|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object chemaxon.struc.CGraph chemaxon.struc.MoleculeGraph chemaxon.struc.SelectionMolecule
A selection object derived from Molecule's ancestor.
Field Summary |
Fields inherited from class chemaxon.struc.MoleculeGraph |
AROM_CHEMAXON, AROM_DAYLIGHT, DIM_MASK, flags, isMultiChiral, orix, oriy, oriz, RMCLEANUP_STEREO |
Fields inherited from class chemaxon.struc.CGraph |
btab, cacheMemory, ctab, edgeCount, edges, fragIds, grinv, grinvCC, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_NONE, sssr, superGraph |
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. |
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 void |
fuse0(CGraph graph)
Adds those nodes and edges of a graph to this one that are not already elements. |
protected boolean |
isRealNodeParent()
Selection molecules are not real node parents. |
protected void |
regenCtabs()
Regenerates connection table and edge table. |
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. |
boolean |
setParity(int[] p)
Sets the parity for the selection. |
boolean |
setParity(int i,
int p)
Sets the parity for a selected atom. |
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.CGraph |
add, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, contains, findEdge, findFrag, findFrags, findNode, fuse, getBtab, getCtab, getEdge, getEdgeCount, getEdgeVector, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getNodeVector, getParent, getSSSR, incGrinvCC, indexOf, indexOf, insertEdge, insertNode, insertNullEdges, insertNullNodes, isEmpty, pack, regenEdges, removeAll, removeAllEdges, removeEdge, removeEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo, toString |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public SelectionMolecule()
Method Detail |
protected boolean isRealNodeParent()
isRealNodeParent
in class CGraph
public void setEdge(int i, CEdge edge)
setEdge
in class CGraph
i
- edge indexedge
- the edge referencepublic void add(CEdge edge)
add
in class CGraph
edge
- the edge objectpublic void swapNodes(int i, int j)
i
- index of the first nodej
- index of the second nodepublic void removeNode(CNode node)
removeNode
in class CGraph
node
- the nodepublic void removeNode(int i)
removeNode
in class CGraph
i
- the node indexpublic void removeEdge(CEdge edge)
removeEdge
in class CGraph
edge
- the edgepublic void removeEdge(int i)
removeEdge
in class CGraph
i
- the edge indexprotected void addNode0(CNode node)
addNode0
in class CGraph
node
- the node referenceprotected void setNode0(int i, CNode node)
setNode0
in class CGraph
i
- node indexnode
- new node referenceprotected void addEdge0(CEdge edge)
addEdge0
in class CGraph
edge
- the edge referenceprotected void regenCtabs()
regenCtabs
in class CGraph
protected void fuse0(CGraph graph)
fuse0
in class CGraph
graph
- the graphpublic void transform(CTransform3D t)
transform
in class MoleculeGraph
t
- the transformation matrixpublic boolean setParity(int i, int p)
setParity
in class MoleculeGraph
p
- the parity for each atom in the selectioni
- the index of the atom whose parity is to be set
StereoConstants.PARITY_ODD
,
StereoConstants.PARITY_EVEN
,
MolBond.UP
,
MolBond.DOWN
,
MoleculeGraph.setParity(int[] p)
public boolean setParity(int[] p)
setParity
in class MoleculeGraph
p
- the parity for each atom in the selection
StereoConstants.PARITY_ODD
,
StereoConstants.PARITY_EVEN
,
MoleculeGraph.isAbsStereo()
,
MoleculeGraph.setAbsStereo(boolean)
,
MolBond.UP
,
MolBond.DOWN
public void clonecopy(CGraph graph)
clonecopy
in class MoleculeGraph
graph
- the target graphpublic java.lang.Object clone()
clone
in class MoleculeGraph
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |