test_class.declarator: SDG = new StructureDiagramGenerator()
test_class.modifier: private static final
test_class.original_string: private static final StructureDiagramGenerator SDG = new StructureDiagramGenerator();
test_class.type: StructureDiagramGenerator
test_class.var_name: SDG
test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
test_class.identifier: StructureDiagramGeneratorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void multipleSalts() throws Exception {
          SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("[K+].[Al+3].[Cl-].[Cl-].[K+].[Cl-].[Cl-].[Al+3].[Cl-].[Pt+2]([NH3])[NH3].[Cl-].[Cl-].[Cl-].[O-][C+]([O-])[O-]");
          layout(mol);
          for (IAtom atom : mol.atoms())
              assertNotNull(atom.getPoint2d());
  
          IAtom platinum = null;
          Set<IAtom> aluminiums = new HashSet<>();
          Set<IAtom> potassiums = new HashSet<>();
          Set<IAtom> chlorines = new HashSet<>();
          Set<IAtom> oxygens = new HashSet<>();
          for (IAtom atom : mol.atoms()) {
              if (atom.getSymbol().equals("Cl"))
                  chlorines.add(atom);
              else if (atom.getSymbol().equals("O"))
                  oxygens.add(atom);
              else if (atom.getSymbol().equals("Al"))
                  aluminiums.add(atom);
              else if (atom.getSymbol().equals("K"))
                  potassiums.add(atom);
              else if (atom.getSymbol().equals("Pt"))
                  platinum = atom;
          }
  
          assertNotNull(platinum);
          assertThat(potassiums.size(), is(2));
          assertThat(oxygens.size(), is(3));
          assertThat(chlorines.size(), is(8));
  
          // platin has two chlorines...
          int ptFound = 0;
          for (IAtom chlorine : chlorines) {
              double delta = chlorine.getPoint2d().distance(platinum.getPoint2d()) - 1.5*SDG.getBondLength();
              if (Math.abs(delta) < 0.01)
                  ptFound++;
          }
          assertThat(ptFound, is(2));
  
          // K+ each have an oxygen
          for (IAtom potassium : potassiums) {
              int kFound = 0;
              for (IAtom oxygen : oxygens) {
                  double delta = oxygen.getPoint2d().distance(potassium.getPoint2d()) - 1.5*SDG.getBondLength();
                  if (Math.abs(delta) < 0.01)
                      kFound++;
              }
              assertThat(kFound, is(1));
          }
  
          // Al+3 each have 3 chlorines
          for (IAtom aluminium : aluminiums) {
              int clFound = 0;
              for (IAtom chlorine : chlorines) {
                  double delta = chlorine.getPoint2d().distance(aluminium.getPoint2d()) - 1.5*SDG.getBondLength();
                  if (Math.abs(delta) < 0.01)
                      clFound++;
              }
              assertThat(clFound, is(3));
          }
      }
test_case.class_method_signature: StructureDiagramGeneratorTest.multipleSalts()
test_case.full_signature: @Test public void multipleSalts()
test_case.identifier: multipleSalts
test_case.invocations: getInstance parseSmiles layout atoms assertNotNull getPoint2d atoms equals getSymbol add equals getSymbol add equals getSymbol add equals getSymbol add equals getSymbol assertNotNull assertThat size is assertThat size is assertThat size is distance getPoint2d getPoint2d getBondLength abs assertThat is distance getPoint2d getPoint2d getBondLength abs assertThat is distance getPoint2d getPoint2d getBondLength abs assertThat is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void multipleSalts()
focal_class.declarator: DEFAULT_BOND_LENGTH           = 1.5
focal_class.modifier: static final
focal_class.original_string: static final double DEFAULT_BOND_LENGTH           = 1.5;
focal_class.type: double
focal_class.var_name: DEFAULT_BOND_LENGTH
focal_class.declarator: SGROUP_BRACKET_PADDING_FACTOR = 0.5
focal_class.modifier: static final
focal_class.original_string: static final double SGROUP_BRACKET_PADDING_FACTOR = 0.5;
focal_class.type: double
focal_class.var_name: SGROUP_BRACKET_PADDING_FACTOR
focal_class.declarator: DEFAULT_BOND_VECTOR      = new Vector2d(0, 1)
focal_class.modifier: private static final
focal_class.original_string: private static final Vector2d                   DEFAULT_BOND_VECTOR      = new Vector2d(0, 1);
focal_class.type: Vector2d
focal_class.var_name: DEFAULT_BOND_VECTOR
focal_class.declarator: DEFAULT_TEMPLATE_LIBRARY = IdentityTemplateLibrary.loadFromResource("custom-templates.smi")
                                                                                                     .add(IdentityTemplateLibrary.loadFromResource("chebi-ring-templates.smi"))
focal_class.modifier: private static final
focal_class.original_string: private static final IdentityTemplateLibrary    DEFAULT_TEMPLATE_LIBRARY = IdentityTemplateLibrary.loadFromResource("custom-templates.smi")
                                                                                                     .add(IdentityTemplateLibrary.loadFromResource("chebi-ring-templates.smi"));
focal_class.type: IdentityTemplateLibrary
focal_class.var_name: DEFAULT_TEMPLATE_LIBRARY
focal_class.declarator: RAD_30                   = Math.toRadians(-30)
focal_class.modifier: private static final
focal_class.original_string: private static final double                     RAD_30                   = Math.toRadians(-30);
focal_class.type: double
focal_class.var_name: RAD_30
focal_class.declarator: logger                   = LoggingToolFactory.createLoggingTool(StructureDiagramGenerator.class)
focal_class.modifier: private static final
focal_class.original_string: private static final ILoggingTool               logger                   = LoggingToolFactory.createLoggingTool(StructureDiagramGenerator.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: LARGEST_FIRST_COMPARATOR = new Comparator<IAtomContainer>() {
          @Override
          public int compare(IAtomContainer o1, IAtomContainer o2) {
              return Integer.compare(o2.getBondCount(), o1.getBondCount());
          }
      }
focal_class.modifier: public static final
focal_class.original_string: public static final Comparator<IAtomContainer> LARGEST_FIRST_COMPARATOR = new Comparator<IAtomContainer>() {
          @Override
          public int compare(IAtomContainer o1, IAtomContainer o2) {
              return Integer.compare(o2.getBondCount(), o1.getBondCount());
          }
      };
focal_class.type: Comparator<IAtomContainer>
focal_class.var_name: LARGEST_FIRST_COMPARATOR
focal_class.declarator: molecule
focal_class.modifier: private
focal_class.original_string: private IAtomContainer molecule;
focal_class.type: IAtomContainer
focal_class.var_name: molecule
focal_class.declarator: sssr
focal_class.modifier: private
focal_class.original_string: private IRingSet       sssr;
focal_class.type: IRingSet
focal_class.var_name: sssr
focal_class.declarator: bondLength = DEFAULT_BOND_LENGTH
focal_class.modifier: private final
focal_class.original_string: private final double bondLength = DEFAULT_BOND_LENGTH;
focal_class.type: double
focal_class.var_name: bondLength
focal_class.declarator: firstBondVector
focal_class.modifier: private
focal_class.original_string: private Vector2d firstBondVector;
focal_class.type: Vector2d
focal_class.var_name: firstBondVector
focal_class.declarator: ringPlacer          = new RingPlacer()
focal_class.modifier: private
focal_class.original_string: private RingPlacer       ringPlacer          = new RingPlacer();
focal_class.type: RingPlacer
focal_class.var_name: ringPlacer
focal_class.declarator: atomPlacer          = new AtomPlacer()
focal_class.modifier: private
focal_class.original_string: private AtomPlacer       atomPlacer          = new AtomPlacer();
focal_class.type: AtomPlacer
focal_class.var_name: atomPlacer
focal_class.declarator: macroPlacer         = null
focal_class.modifier: private
focal_class.original_string: private MacroCycleLayout macroPlacer         = null;
focal_class.type: MacroCycleLayout
focal_class.var_name: macroPlacer
focal_class.declarator: ringSystems         = null
focal_class.modifier: private
focal_class.original_string: private List<IRingSet>   ringSystems         = null;
focal_class.type: List<IRingSet>
focal_class.var_name: ringSystems
focal_class.declarator: afix                = null
focal_class.modifier: private
focal_class.original_string: private Set<IAtom>       afix                = null;
focal_class.type: Set<IAtom>
focal_class.var_name: afix
focal_class.declarator: bfix                = null
focal_class.modifier: private
focal_class.original_string: private Set<IBond>       bfix                = null;
focal_class.type: Set<IBond>
focal_class.var_name: bfix
focal_class.declarator: useIdentTemplates   = true
focal_class.modifier: private
focal_class.original_string: private boolean          useIdentTemplates   = true;
focal_class.type: boolean
focal_class.var_name: useIdentTemplates
focal_class.declarator: alignMappedReaction = true
focal_class.modifier: private
focal_class.original_string: private boolean          alignMappedReaction = true;
focal_class.type: boolean
focal_class.var_name: alignMappedReaction
focal_class.declarator: selectOrientation = true
focal_class.modifier: private
focal_class.original_string: private boolean selectOrientation = true;
focal_class.type: boolean
focal_class.var_name: selectOrientation
focal_class.declarator: identityLibrary
focal_class.modifier: private
focal_class.original_string: private IdentityTemplateLibrary identityLibrary;
focal_class.type: IdentityTemplateLibrary
focal_class.var_name: identityLibrary
focal_class.declarator: FRAGMENT_CHARGE = "FragmentCharge"
focal_class.modifier: private static final
focal_class.original_string: private static final String FRAGMENT_CHARGE = "FragmentCharge";
focal_class.type: String
focal_class.var_name: FRAGMENT_CHARGE
focal_class.file: tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
focal_class.identifier: StructureDiagramGenerator
focal_class.class_method_signature: StructureDiagramGenerator.StructureDiagramGenerator()
focal_class.full_signature: public  StructureDiagramGenerator()
focal_class.identifier: StructureDiagramGenerator
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  StructureDiagramGenerator()
focal_class.class_method_signature: StructureDiagramGenerator.StructureDiagramGenerator(IdentityTemplateLibrary identityLibrary)
focal_class.full_signature: private  StructureDiagramGenerator(IdentityTemplateLibrary identityLibrary)
focal_class.identifier: StructureDiagramGenerator
focal_class.modifiers: private
focal_class.parameters: (IdentityTemplateLibrary identityLibrary)
focal_class.signature:  StructureDiagramGenerator(IdentityTemplateLibrary identityLibrary)
focal_class.class_method_signature: StructureDiagramGenerator.StructureDiagramGenerator(IAtomContainer molecule)
focal_class.full_signature: public  StructureDiagramGenerator(IAtomContainer molecule)
focal_class.identifier: StructureDiagramGenerator
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.signature:  StructureDiagramGenerator(IAtomContainer molecule)
focal_class.class_method_signature: StructureDiagramGenerator.generateCoordinates(IAtomContainer mol)
focal_class.full_signature: public final void generateCoordinates(IAtomContainer mol)
focal_class.identifier: generateCoordinates
focal_class.modifiers: public final
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void generateCoordinates(IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.generateCoordinates(final IReaction reaction)
focal_class.full_signature: public final void generateCoordinates(final IReaction reaction)
focal_class.identifier: generateCoordinates
focal_class.modifiers: public final
focal_class.parameters: (final IReaction reaction)
focal_class.return: void
focal_class.signature: void generateCoordinates(final IReaction reaction)
focal_class.class_method_signature: StructureDiagramGenerator.select(Collection<Map<Integer, IAtom>> refs)
focal_class.full_signature: private Map<Integer, IAtom> select(Collection<Map<Integer, IAtom>> refs)
focal_class.identifier: select
focal_class.modifiers: private
focal_class.parameters: (Collection<Map<Integer, IAtom>> refs)
focal_class.return: Map<Integer, IAtom>
focal_class.signature: Map<Integer, IAtom> select(Collection<Map<Integer, IAtom>> refs)
focal_class.class_method_signature: StructureDiagramGenerator.setMolecule(IAtomContainer mol, boolean clone)
focal_class.full_signature: public void setMolecule(IAtomContainer mol, boolean clone)
focal_class.identifier: setMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer mol, boolean clone)
focal_class.return: void
focal_class.signature: void setMolecule(IAtomContainer mol, boolean clone)
focal_class.class_method_signature: StructureDiagramGenerator.setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix)
focal_class.full_signature: public void setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix)
focal_class.identifier: setMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix)
focal_class.return: void
focal_class.signature: void setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix)
focal_class.class_method_signature: StructureDiagramGenerator.setUseTemplates(boolean useTemplates)
focal_class.full_signature: @Deprecated public void setUseTemplates(boolean useTemplates)
focal_class.identifier: setUseTemplates
focal_class.modifiers: @Deprecated public
focal_class.parameters: (boolean useTemplates)
focal_class.return: void
focal_class.signature: void setUseTemplates(boolean useTemplates)
focal_class.class_method_signature: StructureDiagramGenerator.setUseIdentityTemplates(boolean use)
focal_class.full_signature: public void setUseIdentityTemplates(boolean use)
focal_class.identifier: setUseIdentityTemplates
focal_class.modifiers: public
focal_class.parameters: (boolean use)
focal_class.return: void
focal_class.signature: void setUseIdentityTemplates(boolean use)
focal_class.class_method_signature: StructureDiagramGenerator.getUseTemplates()
focal_class.full_signature: @Deprecated public boolean getUseTemplates()
focal_class.identifier: getUseTemplates
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean getUseTemplates()
focal_class.class_method_signature: StructureDiagramGenerator.setTemplateHandler(TemplateHandler templateHandler)
focal_class.full_signature: @Deprecated public void setTemplateHandler(TemplateHandler templateHandler)
focal_class.identifier: setTemplateHandler
focal_class.modifiers: @Deprecated public
focal_class.parameters: (TemplateHandler templateHandler)
focal_class.return: void
focal_class.signature: void setTemplateHandler(TemplateHandler templateHandler)
focal_class.class_method_signature: StructureDiagramGenerator.getTemplateHandler()
focal_class.full_signature: @Deprecated public TemplateHandler getTemplateHandler()
focal_class.identifier: getTemplateHandler
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: TemplateHandler
focal_class.signature: TemplateHandler getTemplateHandler()
focal_class.class_method_signature: StructureDiagramGenerator.setMolecule(IAtomContainer molecule)
focal_class.full_signature: public void setMolecule(IAtomContainer molecule)
focal_class.identifier: setMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: void
focal_class.signature: void setMolecule(IAtomContainer molecule)
focal_class.class_method_signature: StructureDiagramGenerator.setAlignMappedReaction(boolean align)
focal_class.full_signature: public void setAlignMappedReaction(boolean align)
focal_class.identifier: setAlignMappedReaction
focal_class.modifiers: public
focal_class.parameters: (boolean align)
focal_class.return: void
focal_class.signature: void setAlignMappedReaction(boolean align)
focal_class.class_method_signature: StructureDiagramGenerator.getMolecule()
focal_class.full_signature: public IAtomContainer getMolecule()
focal_class.identifier: getMolecule
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getMolecule()
focal_class.class_method_signature: StructureDiagramGenerator.generateExperimentalCoordinates()
focal_class.full_signature: @Deprecated public void generateExperimentalCoordinates()
focal_class.identifier: generateExperimentalCoordinates
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void generateExperimentalCoordinates()
focal_class.class_method_signature: StructureDiagramGenerator.generateExperimentalCoordinates(Vector2d firstBondVector)
focal_class.full_signature: @Deprecated public void generateExperimentalCoordinates(Vector2d firstBondVector)
focal_class.identifier: generateExperimentalCoordinates
focal_class.modifiers: @Deprecated public
focal_class.parameters: (Vector2d firstBondVector)
focal_class.return: void
focal_class.signature: void generateExperimentalCoordinates(Vector2d firstBondVector)
focal_class.class_method_signature: StructureDiagramGenerator.generateCoordinates(Vector2d firstBondVector)
focal_class.full_signature: public void generateCoordinates(Vector2d firstBondVector)
focal_class.identifier: generateCoordinates
focal_class.modifiers: public
focal_class.parameters: (Vector2d firstBondVector)
focal_class.return: void
focal_class.signature: void generateCoordinates(Vector2d firstBondVector)
focal_class.class_method_signature: StructureDiagramGenerator.generateCoordinates(Vector2d firstBondVector, boolean isConnected, boolean isSubLayout)
focal_class.full_signature: private void generateCoordinates(Vector2d firstBondVector, boolean isConnected, boolean isSubLayout)
focal_class.identifier: generateCoordinates
focal_class.modifiers: private
focal_class.parameters: (Vector2d firstBondVector, boolean isConnected, boolean isSubLayout)
focal_class.return: void
focal_class.signature: void generateCoordinates(Vector2d firstBondVector, boolean isConnected, boolean isSubLayout)
focal_class.class_method_signature: StructureDiagramGenerator.hasFixedPart(final IAtomContainer mol)
focal_class.full_signature: private boolean hasFixedPart(final IAtomContainer mol)
focal_class.identifier: hasFixedPart
focal_class.modifiers: private
focal_class.parameters: (final IAtomContainer mol)
focal_class.return: boolean
focal_class.signature: boolean hasFixedPart(final IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.seedLayout()
focal_class.full_signature: private void seedLayout()
focal_class.identifier: seedLayout
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void seedLayout()
focal_class.class_method_signature: StructureDiagramGenerator.prepareRingSystems()
focal_class.full_signature: private int prepareRingSystems()
focal_class.identifier: prepareRingSystems
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int prepareRingSystems()
focal_class.class_method_signature: StructureDiagramGenerator.assignStereochem(IAtomContainer molecule)
focal_class.full_signature: private void assignStereochem(IAtomContainer molecule)
focal_class.identifier: assignStereochem
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: void
focal_class.signature: void assignStereochem(IAtomContainer molecule)
focal_class.class_method_signature: StructureDiagramGenerator.refinePlacement(IAtomContainer molecule)
focal_class.full_signature: private void refinePlacement(IAtomContainer molecule)
focal_class.identifier: refinePlacement
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: void
focal_class.signature: void refinePlacement(IAtomContainer molecule)
focal_class.class_method_signature: StructureDiagramGenerator.finalizeLayout(IAtomContainer mol)
focal_class.full_signature: private void finalizeLayout(IAtomContainer mol)
focal_class.identifier: finalizeLayout
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void finalizeLayout(IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.calcDirectionHistogram(IAtomContainer mol,
                                                 int[] counts,
                                                 int lim)
focal_class.full_signature: private static void calcDirectionHistogram(IAtomContainer mol,
                                                 int[] counts,
                                                 int lim)
focal_class.identifier: calcDirectionHistogram
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer mol,
                                                 int[] counts,
                                                 int lim)
focal_class.return: void
focal_class.signature: void calcDirectionHistogram(IAtomContainer mol,
                                                 int[] counts,
                                                 int lim)
focal_class.class_method_signature: StructureDiagramGenerator.selectOrientation(IAtomContainer mol, double widthDiff, int alignDiff)
focal_class.full_signature: private void selectOrientation(IAtomContainer mol, double widthDiff, int alignDiff)
focal_class.identifier: selectOrientation
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, double widthDiff, int alignDiff)
focal_class.return: void
focal_class.signature: void selectOrientation(IAtomContainer mol, double widthDiff, int alignDiff)
focal_class.class_method_signature: StructureDiagramGenerator.adjustForHydrogen(IAtom atom, IAtomContainer mol)
focal_class.full_signature: private final double adjustForHydrogen(IAtom atom, IAtomContainer mol)
focal_class.identifier: adjustForHydrogen
focal_class.modifiers: private final
focal_class.parameters: (IAtom atom, IAtomContainer mol)
focal_class.return: double
focal_class.signature: double adjustForHydrogen(IAtom atom, IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.getAprxBounds(IAtomContainer mol)
focal_class.full_signature: private final double[] getAprxBounds(IAtomContainer mol)
focal_class.identifier: getAprxBounds
focal_class.modifiers: private final
focal_class.parameters: (IAtomContainer mol)
focal_class.return: double[]
focal_class.signature: double[] getAprxBounds(IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer> frags)
focal_class.full_signature: private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer> frags)
focal_class.identifier: generateFragmentCoordinates
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, List<IAtomContainer> frags)
focal_class.return: void
focal_class.signature: void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer> frags)
focal_class.class_method_signature: StructureDiagramGenerator.lengthenIonicBonds(List<IBond> ionicBonds, IAtomContainer fragment)
focal_class.full_signature: private void lengthenIonicBonds(List<IBond> ionicBonds, IAtomContainer fragment)
focal_class.identifier: lengthenIonicBonds
focal_class.modifiers: private
focal_class.parameters: (List<IBond> ionicBonds, IAtomContainer fragment)
focal_class.return: void
focal_class.signature: void lengthenIonicBonds(List<IBond> ionicBonds, IAtomContainer fragment)
focal_class.class_method_signature: StructureDiagramGenerator.mergeAtomicIons(final List<IAtomContainer> frags)
focal_class.full_signature: private List<IAtomContainer> mergeAtomicIons(final List<IAtomContainer> frags)
focal_class.identifier: mergeAtomicIons
focal_class.modifiers: private
focal_class.parameters: (final List<IAtomContainer> frags)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> mergeAtomicIons(final List<IAtomContainer> frags)
focal_class.class_method_signature: StructureDiagramGenerator.selectIons(IAtomContainer frag, int sign)
focal_class.full_signature: private List<IAtom> selectIons(IAtomContainer frag, int sign)
focal_class.identifier: selectIons
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer frag, int sign)
focal_class.return: List<IAtom>
focal_class.signature: List<IAtom> selectIons(IAtomContainer frag, int sign)
focal_class.class_method_signature: StructureDiagramGenerator.makeIonicBonds(final List<IAtomContainer> frags)
focal_class.full_signature: private List<IBond> makeIonicBonds(final List<IAtomContainer> frags)
focal_class.identifier: makeIonicBonds
focal_class.modifiers: private
focal_class.parameters: (final List<IAtomContainer> frags)
focal_class.return: List<IBond>
focal_class.signature: List<IBond> makeIonicBonds(final List<IAtomContainer> frags)
focal_class.class_method_signature: StructureDiagramGenerator.nullAsZero(Integer x)
focal_class.full_signature: private static int nullAsZero(Integer x)
focal_class.identifier: nullAsZero
focal_class.modifiers: private static
focal_class.parameters: (Integer x)
focal_class.return: int
focal_class.signature: int nullAsZero(Integer x)
focal_class.class_method_signature: StructureDiagramGenerator.toList(IAtomContainerSet frags)
focal_class.full_signature: private List<IAtomContainer> toList(IAtomContainerSet frags)
focal_class.identifier: toList
focal_class.modifiers: private
focal_class.parameters: (IAtomContainerSet frags)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> toList(IAtomContainerSet frags)
focal_class.class_method_signature: StructureDiagramGenerator.generateCoordinates()
focal_class.full_signature: public void generateCoordinates()
focal_class.identifier: generateCoordinates
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void generateCoordinates()
focal_class.class_method_signature: StructureDiagramGenerator.lookupRingSystem(IRingSet rs, IAtomContainer molecule, boolean anon)
focal_class.full_signature: private boolean lookupRingSystem(IRingSet rs, IAtomContainer molecule, boolean anon)
focal_class.identifier: lookupRingSystem
focal_class.modifiers: private
focal_class.parameters: (IRingSet rs, IAtomContainer molecule, boolean anon)
focal_class.return: boolean
focal_class.signature: boolean lookupRingSystem(IRingSet rs, IAtomContainer molecule, boolean anon)
focal_class.class_method_signature: StructureDiagramGenerator.isHydrogen(IAtom atom)
focal_class.full_signature: private static boolean isHydrogen(IAtom atom)
focal_class.identifier: isHydrogen
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isHydrogen(IAtom atom)
focal_class.class_method_signature: StructureDiagramGenerator.clearHydrogenCounts(IAtomContainer container)
focal_class.full_signature: private static IAtomContainer clearHydrogenCounts(IAtomContainer container)
focal_class.identifier: clearHydrogenCounts
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer clearHydrogenCounts(IAtomContainer container)
focal_class.class_method_signature: StructureDiagramGenerator.layoutRingSet(Vector2d firstBondVector, IRingSet rs)
focal_class.full_signature: private int layoutRingSet(Vector2d firstBondVector, IRingSet rs)
focal_class.identifier: layoutRingSet
focal_class.modifiers: private
focal_class.parameters: (Vector2d firstBondVector, IRingSet rs)
focal_class.return: int
focal_class.signature: int layoutRingSet(Vector2d firstBondVector, IRingSet rs)
focal_class.class_method_signature: StructureDiagramGenerator.getRingSetCore(IRingSet rs)
focal_class.full_signature: private IRingSet getRingSetCore(IRingSet rs)
focal_class.identifier: getRingSetCore
focal_class.modifiers: private
focal_class.parameters: (IRingSet rs)
focal_class.return: IRingSet
focal_class.signature: IRingSet getRingSetCore(IRingSet rs)
focal_class.class_method_signature: StructureDiagramGenerator.isMacroCycle(IRing ring, IRingSet rs)
focal_class.full_signature: private boolean isMacroCycle(IRing ring, IRingSet rs)
focal_class.identifier: isMacroCycle
focal_class.modifiers: private
focal_class.parameters: (IRing ring, IRingSet rs)
focal_class.return: boolean
focal_class.signature: boolean isMacroCycle(IRing ring, IRingSet rs)
focal_class.class_method_signature: StructureDiagramGenerator.layoutAcyclicParts()
focal_class.full_signature: private void layoutAcyclicParts()
focal_class.identifier: layoutAcyclicParts
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void layoutAcyclicParts()
focal_class.class_method_signature: StructureDiagramGenerator.layoutCyclicParts()
focal_class.full_signature: private void layoutCyclicParts()
focal_class.identifier: layoutCyclicParts
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void layoutCyclicParts()
focal_class.class_method_signature: StructureDiagramGenerator.getUnplacedAtoms(IAtom atom)
focal_class.full_signature: private IAtomContainer getUnplacedAtoms(IAtom atom)
focal_class.identifier: getUnplacedAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getUnplacedAtoms(IAtom atom)
focal_class.class_method_signature: StructureDiagramGenerator.getPlacedAtoms(IAtom atom)
focal_class.full_signature: private IAtomContainer getPlacedAtoms(IAtom atom)
focal_class.identifier: getPlacedAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getPlacedAtoms(IAtom atom)
focal_class.class_method_signature: StructureDiagramGenerator.getNextAtomWithAliphaticUnplacedNeigbors()
focal_class.full_signature: private IAtom getNextAtomWithAliphaticUnplacedNeigbors()
focal_class.identifier: getNextAtomWithAliphaticUnplacedNeigbors
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: IAtom
focal_class.signature: IAtom getNextAtomWithAliphaticUnplacedNeigbors()
focal_class.class_method_signature: StructureDiagramGenerator.getNextBondWithUnplacedRingAtom()
focal_class.full_signature: private IBond getNextBondWithUnplacedRingAtom()
focal_class.identifier: getNextBondWithUnplacedRingAtom
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: IBond
focal_class.signature: IBond getNextBondWithUnplacedRingAtom()
focal_class.class_method_signature: StructureDiagramGenerator.placeFirstBond(IBond bond, Vector2d bondVector)
focal_class.full_signature: private IAtomContainer placeFirstBond(IBond bond, Vector2d bondVector)
focal_class.identifier: placeFirstBond
focal_class.modifiers: private
focal_class.parameters: (IBond bond, Vector2d bondVector)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer placeFirstBond(IBond bond, Vector2d bondVector)
focal_class.class_method_signature: StructureDiagramGenerator.allPlaced(IRingSet rings)
focal_class.full_signature: private boolean allPlaced(IRingSet rings)
focal_class.identifier: allPlaced
focal_class.modifiers: private
focal_class.parameters: (IRingSet rings)
focal_class.return: boolean
focal_class.signature: boolean allPlaced(IRingSet rings)
focal_class.class_method_signature: StructureDiagramGenerator.getRingAtom(IBond bond)
focal_class.full_signature: private IAtom getRingAtom(IBond bond)
focal_class.identifier: getRingAtom
focal_class.modifiers: private
focal_class.parameters: (IBond bond)
focal_class.return: IAtom
focal_class.signature: IAtom getRingAtom(IBond bond)
focal_class.class_method_signature: StructureDiagramGenerator.getRingSystemOfAtom(List ringSystems, IAtom ringAtom)
focal_class.full_signature: private IRingSet getRingSystemOfAtom(List ringSystems, IAtom ringAtom)
focal_class.identifier: getRingSystemOfAtom
focal_class.modifiers: private
focal_class.parameters: (List ringSystems, IAtom ringAtom)
focal_class.return: IRingSet
focal_class.signature: IRingSet getRingSystemOfAtom(List ringSystems, IAtom ringAtom)
focal_class.class_method_signature: StructureDiagramGenerator.resetUnplacedRings()
focal_class.full_signature: private void resetUnplacedRings()
focal_class.identifier: resetUnplacedRings
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void resetUnplacedRings()
focal_class.class_method_signature: StructureDiagramGenerator.setBondLength(double bondLength)
focal_class.full_signature: @Deprecated public void setBondLength(double bondLength)
focal_class.identifier: setBondLength
focal_class.modifiers: @Deprecated public
focal_class.parameters: (double bondLength)
focal_class.return: void
focal_class.signature: void setBondLength(double bondLength)
focal_class.class_method_signature: StructureDiagramGenerator.getBondLength()
focal_class.full_signature: public double getBondLength()
focal_class.identifier: getBondLength
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getBondLength()
focal_class.class_method_signature: StructureDiagramGenerator.getOtherBondAtom(IAtom atom, IBond bond)
focal_class.full_signature: public IAtom getOtherBondAtom(IAtom atom, IBond bond)
focal_class.identifier: getOtherBondAtom
focal_class.modifiers: public
focal_class.parameters: (IAtom atom, IBond bond)
focal_class.return: IAtom
focal_class.signature: IAtom getOtherBondAtom(IAtom atom, IBond bond)
focal_class.class_method_signature: StructureDiagramGenerator.placeMultipleGroups(IAtomContainer mol)
focal_class.full_signature: private void placeMultipleGroups(IAtomContainer mol)
focal_class.identifier: placeMultipleGroups
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void placeMultipleGroups(IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.safeUnbox(Integer x)
focal_class.full_signature: private int safeUnbox(Integer x)
focal_class.identifier: safeUnbox
focal_class.modifiers: private
focal_class.parameters: (Integer x)
focal_class.return: int
focal_class.signature: int safeUnbox(Integer x)
focal_class.class_method_signature: StructureDiagramGenerator.getPositionalRingBondPref(IBond bond, IAtomContainer mol)
focal_class.full_signature: private int getPositionalRingBondPref(IBond bond, IAtomContainer mol)
focal_class.identifier: getPositionalRingBondPref
focal_class.modifiers: private
focal_class.parameters: (IBond bond, IAtomContainer mol)
focal_class.return: int
focal_class.signature: int getPositionalRingBondPref(IBond bond, IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.placePositionalVariation(final IAtomContainer mol)
focal_class.full_signature: private void placePositionalVariation(final IAtomContainer mol)
focal_class.identifier: placePositionalVariation
focal_class.modifiers: private
focal_class.parameters: (final IAtomContainer mol)
focal_class.return: void
focal_class.signature: void placePositionalVariation(final IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.visit(Set<Integer> visited, int[][] g, int v)
focal_class.full_signature: private static void visit(Set<Integer> visited, int[][] g, int v)
focal_class.identifier: visit
focal_class.modifiers: private static
focal_class.parameters: (Set<Integer> visited, int[][] g, int v)
focal_class.return: void
focal_class.signature: void visit(Set<Integer> visited, int[][] g, int v)
focal_class.class_method_signature: StructureDiagramGenerator.aggregateMulticenterSgroups(List<Sgroup> sgroups)
focal_class.full_signature: private static Multimap<Set<IAtom>, IAtom> aggregateMulticenterSgroups(List<Sgroup> sgroups)
focal_class.identifier: aggregateMulticenterSgroups
focal_class.modifiers: private static
focal_class.parameters: (List<Sgroup> sgroups)
focal_class.return: Multimap<Set<IAtom>, IAtom>
focal_class.signature: Multimap<Set<IAtom>, IAtom> aggregateMulticenterSgroups(List<Sgroup> sgroups)
focal_class.class_method_signature: StructureDiagramGenerator.numRingBonds(IAtomContainer mol, IAtom atom)
focal_class.full_signature: private static int numRingBonds(IAtomContainer mol, IAtom atom)
focal_class.identifier: numRingBonds
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer mol, IAtom atom)
focal_class.return: int
focal_class.signature: int numRingBonds(IAtomContainer mol, IAtom atom)
focal_class.class_method_signature: StructureDiagramGenerator.updateMinMax(double[] minmax, Point2d p)
focal_class.full_signature: private void updateMinMax(double[] minmax, Point2d p)
focal_class.identifier: updateMinMax
focal_class.modifiers: private
focal_class.parameters: (double[] minmax, Point2d p)
focal_class.return: void
focal_class.signature: void updateMinMax(double[] minmax, Point2d p)
focal_class.class_method_signature: StructureDiagramGenerator.placeSgroupBrackets(IAtomContainer mol)
focal_class.full_signature: private void placeSgroupBrackets(IAtomContainer mol)
focal_class.identifier: placeSgroupBrackets
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void placeSgroupBrackets(IAtomContainer mol)
focal_class.class_method_signature: StructureDiagramGenerator.angle(IBond bond)
focal_class.full_signature: private static double angle(IBond bond)
focal_class.identifier: angle
focal_class.modifiers: private static
focal_class.parameters: (IBond bond)
focal_class.return: double
focal_class.signature: double angle(IBond bond)
focal_class.class_method_signature: StructureDiagramGenerator.newCrossingBracket(IBond bond, Multimap<IBond,Sgroup> bonds, Map<IBond,Integer> counter, boolean vert)
focal_class.full_signature: private SgroupBracket newCrossingBracket(IBond bond, Multimap<IBond,Sgroup> bonds, Map<IBond,Integer> counter, boolean vert)
focal_class.identifier: newCrossingBracket
focal_class.modifiers: private
focal_class.parameters: (IBond bond, Multimap<IBond,Sgroup> bonds, Map<IBond,Integer> counter, boolean vert)
focal_class.return: SgroupBracket
focal_class.signature: SgroupBracket newCrossingBracket(IBond bond, Multimap<IBond,Sgroup> bonds, Map<IBond,Integer> counter, boolean vert)
focal_class.class_method_signature: StructureDiagramGenerator.hasBrackets(Sgroup sgroup)
focal_class.full_signature: private static boolean hasBrackets(Sgroup sgroup)
focal_class.identifier: hasBrackets
focal_class.modifiers: private static
focal_class.parameters: (Sgroup sgroup)
focal_class.return: boolean
focal_class.signature: boolean hasBrackets(Sgroup sgroup)
focal_method.body: public double getBondLength() {
          return bondLength;
      }
focal_method.class_method_signature: StructureDiagramGenerator.getBondLength()
focal_method.full_signature: public double getBondLength()
focal_method.identifier: getBondLength
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: double
focal_method.signature: double getBondLength()