chemaxon.struc
Class CGraph

java.lang.Object
  chemaxon.struc.CGraph

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

Direct Known Subclasses:

MoleculeGraph

public class CGraph

extends java.lang.Object

implements java.lang.Cloneable, java.io.Serializable

Chemical graph.

Version:

3.5.5, 03/08/2005

Author:

Peter Csizmadia

See Also:

CNode, CEdge, Serialized Form

Field Summary

protected int[][]	btab Bond table.
protected java.util.Vector	cacheMemory
protected int[][]	ctab Connection table.
protected int	edgeCount The number of edges.
protected CEdge[]	edges The edges (bonds).
protected int[]	fragIds Fragment identifiers.
protected int[]	grinv Graph invariants.
protected long	grinvCC Graph invariant change count.
protected static int	INITIAL_CAPACITY Initial capacity of the nodes and edges vectors.
protected int	nFrags Number of disconnected fragments.
protected int	nGrinv Number of different graph invariants.
protected int	nodeCount The number of nodes.
protected CNode[]	nodes The nodes (atoms).
protected CGraph	parentGraph The structure that contains this graph as a substructure.
static int	RMCLEANUP_ALL Perform all clean-up methods when removing a node or an edge.
static int	RMCLEANUP_EDGES When removing a node or an edge, also remove the edge(s) from the node object(s).
static int	RMCLEANUP_NONE Do not perform any clean-up methods when removing a node or an edge.
protected int[][]	sssr SSSR ring node indexes.
protected CGraph	superGraph Parent of all parents.

Constructor Summary

CGraph()
Constructs a chemical graph.

CGraph(CGraph p)
Constructs a chemical graph.

CGraph(CGraph p, int n, int e)
Constructs a fragment with the specified number of nodes and edges

Method Summary

void	add(CEdge edge) Adds an edge to the graph.
void	add(CNode node) Adds a node to the graph.
protected void	addEdge0(CEdge edge) Adds an edge.
protected int	addEdgeWithoutChangingIt(CEdge edge) Adds an edge without setting its parentGraph and index fields.
protected void	addNode0(CNode node) Adds a node.
protected int	addNodeWithoutChangingIt(CNode node) Adds a node without setting its parentGraph and index fields.
java.lang.Object	clone() Makes an identical copy of the molecule.
protected void	clonecopy(CGraph graph) Copies the clones of nodes and edges of this graph to another one.
void	clonelesscopy(CGraph graph) Copy to selection.
boolean	contains(CGraph graph) Does the graph contain the specified fragment?
boolean	contains(java.lang.Object o) Checks if the graph contains the specified node or edge.
protected int	findEdge(CEdge edge) Finds an edge in the edgess array.
void	findFrag(int i, CGraph frag) Determines the subgraph connected to the specified node.
CGraph[]	findFrags(java.lang.Class cl) Determines the disconnected fragments and puts them into an array.
protected int	findNode(CNode node) Finds a node in the nodes array.
void	fuse(CGraph graph) Adds those nodes and edges of a graph to this one that are not already elements.
protected void	fuse0(CGraph graph) Adds those nodes and edges of a graph to this one that are not already elements.
int[][]	getBtab() Gets the edge (bond) table.
int[][]	getCtab() Gets the connection table.
CEdge	getEdge(int i) Gets an edge.
CEdge[]	getEdgeArray() Creates an array of edges.
int	getEdgeCount() Gets the number of edges.
java.util.Vector	getEdgeVector() Gets the edges.
CGraph	getForefather() Gets the first parent.
int	getFragCount() Returns the number of fragments.
int[]	getFragIds() Gets an array containing the fragment id for each node.
protected int[]	getGrinv() Gets the graph invariants array.
int	getGrinv(int[] gi) Gets the graph invariants.
long	getGrinvCC() Gets the graph invariant change count.
java.lang.Object	getLock() Gets the lock object for synchronization.
CNode	getNode(int i) Gets a node.
int	getNodeCount() Gets the number of nodes.
java.util.Vector	getNodeVector() Gets the nodes.
CGraph	getParent() Gets the parent graph that contains this substructure.
int[][]	getSSSR() Gets the Smallest Set of Smallest Ring node indexes array.
protected void	incGrinvCC() Increases the graph invariant change count and sets grinv to null.
int	indexOf(CEdge edge) Gets the index of the specified edge.
int	indexOf(CNode node) Gets the index of the specified node.
void	insertEdge(int i, CEdge edge) Inserts the edge at the specified index.
void	insertNode(int i, CNode node) Inserts the node at the specified index.
protected void	insertNullEdges(int i, int count) Insert nulls into the bond array.
protected void	insertNullNodes(int i, int count) Insert nulls into the atom array.
boolean	isEmpty() Ask if the graph is empty or not.
protected boolean	isRealNodeParent() Can it be a real node parent?
boolean	isSimilarTo(CGraph g) Checks if the graph is similar to another graph.
protected void	makeItSimilar(CGraph g) Empty method.
void	mergeNodes(CNode that, CNode a) Merges edges of a node with another node, then adds the node to the molecule.
CGraph	newInstance() Creates a new CGraph object.
void	pack() Reduce memory usage.
protected void	regenCtabs() Regenerates connection table and edge table.
void	regenEdges() Regenerates the edge vector: remove its elements, then put the edge objects from the nodes into it.
void	removeAll() Removes all the nodes and edges.
void	removeAllEdges() Removes all edges.
void	removeEdge(CEdge edge) Removes an edge by reference.
protected void	removeEdge(CEdge edge, int cleanupFlags) Removes an edge by reference.
void	removeEdge(int i) Removes an edge from the graph.
protected void	removeEdge(int i, int cleanupFlags) Removes an edge from the graph.
void	removeNode(CNode node) Removes a node and its edges.
void	removeNode(CNode node, int cleanupFlags) Removes a node and its edges with extra clean-up options.
void	removeNode(int i) Removes a node and its edges from the graph.
void	removeNode(int i, int cleanupFlags) Removes a node and its edges with extra clean-up options.
protected void	resetCtab() An operation performed that changed the connection table and the graph invariants.
protected void	resetGrinvInParents() Graph invariants must be recalculated for this graph and all parent graphs.
protected java.lang.Object[]	restoreCache(int n) Restores caches like connection table, bond table, etc.
protected java.lang.Object[]	saveCache(int n) Saves caches like connection table, bond table, etc.
void	setEdge(int i, CEdge edge) Sets the edge at the specified index.
protected void	setGrinvCC(long g) Sets the graph invariant change count.
void	setNode(int i, CNode node) Sets the node at the specified index.
protected void	setNode0(int i, CNode node) Sets the node at the specified index.
void	sortEdgesAccordingTo(CEdge[] order) Sorts edges in the same order as they appear in another chemical graph.
java.lang.String	toString() Overrides Object.toString() to ease debugging.

Methods inherited from class java.lang.Object

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

Field Detail

INITIAL_CAPACITY

protected static final int INITIAL_CAPACITY

Initial capacity of the nodes and edges vectors.

See Also:

Constant Field Values

RMCLEANUP_NONE

public static final int RMCLEANUP_NONE

Do not perform any clean-up methods when removing a node or an edge.

Since:

Marvin 3.1

See Also:

removeNode(CNode, int), removeNode(int, int), removeEdge(CEdge, int), removeEdge(int, int), Constant Field Values

RMCLEANUP_ALL

public static final int RMCLEANUP_ALL

Perform all clean-up methods when removing a node or an edge.

Since:

Marvin 3.1

See Also:

removeNode(CNode, int), removeNode(int, int), removeEdge(CEdge, int), removeEdge(int, int), Constant Field Values

RMCLEANUP_EDGES

public static final int RMCLEANUP_EDGES

When removing a node or an edge, also remove the edge(s) from the node object(s).

Since:

Marvin 3.1

See Also:

removeNode(CNode, int), removeNode(int, int), removeEdge(CEdge, int), removeEdge(int, int), Constant Field Values

superGraph

protected transient CGraph superGraph

Parent of all parents.

parentGraph

protected transient CGraph parentGraph

The structure that contains this graph as a substructure.

nodes

protected transient CNode[] nodes

The nodes (atoms).

nodeCount

protected transient int nodeCount

The number of nodes.

edges

protected transient CEdge[] edges

The edges (bonds).

edgeCount

protected transient int edgeCount

The number of edges.

sssr

protected transient int[][] sssr

SSSR ring node indexes.

ctab

protected transient int[][] ctab

Connection table.

btab

protected transient int[][] btab

Bond table.

fragIds

protected transient int[] fragIds

Fragment identifiers.

nFrags

protected transient int nFrags

Number of disconnected fragments.

grinv

protected transient int[] grinv

Graph invariants.

nGrinv

protected transient int nGrinv

Number of different graph invariants.

grinvCC

protected transient long grinvCC

Graph invariant change count. The number of times the graph invariants may have changed since the creation of the molecule.

cacheMemory

protected transient java.util.Vector cacheMemory

Constructor Detail

CGraph

public CGraph(CGraph p,
              int n,
              int e)

Constructs a fragment with the specified number of nodes and edges

Parameters:

p - the parent graph or null

n - no reallocation needed until the number of nodes is less than this value

e - no reallocation needed until the number of edges is less than this value

CGraph

public CGraph(CGraph p)

Constructs a chemical graph.

Parameters:

p - the parent graph or null

CGraph

public CGraph()

Constructs a chemical graph.

Method Detail

isRealNodeParent

protected boolean isRealNodeParent()

Can it be a real node parent?

Returns:

true

Since:

Marvin 3.0

getNodeVector

public java.util.Vector getNodeVector()

Gets the nodes.

Returns:

a node vector

getEdgeVector

public java.util.Vector getEdgeVector()

Gets the edges.

Returns:

an edge vector

getNodeCount

public int getNodeCount()

Gets the number of nodes.

Returns:

number of nodes

getNode

public CNode getNode(int i)

Gets a node.

Parameters:

i - node index

Returns:

the node object

Since:

Marvin 2.6

setNode

public void setNode(int i,
                    CNode node)

Sets the node at the specified index.

Parameters:

i - node index

node - new node reference

Since:

Marvin 2.9

insertNode

public final void insertNode(int i,
                             CNode node)

Inserts the node at the specified index.

Parameters:

i - node index

node - new node reference

Since:

Marvin 3.4

insertNullNodes

protected void insertNullNodes(int i,
                               int count)

Insert nulls into the atom array.

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 3.4

insertEdge

public final void insertEdge(int i,
                             CEdge edge)

Inserts the edge at the specified index.

Parameters:

i - edge index

edge - new edge reference

Since:

Marvin 3.5.5

insertNullEdges

protected void insertNullEdges(int i,
                               int count)

Insert nulls into the bond array.

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 3.5.5

getEdgeCount

public int getEdgeCount()

Gets the number of edges.

Returns:

number of edges

getEdge

public CEdge getEdge(int i)

Gets an edge.

Parameters:

i - edge index

Returns:

the edge object

Since:

Marvin 2.6

setEdge

public void setEdge(int i,
                    CEdge edge)

Sets the edge at the specified index.

Parameters:

i - edge index

edge - the edge reference

Since:

Marvin 2.9

add

public void add(CNode node)

Adds a node to the graph.

Parameters:

node - the node object

add

public void add(CEdge edge)

Adds an edge to the graph. If the graph is a superGraph, the edge is also added to its endpoints (two CNode objects).

Parameters:

edge - the edge object

removeNode

public void removeNode(CNode node)

Removes a node and its edges.

Parameters:

node - the node

Since:

Marvin 2.5

removeNode

public void removeNode(int i)

Removes a node and its edges from the graph.

Parameters:

i - the node index

Since:

Marvin 2.5

removeEdge

public void removeEdge(CEdge edge)

Removes an edge by reference.

Parameters:

edge - the edge

Since:

Marvin 2.5

removeEdge

public void removeEdge(int i)

Removes an edge from the graph.

Parameters:

i - the edge index

Since:

Marvin 2.5

removeAllEdges

public void removeAllEdges()

Removes all edges.

removeAll

public void removeAll()

Removes all the nodes and edges.

regenEdges

public void regenEdges()

Regenerates the edge vector: remove its elements, then put the edge objects from the nodes into it.

getEdgeArray

public CEdge[] getEdgeArray()

Creates an array of edges.

Returns:

array of edge objects

Since:

Marvin 3.5, 09/02/2004

sortEdgesAccordingTo

public void sortEdgesAccordingTo(CEdge[] order)

Sorts edges in the same order as they appear in another chemical graph.

Parameters:

order - the edges in the other graph

Since:

Marvin 3.5, 09/02/2004

indexOf

public int indexOf(CNode node)

Gets the index of the specified node.

Parameters:

node - the node

Returns:

the index, or -1 if not found

Since:

Marvin 2.7

indexOf

public int indexOf(CEdge edge)

Gets the index of the specified edge.

Parameters:

edge - the edge

Returns:

the index, or -1 if not found

Since:

Marvin 2.7

contains

public boolean contains(java.lang.Object o)

Checks if the graph contains the specified node or edge.

Parameters:

o - the node or edge object

Returns:

true if the graph contains the object, false otherwise

isEmpty

public boolean isEmpty()

Ask if the graph is empty or not.

Returns:

true if the graph does not contain any nodes or edges.

isSimilarTo

public boolean isSimilarTo(CGraph g)

Checks if the graph is similar to another graph. Two graphs are similar if

1. they have the same number of nodes and edges,
2. for each node ai in the first graph, there is a corresponding node aj in the other graph, with the same graph invariant, "equal properties" and "similar edges".

Returns:

true if the graphs are similar, false otherwise

Since:

Marvin 3.4.1, 07/21/2004

See Also:

CNode.haveEqualProperties(CNode), CNode.haveSimilarEdges(CNode)

removeNode

public void removeNode(CNode node,
                       int cleanupFlags)

Removes a node and its edges with extra clean-up options. This method is for internal use only. Use removeNode(CNode) instead unless you are sure what you are doing.

Parameters:

node - the node

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

removeNode

public void removeNode(int i,
                       int cleanupFlags)

Removes a node and its edges with extra clean-up options. This method is for internal use only. Use removeNode(int) instead unless you are sure what you are doing.

Parameters:

i - the node index

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

removeEdge

protected void removeEdge(CEdge edge,
                          int cleanupFlags)

Removes an edge by reference.

Parameters:

edge - the edge

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

removeEdge

protected void removeEdge(int i,
                          int cleanupFlags)

Removes an edge from the graph.

Parameters:

i - the edge index

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

fuse0

protected void fuse0(CGraph graph)

Adds those nodes and edges of a graph to this one that are not already elements.

Parameters:

graph - the graph

fuse

public void fuse(CGraph graph)

Adds those nodes and edges of a graph to this one that are not already elements.

Parameters:

graph - the other graph

mergeNodes

public void mergeNodes(CNode that,
                       CNode a)

Merges edges of a node with another node, then adds the node to the molecule.

Parameters:

that - the node

a - the other node

contains

public boolean contains(CGraph graph)

Does the graph contain the specified fragment?

Parameters:

graph - the fragment

Returns:

true if it contains the graph, false if not

clonecopy

protected void clonecopy(CGraph graph)

Copies the clones of nodes and edges of this graph to another one.

Parameters:

graph - the target graph

clonelesscopy

public void clonelesscopy(CGraph graph)

Copy to selection. Copies without cloning.

Parameters:

graph - the target graph (the selection)

clone

public java.lang.Object clone()

Makes an identical copy of the molecule. The new molecule will not be subgraph of the parentGraph of the original one. It will be its own superGraph.

Returns:

the clone

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object.

Returns:

a string representation of the object

getSSSR

public final int[][] getSSSR()

Gets the Smallest Set of Smallest Ring node indexes array. If the SSSR array is not calculated for the molecule, then create it. sssr[i][j] is the j-th node index at the i-th SSSR ring in the molecule.

Returns:

the sssr node index arrays

Since:

Marvin 3.0

getCtab

public int[][] getCtab()

Gets the connection table. If there is no connection table for the graph, then creates it. ctab[i][j] will be the index of the jth neighbor of the ith node.

Returns:

the ctab array

Since:

Marvin 2.6

getBtab

public int[][] getBtab()

Gets the edge (bond) table. If there is no edge table for the molecule, then create it. btab[i][j] will be the index of the edge between nodes i and j, or -1 if there is no edge.

Returns:

the btab array

Since:

Marvin 2.6

getGrinv

public int getGrinv(int[] gi)

Gets the graph invariants.

Parameters:

gi - the output array

Returns:

zero

getGrinv

protected int[] getGrinv()

Gets the graph invariants array.

Returns:

the grinv field

Since:

Marvin 3.0

getGrinvCC

public final long getGrinvCC()

Gets the graph invariant change count. Returns the number of times the graph invariants may have changed since the creation of the molecule.

Returns:

graph invariant change count

setGrinvCC

protected final void setGrinvCC(long g)

Sets the graph invariant change count.

Parameters:

g - graph invariant change count

Since:

Marvin 3.4

incGrinvCC

protected final void incGrinvCC()

Increases the graph invariant change count and sets grinv to null.

Since:

Marvin 3.5

resetGrinvInParents

protected final void resetGrinvInParents()

Graph invariants must be recalculated for this graph and all parent graphs.

getFragCount

public final int getFragCount()

Returns the number of fragments.

Returns:

the number of fragments

Since:

Marvin 3.01

getFragIds

public final int[] getFragIds()

Gets an array containing the fragment id for each node.

Returns:

array of fragment identifiers

Since:

Marvin 2.6

findFrags

public final CGraph[] findFrags(java.lang.Class cl)

Determines the disconnected fragments and puts them into an array. Atoms are removed from the original molecule object unless the fragment class is SelectionMolecule.class. The original node order is preserved in the returned fragments. Fragment order is also determined by the original node order. The first fragment is the one containing node 0, the second fragment is the one containing the smallest indexed node not in the first fragment, etc.

Parameters:

cl - create fragment objects of this class

Returns:

array of fragments

Since:

Marvin 3.0

findFrag

public final void findFrag(int i,
                           CGraph frag)

Determines the subgraph connected to the specified node. Subsequent calls with different node (i) argument are possible because only those nodes and edges are added that are still not elements of frag. Nodes are removed from the original graph object unless the frag is a SelectionMolecule.

Parameters:

i - node index

frag - add the nodes and edges to this CGraph

Since:

Marvin 2.6

getLock

public final java.lang.Object getLock()

Gets the lock object for synchronization. The lock object is the top parent.

Returns:

the lock object

Since:

Marvin 2.6

getParent

public final CGraph getParent()

Gets the parent graph that contains this substructure.

Returns:

the parent, or null if this is the supergraph

Since:

Marvin 2.6

getForefather

public final CGraph getForefather()

Gets the first parent.

Returns:

parent of all parents

Since:

Marvin 2.9.11

pack

public void pack()

Reduce memory usage.

newInstance

public CGraph newInstance()

Creates a new CGraph object.

Returns:

new CGraph object

makeItSimilar

protected void makeItSimilar(CGraph g)

Empty method.

Parameters:

g - a CGraph object

resetCtab

protected void resetCtab()

An operation performed that changed the connection table and the graph invariants.

Since:

Marvin 2.6

findNode

protected final int findNode(CNode node)

Finds a node in the nodes array.

Returns:

the node index or -1 if not found

findEdge

protected final int findEdge(CEdge edge)

Finds an edge in the edgess array.

Returns:

the edge index or -1 if not found

regenCtabs

protected void regenCtabs()

Regenerates connection table and edge table.

Since:

Marvin 2.6

addNode0

protected void addNode0(CNode node)

Adds a node.

Parameters:

node - the node reference

addNodeWithoutChangingIt

protected final int addNodeWithoutChangingIt(CNode node)

Adds a node without setting its parentGraph and index fields.

Parameters:

node - the node reference

Returns:

the new node index

setNode0

protected void setNode0(int i,
                        CNode node)

Sets the node at the specified index.

Parameters:

i - node index

node - new node reference

Since:

Marvin 2.10.5

addEdge0

protected void addEdge0(CEdge edge)

Adds an edge.

Parameters:

edge - the edge reference

addEdgeWithoutChangingIt

protected final int addEdgeWithoutChangingIt(CEdge edge)

Adds an edge without setting its parentGraph and index fields.

Parameters:

edge - the edge reference

Returns:

the new edge index

saveCache

protected java.lang.Object[] saveCache(int n)

Saves caches like connection table, bond table, etc.

Since:

Marvin 3.4

restoreCache

protected java.lang.Object[] restoreCache(int n)

Restores caches like connection table, bond table, etc.

Since:

Marvin 3.4