chemaxon.struc
Class SelectionMolecule

java.lang.Object
  chemaxon.struc.CGraph
      chemaxon.struc.MoleculeGraph
          chemaxon.struc.SelectionMolecule

All Implemented Interfaces:

MTransformable, chemaxon.struc.ReadableMolecule, StereoConstants, java.io.Serializable, java.lang.Cloneable

public class SelectionMolecule
extends MoleculeGraph

A selection object derived from Molecule's ancestor.

Since:

Marvin 3.0

Version:

5.1, 03/07/2008

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.MoleculeGraph

AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, useOnlyFirstAtomInStereoCalculation

Fields inherited from class chemaxon.struc.CGraph

btab, CACHE_REMOVE_ALL, CACHE_REMOVE_CACHEMEMORY, cacheMemory, cssr, ctab, edgeCount, edges, fragIds, grinv, grinvCC, grinvOptions, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_NONE, sssr, sssr2idx, sssrl2idx, superGraph

Fields inherited from interface chemaxon.struc.ReadableMolecule

HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS

Constructor Summary

SelectionMolecule()

Method Summary

void	add(CEdge edge) Adds an edge to the graph.
protected void	addEdge0(CEdge edge) Adds an edge.
protected void	addNode0(CNode node) Adds a node.
protected void	checkEdgeConsistency() Empty implementation, edge consistency is not checked in case of selections.
boolean	clean(int dim, java.lang.String opts, MProgressMonitor pmon) Calculates atom coordinates.
java.lang.Object	clone() Create a clone of the selection.
void	clonecopy(CGraph graph) Copies the clones of nodes and edges of this graph to another one.
protected boolean	clonecopyCGraphWithoutSgroups(int[] iatoms, CEdge[] cedges, int nb, CGraph g) Copies the specified atoms and bonds of this graph to another one.
protected void	fuse0(CGraph g, boolean check) Adds those nodes and edges of a graph to this one that are not already elements.
protected boolean	isGrinvCCValid() Tests whether the graph invariant change count is valid.
protected boolean	isRealNodeParent() Selection molecules are not real node parents.
protected void	regenCtabs() Regenerates connection table and edge table.
protected void	regenFragIds() Searches the disconnected fragments.
void	removeEdge(CEdge edge) Removes an edge by reference.
void	removeEdge(int i) Removes an edge from the graph.
void	removeNode(CNode node) Removes a node and its edges.
void	removeNode(int i) Removes a node and its edges from the graph.
void	setEdge(int i, CEdge edge) Sets the edge at the specified index.
protected void	setNode0(int i, CNode node) Sets the node at the specified index.
void	swapNodes(int i, int j) Swap two nodes.
void	transform(CTransform3D t) Apply a transformation matrix to the atomic coordinates.

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, aromatize, arrangeComponents, bondlength, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clear, clearCachedInfo, clearForImport, clonecopy, clonelesscopy, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, dearomatize, findAtomClone, fixSelfReferringProperty, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEdgeArray, getEdgeVector, getExactMass, getExplicitHcount, getExplicitLonePairCount, getFlags, getFormalCharge, getFormula, getGraphUnion, getGrinv, getGrinv, getGrinv, getGrinvOptions, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMass, getMassno, getName, getNeighbor, getNeighborCount, getNodeVector, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphCount, getSubGraphs, getSubGraphs, getTotalCharge, getVisibleCoords, hasAtomSet, hasBondSet, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, isAbsStereo, isAtom, isBond, isMultiChiral, isOnlyFirstAtomInStereoCalculation, isQuery, isRingBond, isSelfReference, isSimilarTo, isValidLinkNode, makeItSimilar, mergeNodes, moveTo, newInstance, partialClean, partialClean, properties, qpropCheck, removeEdge, removeExplicitLonePairs, removeNode, removeNode, restoreCache, revalidateCoordDependentProps, saveCache, setAbsStereo, setAtomSetSeqs, setBondSetSeqs, setChirality, setDim, setFlags, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocation, setParity, setParity, setParity, setSetSeqs, stereoClean, sumConservedQuantities, toString, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph

add, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, checkConsistency, contains, contains, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findFrags, findInArray, findNode, fuse, fuse, fuse0, getBtab, getCSSR, getCtab, getEdge, getEdgeCount, getEdgeList, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isEmpty, isolate, isolate, isRing, isSymmetric, mergeFrags, pack, regenEdges, removeAll, removeAllEdges, removeEdge, removeIsolatedEdges, removeIsolatedNodes, replaceEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo

Methods inherited from class java.lang.Object

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

Constructor Detail

SelectionMolecule

public SelectionMolecule()

Method Detail

isRealNodeParent

protected boolean isRealNodeParent()

Selection molecules are not real node parents. However, in some special cases a selection molecule can be a node parent.

Overrides:

isRealNodeParent in class CGraph

Returns:

false

Since:

Marvin 3.0

setEdge

public void setEdge(int i,
                    CEdge edge)

Sets the edge at the specified index.

Overrides:

setEdge in class MoleculeGraph

Parameters:

i - edge index

edge - the edge reference

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).

Overrides:

add in class CGraph

Parameters:

edge - the edge object

swapNodes

public void swapNodes(int i,
                      int j)

Swap two nodes.

Parameters:

i - index of the first node

j - index of the second node

Since:

Marvin 3.3, 11/04/2003

removeNode

public void removeNode(CNode node)

Removes a node and its edges.

Overrides:

removeNode in class CGraph

Parameters:

node - the node

removeNode

public void removeNode(int i)

Removes a node and its edges from the graph.

Overrides:

removeNode in class CGraph

Parameters:

i - the node index

removeEdge

public void removeEdge(CEdge edge)

Removes an edge by reference.

Overrides:

removeEdge in class CGraph

Parameters:

edge - the edge

removeEdge

public void removeEdge(int i)

Removes an edge from the graph.

Overrides:

removeEdge in class CGraph

Parameters:

i - the edge index

addNode0

protected void addNode0(CNode node)

Adds a node.

Overrides:

addNode0 in class CGraph

Parameters:

node - the node reference

setNode0

protected void setNode0(int i,
                        CNode node)

Sets the node at the specified index.

Overrides:

setNode0 in class MoleculeGraph

Parameters:

i - node index

node - new node reference

addEdge0

protected void addEdge0(CEdge edge)

Adds an edge.

Overrides:

addEdge0 in class CGraph

Parameters:

edge - the edge reference

regenCtabs

protected void regenCtabs()

Regenerates connection table and edge table.

Overrides:

regenCtabs in class CGraph

Since:

Marvin 3.5.2, 12/16/2004

fuse0

protected void fuse0(CGraph g,
                     boolean check)

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

Overrides:

fuse0 in class MoleculeGraph

Parameters:

g - the graph

check - true if a containment check should be performed to ensure that only those nodes and edges are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped

Since:

Marvin 5.0

transform

public void transform(CTransform3D t)

Apply a transformation matrix to the atomic coordinates.

Specified by:

transform in interface MTransformable

Overrides:

transform in class MoleculeGraph

Parameters:

t - the transformation matrix

clonecopy

public void clonecopy(CGraph graph)

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

Overrides:

clonecopy in class MoleculeGraph

Parameters:

graph - the target graph

clonecopyCGraphWithoutSgroups

protected boolean clonecopyCGraphWithoutSgroups(int[] iatoms,
                                                CEdge[] cedges,
                                                int nb,
                                                CGraph g)

Copies the specified atoms and bonds of this graph to another one.

Overrides:

clonecopyCGraphWithoutSgroups in class MoleculeGraph

Parameters:

iatoms - array of atoms indices to copy

cedges - array of bonds to copy or null to copy edges in cnodes only

nb - number of edges

g - the target graph

Returns:

false if the nodes array contains all edge end points, true if there is at least one external bond

Since:

Marvin 5.0.2, 03/07/2008

clone

public java.lang.Object clone()

Create a clone of the selection.

Overrides:

clone in class MoleculeGraph

Returns:

the clone

clean

public boolean clean(int dim,
                     java.lang.String opts,
                     MProgressMonitor pmon)

Calculates atom coordinates.

Overrides:

clean in class MoleculeGraph

Parameters:

dim - dimensions

opts - cleaning options

pmon - progress monitor or null

Returns:

true for success, false if an error occured

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

Since:

Marvin 4.1, 15/08/2006

See Also:

MoleculeGraph.clean(int, java.lang.String)

regenFragIds

protected final void regenFragIds()

Searches the disconnected fragments. Fragment order is determined by the 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. Provides a proper fragmentation for coordination compounds: keeps the atoms in the sgroupGraph of MulticenterSgroup and its central atom in the same fragment.

Overrides:

regenFragIds in class CGraph

Since:

Marvin 5.0

isGrinvCCValid

protected boolean isGrinvCCValid()

Tests whether the graph invariant change count is valid.

Overrides:

isGrinvCCValid in class CGraph

Returns:

false

Since:

Marvin 5.0, 11/30/2007

checkEdgeConsistency

protected void checkEdgeConsistency()

Empty implementation, edge consistency is not checked in case of selections.

Overrides:

checkEdgeConsistency in class CGraph

Since:

Marvin 5.0, 11/06/2007