Package com.actelion.research.chem.descriptor.pharmacophoretree

Class PharmacophoreTree

java.lang.Object

com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree

public class PharmacophoreTree
extends java.lang.Object

A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon (DOI:10.1023/a:1008068904628). A PharmacophoreTree consists of connected nodes and it's data structure is an undirected tree. No cycles are allowed which distinguishes it from a molecular graph. PharmacophoreTrees facilitates the comparison of chemical structures with respect to their features in 2D.

Author:

joel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PharmacophoreTree.BiGramInt	container of an undirected edge

Field Summary

Fields

Modifier and Type	Field	Description
static int	CUT_LEFT
static int	CUT_NONE
static int	CUT_RIGHT

Constructor Summary

Constructors

Constructor	Description
PharmacophoreTree(java.util.List<PharmacophoreNode> nodes, java.util.List<int[]> edges)

Method Summary

Modifier and Type	Method	Description
void	enumerateExtensionCutFast(int head, int[] cut, java.util.List<java.lang.Integer> subTreeEdgeIndeces, java.util.Set<java.lang.Integer> extensionNodes, java.util.Set<java.lang.Integer> sourceNodes)	retrieve nodes that are part of extension match ("extension nodes") as well as the nodes that are part of a cut subtree (source nodes) from a cut-string
void	enumerateExtensionCutFull(int head, int[] cut, java.util.List<java.lang.Integer> subTreeEdgeIndeces, java.util.List<java.lang.Integer> subTreeParentEdgeIndeces, java.util.List<java.util.List<java.lang.Integer>> sourceTreeEdgeIndeces, java.util.List<java.util.List<java.lang.Integer>> sourceTreeEdgeParentIndeces, java.util.List<java.lang.Integer> sourceTreeHeadNodes, java.util.Set<java.lang.Integer> extensionNodes, java.util.List<java.lang.Integer> cutEdges, java.util.List<java.lang.Integer> cutDirections)	retrieves nodes that are part of extension match ("extension nodes") as well as the different subtrees resulting from the cuts with a list of their edges (in bfs order) as well as the parents of the edges
java.util.List<java.util.Set<java.lang.Integer>>	getAllSubtrees()
double	getDirectSim(PharmacophoreTree pTree2)
java.util.List<int[]>	getEdges()
java.util.List<int[]>	getExtensionCuts(java.util.List<java.lang.Integer> subtreeEdgeIndeces, java.util.List<java.lang.Integer> subtreeEdgeParentIndeces)	get a list of int[] arrays that define an extension cut: Given a subtree with a designated head-node, an extension cut separates an extension match from the remaining subtrees.
int	getLinkNodes()
java.util.List<PharmacophoreNode>	getNodes()
java.util.List<PharmacophoreNode>	getNodes(java.util.Collection<java.lang.Integer> indeces)
java.util.Set<java.lang.Integer>	getNodesFromEdges(java.util.List<java.lang.Integer> edgeIndeces)
void	getPathsFromHeadNode(int headNode, java.util.List<java.util.Set<java.lang.Integer>> paths, java.util.Set<java.lang.Integer> visitedEdges)
double	getSize()
double	getSubTreeSize(java.util.List<java.lang.Integer> edges, int headNode)
int[]	initialCut(int cut, int edge, java.util.List<java.lang.Integer> sourceTreeEdges, java.util.List<java.lang.Integer> sourceTreeEdgeParents, java.util.List<java.lang.Integer> targetTreeEdges, java.util.List<java.lang.Integer> targetTreeEdgeParents)	a cut divides a edge into a target node and a source node: an edge is defined as a tuple of two nodes (a,b), a left cut results in node a being the source node and b being the target node: a-->--b a right cut results in the right node being the source node: a--<--b returns int array with source node as 0th element and target node as 1st element
void	removeNode(PharmacophoreNode node)
void	treeWalkBFS(int headNode, int deletedEdgeIndex, java.util.List<java.lang.Integer> treeEdgesBFS, java.util.List<java.lang.Integer> edgeParentsBFS)	Walks a subtree of the PharmacophoreTree in breadth-first manner starting from a deleted edge and a designated head node.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CUT_NONE

public static final int CUT_NONE

See Also:

Constant Field Values

CUT_RIGHT

public static final int CUT_RIGHT

See Also:

Constant Field Values

CUT_LEFT

public static final int CUT_LEFT

See Also:

Constant Field Values

Constructor Detail

PharmacophoreTree

public PharmacophoreTree(java.util.List<PharmacophoreNode> nodes,
                         java.util.List<int[]> edges)

Method Detail

initialCut

public int[] initialCut(int cut,
                        int edge,
                        java.util.List<java.lang.Integer> sourceTreeEdges,
                        java.util.List<java.lang.Integer> sourceTreeEdgeParents,
                        java.util.List<java.lang.Integer> targetTreeEdges,
                        java.util.List<java.lang.Integer> targetTreeEdgeParents)

a cut divides a edge into a target node and a source node: an edge is defined as a tuple of two nodes (a,b), a left cut results in node a being the source node and b being the target node: a-->--b a right cut results in the right node being the source node: a--<--b returns int array with source node as 0th element and target node as 1st element

Parameters:

cut -

edge -

sourceTreeEdges -

sourceTreeEdgeParents -

targetTreeEdges -

targetTreeEdgeParents -

Returns:

treeWalkBFS

public void treeWalkBFS(int headNode,
                        int deletedEdgeIndex,
                        java.util.List<java.lang.Integer> treeEdgesBFS,
                        java.util.List<java.lang.Integer> edgeParentsBFS)

Walks a subtree of the PharmacophoreTree in breadth-first manner starting from a deleted edge and a designated head node. Returns a list of edge indeces and the parents of the edges.

Parameters:

headNode -

deletedEdgeIndex -

treeEdgesBFS -

edgeParentsBFS -

enumerateExtensionCutFast

public void enumerateExtensionCutFast(int head,
                                      int[] cut,
                                      java.util.List<java.lang.Integer> subTreeEdgeIndeces,
                                      java.util.Set<java.lang.Integer> extensionNodes,
                                      java.util.Set<java.lang.Integer> sourceNodes)

retrieve nodes that are part of extension match ("extension nodes") as well as the nodes that are part of a cut subtree (source nodes) from a cut-string

Parameters:

head -

cut -

subTreeEdgeIndeces -

extensionNodes -

sourceNodes -

enumerateExtensionCutFull

public void enumerateExtensionCutFull(int head,
                                      int[] cut,
                                      java.util.List<java.lang.Integer> subTreeEdgeIndeces,
                                      java.util.List<java.lang.Integer> subTreeParentEdgeIndeces,
                                      java.util.List<java.util.List<java.lang.Integer>> sourceTreeEdgeIndeces,
                                      java.util.List<java.util.List<java.lang.Integer>> sourceTreeEdgeParentIndeces,
                                      java.util.List<java.lang.Integer> sourceTreeHeadNodes,
                                      java.util.Set<java.lang.Integer> extensionNodes,
                                      java.util.List<java.lang.Integer> cutEdges,
                                      java.util.List<java.lang.Integer> cutDirections)

retrieves nodes that are part of extension match ("extension nodes") as well as the different subtrees resulting from the cuts with a list of their edges (in bfs order) as well as the parents of the edges

Parameters:

head -

cut -

subTreeEdgeIndeces -

subTreeParentEdgeIndeces -

sourceTreeEdgeIndeces -

sourceTreeEdgeParentIndeces -

sourceTreeHeadNodes -

extensionNodes -

cutEdges -

cutDirections -

getExtensionCuts

public java.util.List<int[]> getExtensionCuts(java.util.List<java.lang.Integer> subtreeEdgeIndeces,
                                              java.util.List<java.lang.Integer> subtreeEdgeParentIndeces)

get a list of int[] arrays that define an extension cut: Given a subtree with a designated head-node, an extension cut separates an extension match from the remaining subtrees. The extension cut defines for every edge of the input subtrees their status: 0 -> edge contained in extension match 1 -> edge is cut -1 -> edge is part of a cut subtree

Parameters:

subtreeEdgeIndeces -

subtreeEdgeParentIndeces -

Returns:

getNodesFromEdges

public java.util.Set<java.lang.Integer> getNodesFromEdges(java.util.List<java.lang.Integer> edgeIndeces)

getNodes

public java.util.List<PharmacophoreNode> getNodes(java.util.Collection<java.lang.Integer> indeces)

getNodes

public java.util.List<PharmacophoreNode> getNodes()

getEdges

public java.util.List<int[]> getEdges()

getLinkNodes

public int getLinkNodes()

removeNode

public void removeNode(PharmacophoreNode node)

getSize

public double getSize()

getSubTreeSize

public double getSubTreeSize(java.util.List<java.lang.Integer> edges,
                             int headNode)

getDirectSim

public double getDirectSim(PharmacophoreTree pTree2)

getAllSubtrees

public java.util.List<java.util.Set<java.lang.Integer>> getAllSubtrees()

getPathsFromHeadNode

public void getPathsFromHeadNode(int headNode,
                                 java.util.List<java.util.Set<java.lang.Integer>> paths,
                                 java.util.Set<java.lang.Integer> visitedEdges)