature: public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.identifier: getPlacedHeavyAtom
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtom atom)
focal_class.return: IAtom
focal_class.signature: IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)
focal_class.full_signature: public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)
focal_class.identifier: getPlacedHeavyAtom
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtom atomA, IAtom atomB)
focal_class.return: IAtom
focal_class.signature: IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)
focal_class.class_method_signature: AtomPlacer3D.getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom)
focal_class.full_signature: public IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom)
focal_class.identifier: getPlacedHeavyAtoms
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, IAtom atom)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.numberOfUnplacedHeavyAtoms(IAtomContainer ac)
focal_class.full_signature: public int numberOfUnplacedHeavyAtoms(IAtomContainer ac)
focal_class.identifier: numberOfUnplacedHeavyAtoms
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac)
focal_class.return: int
focal_class.signature: int numberOfUnplacedHeavyAtoms(IAtomContainer ac)
focal_class.class_method_signature: AtomPlacer3D.getAllPlacedAtoms(IAtomContainer molecule)
focal_class.full_signature: private IAtomContainer getAllPlacedAtoms(IAtomContainer molecule)
focal_class.identifier: getAllPlacedAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAllPlacedAtoms(IAtomContainer molecule)
focal_class.class_method_signature: AtomPlacer3D.allHeavyAtomsPlaced(IAtomContainer ac)
focal_class.full_signature: public boolean allHeavyAtomsPlaced(IAtomContainer ac)
focal_class.identifier: allHeavyAtomsPlaced
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac)
focal_class.return: boolean
focal_class.signature: boolean allHeavyAtomsPlaced(IAtomContainer ac)
focal_class.class_method_signature: AtomPlacer3D.isUnplacedHeavyAtom(IAtom atom)
focal_class.full_signature:  boolean isUnplacedHeavyAtom(IAtom atom)
focal_class.identifier: isUnplacedHeavyAtom
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isUnplacedHeavyAtom(IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.isPlacedHeavyAtom(IAtom atom)
focal_class.full_signature:  boolean isPlacedHeavyAtom(IAtom atom)
focal_class.identifier: isPlacedHeavyAtom
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isPlacedHeavyAtom(IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.isAliphaticHeavyAtom(IAtom atom)
focal_class.full_signature:  boolean isAliphaticHeavyAtom(IAtom atom)
focal_class.identifier: isAliphaticHeavyAtom
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isAliphaticHeavyAtom(IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.isRingHeavyAtom(IAtom atom)
focal_class.full_signature:  boolean isRingHeavyAtom(IAtom atom)
focal_class.identifier: isRingHeavyAtom
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isRingHeavyAtom(IAtom atom)
focal_class.class_method_signature: AtomPlacer3D.isHeavyAtom(IAtom atom)
focal_class.full_signature:  boolean isHeavyAtom(IAtom atom)
focal_class.identifier: isHeavyAtom
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isHeavyAtom(IAtom atom)
focal_method.body: public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) {
          List<IBond> bonds = molecule.getConnectedBondsList(atom);
          for (IBond bond : bonds) {
              IAtom connectedAtom = bond.getOther(atom);
              if (isPlacedHeavyAtom(connectedAtom)) {
                  return connectedAtom;
              }
          }
          return null;
      }
focal_method.class_method_signature: AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_method.full_signature: public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
focal_method.identifier: getPlacedHeavyAtom
focal_method.invocations: getConnectedBondsList getOther isPlacedHeavyAtom
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer molecule, IAtom atom)
focal_method.return: IAtom
focal_method.signature: IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)