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java.lang.Object chemaxon.struc.CNode chemaxon.struc.MolAtom chemaxon.struc.sgroup.SgroupAtom
S-group.
Field Summary |
Fields inherited from class chemaxon.struc.MolAtom |
AAMAP_MASK, AAMAP_MAX, AAMAP_OFF, ALIPHATIC, ANY, AROMATIC, AROMATIC_OR_ALIPHATIC, ATOM_TYPE_COUNT, ATTACH_BOTH, ATTACH1, ATTACH2, CHARGED_H, ELEMENT_COUNT, EMPTY, FIX_CHARGE, HETERO, HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN, ISOTOPE_H, LIST, LONELY_H, LP, MAPPED_H, NOTLIST, PSEUDO, RAD_COUNT_MASK, RAD_MASK, RAD_OFF, RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3, RADICAL_H, RESSEQ_MAX, RESTYPE_MAX, RGROUP, RGROUP_MAX, RXNSTEREO_INVERSION, RXNSTEREO_NONE, RXNSTEREO_RETENTION, SETSEQ_MAX, SGROUP, SMARTS_H_DAYLIGHT_COMP_MODE, SMARTS_H_MARVIN_COMP_MODE, VALCHK_ATTACH, VALENCE_CHECKED, xCoordinate, yCoordinate, zCoordinate |
Fields inherited from class chemaxon.struc.CNode |
edges, nedges |
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 | |
SgroupAtom(SuperatomSgroup sg)
Constructs a superatom for a superatom type S-group. |
Method Summary | |
protected void |
add(CEdge edge)
Add an edge if it had not been already added. |
java.lang.Object |
clone()
Clones the S-group superatom. |
SgroupAtom |
cloneFromSgroupCopy()
Clones the S-group superatom partially. |
protected void |
copy(CNode node)
Make a copy of this S-group superatom. |
protected void |
copyFromSgroupCopy(SgroupAtom sa)
Make a copy of this S-group superatom. |
protected int |
countAllAtoms()
Counts all atoms represented by this atom. |
java.lang.String |
getAtomSymbol(int style,
int flags,
int[] lcenter,
CTransform3D preTransform)
Gets the string representation of the atom symbol. |
SuperatomSgroup |
getSgroup()
Gets the S-group corresponding to this superatom. |
protected void |
removeAllEdges()
Remove all edges. |
protected void |
removeEdge(int i)
Removes a bond. |
protected static void |
setNode1(CEdge edge,
CNode newnode)
Sets the first node of an edge. |
protected static void |
setNode2(CEdge edge,
CNode newnode)
Sets the second node of an edge. |
Methods inherited from class chemaxon.struc.CNode |
getEdge, getEdgeCount, getEdgeTo, getLigand, getLock, getParent, haveSimilarEdges, indexOf, isBoundTo, pack, removeEdge, sringsize |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public SgroupAtom(SuperatomSgroup sg)
sg
- the S-groupMethod Detail |
public SuperatomSgroup getSgroup()
public java.lang.String getAtomSymbol(int style, int flags, int[] lcenter, CTransform3D preTransform)
getAtomSymbol
in class MolAtom
style
- neglectedflags
- neglectedpreTransform
- neglectedlcenter
- neglected
public java.lang.Object clone()
clone
in class MolAtom
protected void copy(CNode node)
copy
in class MolAtom
node
- the target atompublic SgroupAtom cloneFromSgroupCopy()
protected void copyFromSgroupCopy(SgroupAtom sa)
sa
- the target atomprotected void add(CEdge edge)
add
in class MolAtom
edge
- the edge to addprotected void removeEdge(int i)
removeEdge
in class MolAtom
i
- bond indexprotected static void setNode1(CEdge edge, CNode newnode)
edge
- the edgenewnode
- the new node valueprotected static void setNode2(CEdge edge, CNode newnode)
edge
- the edgenewnode
- the new node valueprotected void removeAllEdges()
removeAllEdges
in class CNode
protected int countAllAtoms()
countAllAtoms
in class MolAtom
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