chemaxon.struc.sgroup
Class SgroupAtom

java.lang.Object
  chemaxon.struc.CNode
      chemaxon.struc.MolAtom
          chemaxon.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