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 ionicBondsInSodiumBenzoate() throws Exception {
          SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("[Na+].[O-]C(=O)c1ccccc1");
          layout(mol);
          for (IAtom atom : mol.atoms())
              assertNotNull(atom.getPoint2d());
          assertThat(mol.getAtom(0).getPoint2d().distance(mol.getAtom(1).getPoint2d()),
                     closeTo(1.5*SDG.getBondLength(), 0.001));
      }
test_case.class_method_signature: StructureDiagramGeneratorTest.ionicBondsInSodiumBenzoate()
test_case.full_signature: @Test public void ionicBondsInSodiumBenzoate()
test_case.identifier: ionicBondsInSodiumBenzoate
test_case.invocations: getInstance parseSmiles layout atoms assertNotNull getPoint2d assertThat distance getPoint2d getAtom getPoint2d getAtom closeTo getBondLength
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void ionicBondsInSodiumBenzoate()
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()