chemaxon.struc.sgroup
Class SgroupAtom

java.lang.Object
  extended bychemaxon.struc.CNode
      extended bychemaxon.struc.MolAtom
          extended bychemaxon.struc.sgroup.SgroupAtom
All Implemented Interfaces:
java.lang.Cloneable, java.io.Serializable, StereoConstants

public class SgroupAtom
extends MolAtom

S-group.

Since:
3.0, 11/05/2002
Version:
3.1.4, 06/06/2003
Author:
Peter Csizmadia
See Also:
Serialized Form

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, 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, 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(CNode node)
          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 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.MolAtom
bondweights, clear, clearCalcstr, covalentRadiusOf, electronegOf, getAliasstr, getAtno, getAtomLabels, getAtomMap, getAttach, getBond, getBondCount, getCalcrgb, getCalcrgbs, getCalcstr, getCharge, getExplicitHcount, getFlags, getHybridizationState, getImplicitHcount, getList, getLocation, getLocation, getMass, getMassno, getQProp, getQPropAsInt, getQueryAromaticity, getQueryLabel, getQuerystr, getRadical, getRadicalCount, getReactionStereo, getRelativeNegativity, getResidueAtomId, getResidueSeq, getResidueType, getRgroup, getSetSeq, getStereoCare, getStereoGroupNumber, getStereoGroupType, getSymbol, getValence, getX, getY, getZ, hasAromaticBond, hasQProps, hasQueryBonds, hasSMARTSProps, hasSMARTSPropsExcluding, hasValenceError, insideLabel, ionChargeOf, isArrowEnd, isImplicitizableH, isNobleGas, isotopeType, isPseudo, isQProp, isQuery, isSameParityClass, isSelected, nameOf, naturalWeightOf, negOxOf, numOf, numoxstatesOf, oxstateOf, paritySign, posOxOf, qpropCheck, removeEdge, residueSymbolOf, residueTypeOf, setAliasstr, setAtno, setAtomMap, setAttach, setCalcrgbs, setCalcstr, setCharge, setCorners, setFlags, setFlags, setHybridizationState, setImplicitHcount, setList, setList, setLocation, setMassno, setMassnoIfKnown, setQProp, setQProp, setQueryAromaticity, setQuerystr, setRadical, setReactionStereo, setResidueAtomId, setResidueSeq, setResidueType, setRgroup, setSelected, setSetSeq, setSMARTS, setStereoGroupNumber, setStereoGroupType, setValenceError, setX, setXY, setXYZ, setY, setZ, symbolOf, toString, twicesumbonds, valenceCheck
 
Methods inherited from class chemaxon.struc.CNode
getEdge, getEdgeCount, getLigand, getLock, getParent, indexOf, isBoundTo, pack, removeEdge, sringsize, toString
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SgroupAtom

public SgroupAtom(SuperatomSgroup sg)
Constructs a superatom for a superatom type S-group.

Parameters:
sg - the S-group
Method Detail

getSgroup

public SuperatomSgroup getSgroup()
Gets the S-group corresponding to this superatom.

Returns:
the S-group

getAtomSymbol

public java.lang.String getAtomSymbol(int style,
                                      int flags,
                                      int[] lcenter,
                                      CTransform3D preTransform)
Gets the string representation of the atom symbol.

Overrides:
getAtomSymbol in class MolAtom
Parameters:
style - neglected
flags - neglected
preTransform - neglected
lcenter - neglected
Returns:
the S-group subscript

clone

public java.lang.Object clone()
Clones the S-group superatom.

Overrides:
clone in class MolAtom
Returns:
the clone

copy

protected void copy(CNode node)
Make a copy of this S-group superatom.

Overrides:
copy in class MolAtom
Parameters:
node - the target atom

cloneFromSgroupCopy

public SgroupAtom cloneFromSgroupCopy()
Clones the S-group superatom partially. This method is needed to prevent infinite recursion when cloning from SuperatomSgroup.copy.

Returns:
the clone

copyFromSgroupCopy

protected void copyFromSgroupCopy(CNode node)
Make a copy of this S-group superatom. Clones the S-group superatom partially. This method is needed to prevent infinite recursion when cloning from SuperatomSgroup.copy.

Parameters:
node - the target atom

add

protected void add(CEdge edge)
Add an edge if it had not been already added. Overridden to enable access from other classes of this package.

Overrides:
add in class MolAtom
Parameters:
edge - the edge to add

setNode1

protected static void setNode1(CEdge edge,
                               CNode newnode)
Sets the first node of an edge. Overridden to enable access from other classes of this package.

Parameters:
edge - the edge
newnode - the new node value

setNode2

protected static void setNode2(CEdge edge,
                               CNode newnode)
Sets the second node of an edge. Overridden to enable access from other classes of this package.

Parameters:
edge - the edge
newnode - the new node value

removeAllEdges

protected void removeAllEdges()
Remove all edges.

Overrides:
removeAllEdges in class CNode

countAllAtoms

protected int countAllAtoms()
Counts all atoms represented by this atom.

Overrides:
countAllAtoms in class MolAtom
Returns:
the number of atoms in the S-group