Modifier and Type | Interface and Description |
---|---|
interface |
Centre<A>
Defines a stereo centre (normally on an atom or bond) that provides access and mutation of the centres descriptor.
|
Modifier and Type | Method and Description |
---|---|
Ligand<A> |
Digraph.getRoot()
Access the root ligand of this digraph.
|
Modifier and Type | Method and Description |
---|---|
<A> java.util.List<java.util.List<Ligand<A>>> |
Priority.createBins(java.util.List<Ligand<A>> ligands) |
java.util.List<java.util.List<Ligand<A>>> |
LigandSorter.getGroups(java.util.List<Ligand<A>> sorted) |
java.util.List<Ligand<A>> |
Ligand.getLigands()
Access the child ligands.
|
java.util.List<Ligand<A>> |
ConnectionProvider.getLigands(A atom) |
java.util.List<Ligand<A>> |
Digraph.getLigands(A atom)
Access all created ligands for the provided atom.
|
java.util.List<Ligand<A>> |
ConnectionProvider.getLigands(Ligand<A> ligand) |
java.util.List<Ligand<A>> |
Digraph.getProximal()
Access the proximal ligands next to the root.
|
Modifier and Type | Method and Description |
---|---|
Comparison |
PriorityRule.compareLigands(Ligand<A> o1,
Ligand<A> o2)
Analogous to
Comparator.compare(Object, Object) the prioritise method combines the Descriptor.Type to the
order and can indicate what comparison method was used. |
Comparison |
PriorityRule.compareLigands(Ligand<A> o1,
Ligand<A> o2)
Analogous to
Comparator.compare(Object, Object) the prioritise method combines the Descriptor.Type to the
order and can indicate what comparison method was used. |
java.util.List<Arc<A>> |
ConnectionProvider.getArcs(Ligand<A> ligand) |
java.util.List<Ligand<A>> |
ConnectionProvider.getLigands(Ligand<A> ligand) |
Arc<A> |
ConnectionProvider.getParentArc(Ligand<A> ligand) |
int |
Abstract2DSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
Abstract2DSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
Abstract2DSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
Abstract2DSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
SignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4)
When wedge and hatch bonds are involed
|
int |
SignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4)
When wedge and hatch bonds are involed
|
int |
SignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4)
When wedge and hatch bonds are involed
|
int |
SignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4)
When wedge and hatch bonds are involed
|
int |
PriorityRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
int |
PriorityRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
void |
ConnectionProvider.reroot(Ligand<A> ligand) |
void |
Digraph.reroot(Ligand<A> ligand)
Reroot the digraph on the provided ligand.
|
Modifier and Type | Method and Description |
---|---|
<A> java.util.List<java.util.List<Ligand<A>>> |
Priority.createBins(java.util.List<Ligand<A>> ligands) |
java.util.List<java.util.List<Ligand<A>>> |
LigandSorter.getGroups(java.util.List<Ligand<A>> sorted) |
Descriptor |
Centre.perceive(java.util.List<Ligand<A>> proximal,
PriorityRule<A> rule,
SignCalculator<A> calculator) |
Priority |
LigandSorter.prioritise(java.util.List<Ligand<A>> ligands)
Sorts the provided ligands and indicates if all the ligands are different (i.e.
|
Priority |
PriorityRule.prioritise(java.util.List<Ligand<A>> ligands)
Prioritises ligands using the provided sorter and indicates whether the ligands were unique.
|
Modifier and Type | Method and Description |
---|---|
int |
ThreeDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
ThreeDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
ThreeDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
ThreeDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
TwoDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
TwoDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
TwoDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
int |
TwoDimensionalSignCalculator.getSign(Ligand<A> a1,
Ligand<A> a2,
Ligand<A> a3,
Ligand<A> a4) |
Modifier and Type | Method and Description |
---|---|
Ligand<A> |
Arc.getHead() |
Ligand<A> |
AbstractDigraph.getRoot() |
Ligand<A> |
Arc.getTail() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Ligand<A>> |
AbstractDigraph.getLigands(A atom) |
java.util.List<Ligand<A>> |
AbstractDigraph.getLigands(Ligand<A> ligand) |
java.util.List<Ligand<A>> |
AbstractDigraph.getProximal() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Arc<A>> |
AbstractDigraph.getArcs(Ligand<A> ligand) |
java.util.List<Ligand<A>> |
AbstractDigraph.getLigands(Ligand<A> ligand) |
Arc<A> |
AbstractDigraph.getParentArc(Ligand<A> ligand) |
void |
AbstractDigraph.reroot(Ligand<A> ligand) |
Constructor and Description |
---|
AbstractDigraph(Ligand<A> root) |
AbstractDigraph(Ligand<A> root,
DescriptorManager<A> manager) |
Arc(Ligand<A> tail,
Ligand<A> head,
MutableDescriptor descriptor) |
Arc(Ligand<A> tail,
Ligand<A> head,
MutableDescriptor descriptor) |
Arc(Ligand<A> tail,
Ligand<A> head,
MutableDescriptor descriptor,
int depth) |
Arc(Ligand<A> tail,
Ligand<A> head,
MutableDescriptor descriptor,
int depth) |
ConnectionTableDigraph(Ligand<A> root,
DescriptorManager<A> manager,
ConnectionTable<A> table) |
Modifier and Type | Class and Description |
---|---|
class |
AbstractLigand<A> |
class |
NonterminalLigand<A> |
class |
PlanarCentre<A> |
class |
TerminalLigand<A> |
class |
TetrahedralCentre<A> |
Modifier and Type | Method and Description |
---|---|
java.util.List<Ligand<A>> |
AbstractLigand.getLigands() |
java.util.List<Ligand<A>> |
PlanarCentre.getLigands() |
java.util.List<Ligand<A>> |
TerminalLigand.getLigands() |
Modifier and Type | Method and Description |
---|---|
Descriptor |
PlanarCentre.perceive(java.util.List<Ligand<A>> proximal,
PriorityRule<A> rule,
SignCalculator<A> calculator) |
Descriptor |
TetrahedralCentre.perceive(java.util.List<Ligand<A>> proximal,
PriorityRule<A> rule,
SignCalculator<A> calculator) |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.util.List<Ligand<A>>> |
InsertionSorter.getGroups(java.util.List<Ligand<A>> sorted) |
Modifier and Type | Method and Description |
---|---|
int |
AtomicNumberRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the ligands by their atoms atomic numbers.
|
int |
AtomicNumberRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the ligands by their atoms atomic numbers.
|
int |
CombinedRule.compare(Ligand<A> o1,
Ligand<A> o2)
Iteratively compares ligands using the given priority rules.
|
int |
CombinedRule.compare(Ligand<A> o1,
Ligand<A> o2)
Iteratively compares ligands using the given priority rules.
|
int |
DuplicateAtomRule.compare(Ligand<A> o1,
Ligand<A> o2) |
int |
DuplicateAtomRule.compare(Ligand<A> o1,
Ligand<A> o2) |
int |
MassNumberRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the ligands by their atoms mass numbers.
|
int |
MassNumberRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the ligands by their atoms mass numbers.
|
Comparison |
AbstractPriorityRule.compareLigands(Ligand<A> o1,
Ligand<A> o2) |
Comparison |
AbstractPriorityRule.compareLigands(Ligand<A> o1,
Ligand<A> o2) |
Comparison |
CombinedRule.compareLigands(Ligand<A> o1,
Ligand<A> o2)
Iteratively compares ligands using the given priority rules.
|
Comparison |
CombinedRule.compareLigands(Ligand<A> o1,
Ligand<A> o2)
Iteratively compares ligands using the given priority rules.
|
Comparison |
InsertionSorter.compareLigands(Ligand<A> first,
Ligand<A> second) |
Comparison |
InsertionSorter.compareLigands(Ligand<A> first,
Ligand<A> second) |
int |
AbstractPriorityRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
int |
AbstractPriorityRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
Modifier and Type | Method and Description |
---|---|
int |
AbstractPriorityRule.compare(java.util.List<Ligand<A>> first,
java.util.List<Ligand<A>> second)
Compares two lists of ligands.
|
int |
AbstractPriorityRule.compare(java.util.List<Ligand<A>> first,
java.util.List<Ligand<A>> second)
Compares two lists of ligands.
|
java.util.List<java.util.List<Ligand<A>>> |
InsertionSorter.getGroups(java.util.List<Ligand<A>> sorted) |
Priority |
AbstractPriorityRule.prioritise(java.util.List<Ligand<A>> ligands)
Uses the injected ligand sorter to order the ligands.
|
Priority |
InsertionSorter.prioritise(java.util.List<Ligand<A>> ligands)
Sorts in descending order and indicates whether all elements are unique and the type of descriptor used.
|
Modifier and Type | Method and Description |
---|---|
Descriptor |
DescriptorAccessor.getDescriptor(Ligand<A> ligand)
Access the descriptor for the provided ligand.
|
Modifier and Type | Method and Description |
---|---|
Descriptor |
ArcPrimaryDescriptor.getDescriptor(Ligand<A> ligand) |
Descriptor |
AuxiliaryDescriptor.getDescriptor(Ligand<A> ligand) |
Descriptor |
PrimaryDescriptor.getDescriptor(Ligand<A> ligand) |
Modifier and Type | Method and Description |
---|---|
int |
DescriptorRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares ligands on the rank of their descriptors.
|
int |
DescriptorRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares ligands on the rank of their descriptors.
|
int |
PairRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the two ligands based on their generated descriptor pairs.
|
int |
PairRule.compare(Ligand<A> o1,
Ligand<A> o2)
Compares the two ligands based on their generated descriptor pairs.
|
protected java.util.NavigableSet<DescriptorList> |
PairRule.generate(Ligand<A> ligand)
Generates a set of descriptor lists that maintain the like/unlike pairing
whilst descriptors are added.
|
int |
PairRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
int |
PairRule.recursiveCompare(Ligand<A> o1,
Ligand<A> o2) |
Modifier and Type | Method and Description |
---|---|
protected java.util.NavigableSet<DescriptorList> |
PairRule.generate(java.util.Queue<Ligand<A>> queue)
Generates a set of descriptor lists that maintain the like/unlike pairing
whilst descriptors are added.
|