Index (cdk-scaffold 2.8 API)

A B C D E G H I L M N O R S T U V
All Classes and Interfaces|All Packages|Constant Field Values

A

addChild(MoleculeType) - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Adds a child to the network node, i.e. links it to a node on the level below.
addChild(MoleculeType) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Adds a child to the ScaffoldNodeBase, i.e. links it to a ScaffoldNodeBase on the level below
addChild(MoleculeType) - Method in class org.openscience.cdk.tools.scaffold.TreeNode: Adds a child to the tree node, i.e. links it to a node on the level below.
addNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Add a node to the graph structure.
addNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Add ScaffoldNodeBase to the ScaffoldNodeCollectionBase.
addNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Add a node to the graph structure.
addNodeToCollections(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Adds the node to the internal node collections node map, reverse node map, smiles map, and level map.
addNonVirtualOriginSmiles(String) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Adds another string to the NonVirtualOriginSmilesList if it is not already present.
addOriginSmiles(String) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Adds another string to the OriginSmilesList if it is not already present.
addParent(NetworkNode<MoleculeType>) - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Add the parents node and add this node as child to the parent node if not already done.
applyEnumerativeRemoval(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Iteratively removes the terminal rings.
applySchuffenhauerRuleEight(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the eighth Schuffenhauer rule.
applySchuffenhauerRuleEleven(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the eleventh Schuffenhauer rule.
applySchuffenhauerRuleFourAndFive(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the fourth and fifth Schuffenhauer rule.
applySchuffenhauerRuleNine(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the ninth Schuffenhauer rule.
applySchuffenhauerRuleOne(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the first Schuffenhauer rule.
applySchuffenhauerRules(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Iteratively removes the rings of the molecule according to specific rules that are queried hierarchically and returns the scaffolds as list.
applySchuffenhauerRuleSeven(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the seventh Schuffenhauer rule.
applySchuffenhauerRuleSix(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the sixth Schuffenhauer rule.
applySchuffenhauerRuleTen(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the tenth Schuffenhauer rule.
applySchuffenhauerRuleThirteen(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Remove a ring according to the thirteenth Schuffenhauer rule.
applySchuffenhauerRuleThree(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the third Schuffenhauer rule.
applySchuffenhauerRuleTwelve(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the twelfth Schuffenhauer rule.
applySchuffenhauerRuleTwo(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sort out the rings according to the second Schuffenhauer rule.
areOnlyHybridisationsAtAromaticBondsRetained() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: With this setting, only the hybridisation of aromatic atoms can be obtained.
AROMATICITY_MODEL_SETTING_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for which aromaticity model should be used.

B

BASIC_FRAMEWORK - Enum constant in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: All side chains are removed and all atoms are converted into carbons.
BASIC_WIRE_FRAME - Enum constant in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: All side chains are removed, all bonds are converted into single bonds and all atoms are converted into carbons.

C

children - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Children of the Node
containsMolecule(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Checks with the SMILES string whether the molecule is already present in the Scaffold Collection.
containsNode(int) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Indicates whether there is a node with this number in the collection.
CYCLE_FINDER - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Cycle finder used to detect rings.
CYCLE_FINDER_BACKUP - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Backup cycle finder used to detect rings.
CYCLE_FINDER_BACKUP_PROPERTY - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Property is true if the backup cycle finder is to be used instead of the normal cycle finder.

D

DETERMINE_AROMATICITY_SETTING_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for whether the aromaticity should be determined.

E

ELEMENTAL_WIRE_FRAME - Enum constant in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: All side chains are removed and multiple bonds are converted to single bonds, but the atomic elements remain.

G

generateScaffoldNetwork(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Generates a network for each molecule in the list and merges the networks together.
generateScaffoldNetwork(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Iteratively removes the terminal rings.
generateSchuffenhauerForest(List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Decomposes the entered molecules into Scaffolds, creates ScaffoldTrees from them and then assembles these trees if possible.
generateSchuffenhauerTree(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Iteratively removes the rings of the molecule according to specific rules that are queried hierarchically.
getAllNodes() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Get all ScaffoldNodes of the Scaffold
getAllNodesOnLevel(int) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Return all ScaffoldNodes that are at a certain level in the ScaffoldCollection.
getAromaticityModel() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Returns the currently applied Aromaticity model.
getChildren() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the children nodes.
getCycleFinder(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Selects the correct CycleFinder based on ScaffoldGenerator.CYCLE_FINDER_BACKUP_PROPERTY.
getLevel() - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Outputs the level on which the node is located in the graph structure.
getLevel() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Outputs the level on which the node is located in the entire graph structure.
getLevel() - Method in class org.openscience.cdk.tools.scaffold.TreeNode: Outputs the level on which the node is located in the graph structure.
getLinkers(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Returns the linkers of the molecule as a fragment list.
getMatrix() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Outputs an adjacency matrix in which the parent node of each node is marked with 1.
getMatrix() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Outputs an adjacency matrix in which the parent node of each node is marked with a 1.
getMatrix() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Outputs an adjacency matrix in which the parent node of each node is marked with a 1.
getMatrixNode(int) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Returns the node that belongs to a certain row and column number of the matrix.
getMatrixNodes() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Returns the number of the nodes and the nodes of the matrix in ascending order.
getMatrixNodesNumbers() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Gives the number of nodes as they occur in the matrix.
getMaxLevel() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Outputs the maximum level of the collection
getMolecule() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the node molecule.
getMurckoFragment(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Returns the Murcko fragment of each molecule entered.
getNode(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Return the ScaffoldNode that belongs to a specific molecule.
getNonVirtualOriginCount() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the size of the nonVirtualSmilesList NonVirtualOrigin: This node is the direct(without further fragmentation) scaffold of this origin molecule.
getNonVirtualOriginSmilesList() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the nonVirtualOriginSmilesList NonVirtualOrigin: This node is the direct(without further fragmentation) scaffold of this origin molecule.
getOriginCount() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the size of the originSmilesList
getOriginSmilesList() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Get the originSmilesList
getParent() - Method in class org.openscience.cdk.tools.scaffold.TreeNode: Get the parent node.
getParents() - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Get the parents of the node.
getRings(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Extracts the individual rings from the scaffold of the given molecule.
getRingsInternal(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Generates a set of rings depending on the CycleFinder selected by ScaffoldGenerator.getCycleFinder(IAtomContainer).
getRoot() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Outputs root node of the tree.
getRoots() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Outputs root nodes of the network.
getScaffold(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Generates the selected fragment type for the entered molecule and returns it.
getScaffoldInternal(IAtomContainer, boolean, boolean, Aromaticity, ScaffoldGenerator.ScaffoldModeOption) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Generates the selected fragment type for the entered molecule and returns it.
getScaffoldModeSetting() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Returns the currently applied ScaffoldMode.
getSideChains(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Outputs all fragments that are not contained in the generated scaffold in contrast to the unchanged molecule.
getSmilesGenerator() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Returns the currently applied SmilesGenerator.

H

hasFusedAromaticRings(IAtomContainer, List<IAtomContainer>, IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Checks whether the ring of a molecule is in an aromatic fused ring system.
hasNonVirtualOriginSmiles() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Indicates whether the molecule has at least one nonVirtualOrigin.

I

isAromaticityDetermined() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Specifies whether the aromaticity is to be taken into account.
isAtomContainerAromatic(IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Checks the aromaticity of each atom of the input molecule.
isLeaf() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Indicates whether it has children
isOrphan() - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Shows if the node has parents.
isOrphan() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Shows if the node has parents
isOrphan() - Method in class org.openscience.cdk.tools.scaffold.TreeNode: Shows if the node has parents.
isRingAttachedToHeteroatomLinker(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: The ring to be examined is checked to determine whether it is attached to a linker that has a heteroatom at least one end.
isRingRemovable(IAtomContainer, List<IAtomContainer>, IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Checks whether rings may be removed.
isRingTerminal(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Checks whether the tmpRing in the tmpMolecule is terminal.
isRuleSevenApplied() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Indicates whether rule 7 of the Schuffenhauer scaffold tree fragmentation is executed.
isValid() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Tests whether the tree is valid, i.e. has only one root and all nodes are connected.

L

levelMap - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Saves all ScaffoldNodes according to their level.

M

mergeNetwork(ScaffoldNetwork) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Adds another ScaffoldNetwork to the existing one.
mergeTree(ScaffoldTree) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Adds another ScaffoldTree to the existing one if possible.
molecule - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Molecule that can be stored in each node
MURCKO_FRAMEWORK - Enum constant in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: Murcko frameworks are generated.

N

NetworkNode<MoleculeType> - Class in org.openscience.cdk.tools.scaffold: The NetworkNodes are nodes from which a ScaffoldNetwork can be built.
NetworkNode(MoleculeType) - Constructor for class org.openscience.cdk.tools.scaffold.NetworkNode: Creates a NetworkNode
NODE_MAPS_INIT_CAPACITY - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Initial capacity for hash maps storing nodes.
NODE_MAPS_LOAD_FACTOR - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Load factor for hash maps storing nodes.
nodeCounter - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Shows how many nodes have been added so far.
nodeMap - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Saves all ScaffoldNodes and numbers them in ascending order.
nonVirtualOriginSmilesList - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: List of SMILES of the molecules from which this fragment directly originates.

O

org.openscience.cdk.tools.scaffold - package org.openscience.cdk.tools.scaffold
originSmilesList - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: List of SMILES of the molecules from which this fragment originates.

R

removeNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Removes a node.
removeNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Removes a node.
removeNode(ScaffoldNodeBase) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldTree: Removes a node.
removeRing(IAtomContainer, boolean, IAtomContainer) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Removes the given ring from the total molecule and returns it.
removeRingForSchuffenhauerRule(IAtomContainer, List<IAtomContainer>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Removes the selected ring from the last fragment in the list and adds the resulting fragment to this list.
restoreDefaultSettings() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: All settings are set to their default values.
RETAIN_ONLY_HYBRIDISATIONS_AT_AROMATIC_BONDS_SETTING_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for whether hybridisation should only be retained for aromatic bonds.
reverseNodeMap - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Saves all ScaffoldNodes and numbers them in ascending order.
RULE_SEVEN_APPLIED_SETTING_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for whether rule prioritisation rule 7 of the Schuffenhauer scaffold tree fragmentation should be applied.

S

SCAFFOLD - Enum constant in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: Terminal side chains of the molecule are removed except for any atoms non-single bonded directly to linkers or rings, as it is e.g. defined in "The Scaffold Tree − Visualization of the Scaffold Universe by Hierarchical Scaffold Classification".
SCAFFOLD_ATOM_COUNTER_PROPERTY - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Property of the atoms according to which they are counted and identified.
SCAFFOLD_MODE_OPTION_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for which scaffold mode should be used.
ScaffoldGenerator - Class in org.openscience.cdk.tools.scaffold: This class is designed to generate different molecule scaffolds and frameworks.
ScaffoldGenerator() - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: The only constructor of this class.
ScaffoldGenerator.ScaffoldModeOption - Enum Class in org.openscience.cdk.tools.scaffold: Enum with which the type of scaffolds to be generated can be set.
ScaffoldNetwork - Class in org.openscience.cdk.tools.scaffold: Top-level class to organise the NetworkNodes A network can have several roots and leaves.
ScaffoldNetwork() - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Default Constructor
ScaffoldNetwork(SmilesGenerator) - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Constructor
ScaffoldNodeBase<MoleculeType> - Class in org.openscience.cdk.tools.scaffold: Inspired by: Another Tree Structure
Base class of node objects.
ScaffoldNodeBase(MoleculeType) - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Constructor
ScaffoldNodeCollectionBase - Class in org.openscience.cdk.tools.scaffold: Base class of node collection objects.
ScaffoldNodeCollectionBase() - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Default Constructor
ScaffoldNodeCollectionBase(SmilesGenerator) - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Constructor
ScaffoldTree - Class in org.openscience.cdk.tools.scaffold: Top-level class to organise the TreeNodes as a tree.
ScaffoldTree() - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldTree: Default Constructor
ScaffoldTree(SmilesGenerator) - Constructor for class org.openscience.cdk.tools.scaffold.ScaffoldTree: Constructor
setAromaticityModelSetting(Aromaticity) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the applied aromaticity model.
setChildren(List<ScaffoldNodeBase<MoleculeType>>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Set the children node.
setDetermineAromaticitySetting(boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the option to not determine the aromaticity.
setMolecule(MoleculeType) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Set the node molecule.
setNonVirtualOriginSmilesList(List<String>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Set the entire nonVirtualOriginSmilesList.
setOriginSmilesList(List<String>) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase: Set the entire originSmilesList
setParent(TreeNode<MoleculeType>) - Method in class org.openscience.cdk.tools.scaffold.TreeNode: Set the parent node.
setParents(List<NetworkNode<MoleculeType>>) - Method in class org.openscience.cdk.tools.scaffold.NetworkNode: Set the parents of the node.
setRetainOnlyHybridisationsAtAromaticBondsSetting(boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the setting that, only the hybridisation of aromatic atoms is obtained.
setRuleSevenAppliedSetting(boolean) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the option to skip rule 7 of the Schuffenhauer scaffold tree fragmentation.
setScaffoldModeSetting(ScaffoldGenerator.ScaffoldModeOption) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the now used scaffold mode.
setSmilesGeneratorSetting(SmilesGenerator) - Method in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Sets the applied SmilesGenerator.
SMILES_GENERATOR_SETTING_DEFAULT - Static variable in class org.openscience.cdk.tools.scaffold.ScaffoldGenerator: Default setting for which SmilesGenerator should be used.
smilesGenerator - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Generator for the creation of SMILES
smilesMap - Variable in class org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase: Saves all ScaffoldNodes according to their SMILES.

T

TreeNode<MoleculeType> - Class in org.openscience.cdk.tools.scaffold: The TreeNodes are nodes from which a ScaffoldTree can be built.
TreeNode(MoleculeType) - Constructor for class org.openscience.cdk.tools.scaffold.TreeNode: Constructor

U

updateLevelMap() - Method in class org.openscience.cdk.tools.scaffold.ScaffoldNetwork: Updates the assignment of nodes to levels in the level map by iterating over all nodes and enquiring their levels.

V

valueOf(String) - Static method in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption: Returns an array containing the constants of this enum class, in the order they are declared.

A B C D E G H I L M N O R S T U V
All Classes and Interfaces|All Packages|Constant Field Values