test_class.file: base/data/src/test/java/org/openscience/cdk/AtomTest.java
test_class.identifier: AtomTest
test_class.superclass: extends AbstractAtomTest
test_case.body: @Test
      @Override
      public void testCompare_Object() {
          IAtom someAtom = new Atom("C");
          if (someAtom instanceof org.openscience.cdk.Atom) {
              org.openscience.cdk.Atom atom = (org.openscience.cdk.Atom) someAtom;
              Assert.assertTrue(atom.compare(atom));
              IAtom hydrogen = someAtom.getBuilder().newInstance(IAtom.class, "H");
              Assert.assertFalse(atom.compare(hydrogen));
              Assert.assertFalse(atom.compare("C"));
          }
      }
test_case.class_method_signature: AtomTest.testCompare_Object()
test_case.full_signature: @Test @Override public void testCompare_Object()
test_case.identifier: testCompare_Object
test_case.invocations: assertTrue compare newInstance getBuilder assertFalse compare assertFalse compare
test_case.modifiers: @Test @Override public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCompare_Object()
focal_class.declarator: serialVersionUID  = -3137373012494608794L
focal_class.modifier: private static final
focal_class.original_string: private static final long serialVersionUID  = -3137373012494608794L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: point2d           = (Point2d) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Point2d         point2d           = (Point2d) CDKConstants.UNSET;
focal_class.type: Point2d
focal_class.var_name: point2d
focal_class.declarator: point3d           = (Point3d) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Point3d         point3d           = (Point3d) CDKConstants.UNSET;
focal_class.type: Point3d
focal_class.var_name: point3d
focal_class.declarator: fractionalPoint3d = (Point3d) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Point3d         fractionalPoint3d = (Point3d) CDKConstants.UNSET;
focal_class.type: Point3d
focal_class.var_name: fractionalPoint3d
focal_class.declarator: hydrogenCount     = (Integer) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Integer         hydrogenCount     = (Integer) CDKConstants.UNSET;
focal_class.type: Integer
focal_class.var_name: hydrogenCount
focal_class.declarator: stereoParity      = (Integer) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Integer         stereoParity      = (Integer) CDKConstants.UNSET;
focal_class.type: Integer
focal_class.var_name: stereoParity
focal_class.declarator: charge            = (Double) CDKConstants.UNSET
focal_class.modifier: protected
focal_class.original_string: protected Double          charge            = (Double) CDKConstants.UNSET;
focal_class.type: Double
focal_class.var_name: charge
focal_class.file: base/data/src/main/java/org/openscience/cdk/Atom.java
focal_class.identifier: Atom
focal_class.interfaces: implements IAtom, Serializable, Cloneable
focal_class.class_method_signature: Atom.Atom()
focal_class.full_signature: public  Atom()
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Atom()
focal_class.class_method_signature: Atom.Atom(int elem)
focal_class.full_signature: public  Atom(int elem)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (int elem)
focal_class.signature:  Atom(int elem)
focal_class.class_method_signature: Atom.Atom(int elem, int hcnt)
focal_class.full_signature: public  Atom(int elem, int hcnt)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (int elem, int hcnt)
focal_class.signature:  Atom(int elem, int hcnt)
focal_class.class_method_signature: Atom.Atom(int elem, int hcnt, int fchg)
focal_class.full_signature: public  Atom(int elem, int hcnt, int fchg)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (int elem, int hcnt, int fchg)
focal_class.signature:  Atom(int elem, int hcnt, int fchg)
focal_class.class_method_signature: Atom.Atom(String symbol)
focal_class.full_signature: public  Atom(String symbol)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (String symbol)
focal_class.signature:  Atom(String symbol)
focal_class.class_method_signature: Atom.Atom(String elementSymbol, Point3d point3d)
focal_class.full_signature: public  Atom(String elementSymbol, Point3d point3d)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (String elementSymbol, Point3d point3d)
focal_class.signature:  Atom(String elementSymbol, Point3d point3d)
focal_class.class_method_signature: Atom.Atom(String elementSymbol, Point2d point2d)
focal_class.full_signature: public  Atom(String elementSymbol, Point2d point2d)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (String elementSymbol, Point2d point2d)
focal_class.signature:  Atom(String elementSymbol, Point2d point2d)
focal_class.class_method_signature: Atom.Atom(IElement element)
focal_class.full_signature: public  Atom(IElement element)
focal_class.identifier: Atom
focal_class.modifiers: public
focal_class.parameters: (IElement element)
focal_class.signature:  Atom(IElement element)
focal_class.class_method_signature: Atom.getContainer()
focal_class.full_signature: @Override public IAtomContainer getContainer()
focal_class.identifier: getContainer
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getContainer()
focal_class.class_method_signature: Atom.getIndex()
focal_class.full_signature: @Override public int getIndex()
focal_class.identifier: getIndex
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getIndex()
focal_class.class_method_signature: Atom.bonds()
focal_class.full_signature: @Override public Iterable<IBond> bonds()
focal_class.identifier: bonds
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IBond>
focal_class.signature: Iterable<IBond> bonds()
focal_class.class_method_signature: Atom.getBondCount()
focal_class.full_signature: @Override public int getBondCount()
focal_class.identifier: getBondCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getBondCount()
focal_class.class_method_signature: Atom.getBond(IAtom atom)
focal_class.full_signature: @Override public IBond getBond(IAtom atom)
focal_class.identifier: getBond
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: IBond
focal_class.signature: IBond getBond(IAtom atom)
focal_class.class_method_signature: Atom.setCharge(Double charge)
focal_class.full_signature: @Override public void setCharge(Double charge)
focal_class.identifier: setCharge
focal_class.modifiers: @Override public
focal_class.parameters: (Double charge)
focal_class.return: void
focal_class.signature: void setCharge(Double charge)
focal_class.class_method_signature: Atom.getCharge()
focal_class.full_signature: @Override public Double getCharge()
focal_class.identifier: getCharge
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getCharge()
focal_class.class_method_signature: Atom.setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.full_signature: @Override public void setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.identifier: setImplicitHydrogenCount
focal_class.modifiers: @Override public
focal_class.parameters: (Integer hydrogenCount)
focal_class.return: void
focal_class.signature: void setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.class_method_signature: Atom.getImplicitHydrogenCount()
focal_class.full_signature: @Override public Integer getImplicitHydrogenCount()
focal_class.identifier: getImplicitHydrogenCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getImplicitHydrogenCount()
focal_class.class_method_signature: Atom.setPoint2d(Point2d point2d)
focal_class.full_signature: @Override public void setPoint2d(Point2d point2d)
focal_class.identifier: setPoint2d
focal_class.modifiers: @Override public
focal_class.parameters: (Point2d point2d)
focal_class.return: void
focal_class.signature: void setPoint2d(Point2d point2d)
focal_class.class_method_signature: Atom.setPoint3d(Point3d point3d)
focal_class.full_signature: @Override public void setPoint3d(Point3d point3d)
focal_class.identifier: setPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: (Point3d point3d)
focal_class.return: void
focal_class.signature: void setPoint3d(Point3d point3d)
focal_class.class_method_signature: Atom.setFractionalPoint3d(Point3d point3d)
focal_class.full_signature: @Override public void setFractionalPoint3d(Point3d point3d)
focal_class.identifier: setFractionalPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: (Point3d point3d)
focal_class.return: void
focal_class.signature: void setFractionalPoint3d(Point3d point3d)
focal_class.class_method_signature: Atom.setStereoParity(Integer stereoParity)
focal_class.full_signature: @Override public void setStereoParity(Integer stereoParity)
focal_class.identifier: setStereoParity
focal_class.modifiers: @Override public
focal_class.parameters: (Integer stereoParity)
focal_class.return: void
focal_class.signature: void setStereoParity(Integer stereoParity)
focal_class.class_method_signature: Atom.getPoint2d()
focal_class.full_signature: @Override public Point2d getPoint2d()
focal_class.identifier: getPoint2d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point2d
focal_class.signature: Point2d getPoint2d()
focal_class.class_method_signature: Atom.getPoint3d()
focal_class.full_signature: @Override public Point3d getPoint3d()
focal_class.identifier: getPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point3d
focal_class.signature: Point3d getPoint3d()
focal_class.class_method_signature: Atom.getFractionalPoint3d()
focal_class.full_signature: @Override public Point3d getFractionalPoint3d()
focal_class.identifier: getFractionalPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point3d
focal_class.signature: Point3d getFractionalPoint3d()
focal_class.class_method_signature: Atom.getStereoParity()
focal_class.full_signature: @Override public Integer getStereoParity()
focal_class.identifier: getStereoParity
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getStereoParity()
focal_class.class_method_signature: Atom.compare(Object object)
focal_class.full_signature: @Override public boolean compare(Object object)
focal_class.identifier: compare
focal_class.modifiers: @Override public
focal_class.parameters: (Object object)
focal_class.return: boolean
focal_class.signature: boolean compare(Object object)
focal_class.class_method_signature: Atom.isAromatic()
focal_class.full_signature: @Override public boolean isAromatic()
focal_class.identifier: isAromatic
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isAromatic()
focal_class.class_method_signature: Atom.setIsAromatic(boolean arom)
focal_class.full_signature: @Override public void setIsAromatic(boolean arom)
focal_class.identifier: setIsAromatic
focal_class.modifiers: @Override public
focal_class.parameters: (boolean arom)
focal_class.return: void
focal_class.signature: void setIsAromatic(boolean arom)
focal_class.class_method_signature: Atom.isInRing()
focal_class.full_signature: @Override public boolean isInRing()
focal_class.identifier: isInRing
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isInRing()
focal_class.class_method_signature: Atom.setIsInRing(boolean ring)
focal_class.full_signature: @Override public void setIsInRing(boolean ring)
focal_class.identifier: setIsInRing
focal_class.modifiers: @Override public
focal_class.parameters: (boolean ring)
focal_class.return: void
focal_class.signature: void setIsInRing(boolean ring)
focal_class.class_method_signature: Atom.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.class_method_signature: Atom.clone()
focal_class.full_signature: @Override public IAtom clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtom
focal_class.signature: IAtom clone()
focal_class.class_method_signature: Atom.isUpper(char c)
focal_class.full_signature: private static boolean isUpper(char c)
focal_class.identifier: isUpper
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isUpper(char c)
focal_class.class_method_signature: Atom.isLower(char c)
focal_class.full_signature: private static boolean isLower(char c)
focal_class.identifier: isLower
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isLower(char c)
focal_class.class_method_signature: Atom.isDigit(char c)
focal_class.full_signature: private static boolean isDigit(char c)
focal_class.identifier: isDigit
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isDigit(char c)
focal_class.class_method_signature: Atom.parseAtomSymbol(IAtom atom, String str)
focal_class.full_signature: private static boolean parseAtomSymbol(IAtom atom, String str)
focal_class.identifier: parseAtomSymbol
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom, String str)
focal_class.return: boolean
focal_class.signature: boolean parseAtomSymbol(IAtom atom, String str)
focal_class.class_method_signature: Atom.hashCode()
focal_class.full_signature: @Override public int hashCode()
focal_class.identifier: hashCode
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int hashCode()
focal_class.class_method_signature: Atom.equals(Object obj)
focal_class.full_signature: @Override public boolean equals(Object obj)
focal_class.identifier: equals
focal_class.modifiers: @Override public
focal_class.parameters: (Object obj)
focal_class.return: boolean
focal_class.signature: boolean equals(Object obj)
focal_class.superclass: extends AtomType
focal_method.body: @Override
      public boolean compare(Object object) {
          if (!(object instanceof IAtom)) {
              return false;
          }
          if (!super.compare(object)) {
              return false;
          }
          Atom atom = (Atom) object;
          // XXX: floating point comparision!
          if (((point2d == atom.point2d) || ((point2d != null) && (point2d.equals(atom.point2d))))
              && ((point3d == atom.point3d) || ((point3d != null) && (point3d.equals(atom.point3d))))
              && (Objects.equals(hydrogenCount, atom.hydrogenCount)) && (Objects.equals(stereoParity, atom.stereoParity))
              && (Objects.equals(charge, atom.charge))) {
              return true;
          }
          return false;
      }
focal_method.class_method_signature: Atom.compare(Object object)
focal_method.full_signature: @Override public boolean compare(Object object)
focal_method.identifier: compare
focal_method.invocations: compare equals equals equals equals equals
focal_method.modifiers: @Override public
focal_method.parameters: (Object object)
focal_method.return: boolean
focal_method.signature: boolean compare(Object object)