chemaxon.struc.sgroup
Class SgroupAtom

java.lang.Object
  chemaxon.struc.MolAtom
      chemaxon.struc.sgroup.SgroupAtom

All Implemented Interfaces:

CNode, StereoConstants, java.io.Serializable

public class SgroupAtom
extends MolAtom

S-group superatom.

Since:

Marvin 3.0, 11/05/2002

Version:

5.3, 04/27/2009

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

static int	LABEL_AUTO
static int	LABEL_DEFAULT

Fields inherited from class chemaxon.struc.MolAtom

AAMAP_MASK, AAMAP_MAX, AAMAP_OFF, ALIPHATIC, ALL_H, ANY, AROMATIC, AROMATIC_OR_ALIPHATIC, ATOM_TYPE_COUNT, ATOM_TYPE_MAX, ATTACH_BOTH, ATTACH_NONE, ATTACH1, ATTACH2, bondCount, BRIDGEHEAD_H, CHARGED_H, CTSPECIFIC_H, ELEMENT_COUNT, EMPTY, FIX_CHARGE, HCONNECTED_H, HETERO, HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN, ISOTOPE_H, LDIR_ABOVE, LDIR_BELOW, LDIR_LEFT, LDIR_RIGHT, LIST, LONELY_H, LP, MAPPED_H, MULTICENTER, NOTLIST, POLYMERENDGROUP_H, PSEUDO, RAD_COUNT_MASK, RAD_MASK, RAD_OFF, RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3, RAD3_DOUBLET, RAD3_QUARTET, RAD4, RADICAL_CHAR, RADICAL_H, RESSEQ_MAX, RESTYPE_MAX, RGROUP, RGROUP_ATTACHMENT, RGROUP_MAX, RXNSTEREO_INVERSION, RXNSTEREO_NONE, RXNSTEREO_RETENTION, SETSEQ_MAX, SGROUP, SGROUP_H, SGROUPEND_H, SMARTS_H_DAYLIGHT_COMP_MODE, SMARTS_H_MARVIN_COMP_MODE, STAR, SYM_CX, SYM_EXPLH, SYM_IMPLH, SYM_MOLEX, SYM_NEUTRAL, SYM_SMARTS, SYM_SQBRACKETS, theBonds, UNSPECIFIED_AROMATICITY, VALENCE_CHECKED, VALENCE_ERROR, VALENCEERROR_H, WEDGED_H, xCoordinate, yCoordinate, zCoordinate

Fields inherited from interface chemaxon.struc.StereoConstants

ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

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

Method Summary

protected boolean	add(MolBond 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 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.
int	getLabelCenter() Gets the index of the character in the label the bonds should point to.
java.lang.String	getLeftName() Gets the string that will be shown at the left side of the molecule.
java.lang.String	getRightName() Set the string that will be shown at the right side of the molecule.
SuperatomSgroup	getSgroup() Gets the S-group corresponding to this superatom.
java.lang.String	getSymbol() Gets the abbreviated group symbol.
boolean	hasAlternativeName() Checks whether there is an alternative name at all.
protected void	removeAllBonds() Remove all edges.
protected void	removeBond(int i) Removes a bond.
void	set(MolAtom atom) Set properties of this S-group superatom.
protected static void	setAtom1(MolBond edge, MolAtom newnode) Sets the first node of an edge.
protected static void	setAtom2(MolBond edge, MolAtom newnode) Sets the second node of an edge.
protected void	setFromSgroupCopy(SgroupAtom sa) Make a copy of this S-group superatom.
void	setLabelCenter(int k) Sets the index of the character in the label the bonds should point to.
void	setLeftName(java.lang.String s) Set the string that will be shown at the left side of the molecule.
void	setRightName(java.lang.String s) Set the string that will be shown at the right side of the molecule.
void	transform(CTransform3D t, boolean incg) Apply a transformation matrix to the coordinates.

Methods inherited from class chemaxon.struc.MolAtom

addRgroupAttachmentPoint, bondweights, checkAtno, clear, clearExtraLabel, clearProperties, clearQProps, containsPropertyKey, covalentRadiusOf, decQProp, decValenceProp, electronegOf, getAliasstr, getAtno, getAtomicNumber, getAtomMap, getAttach, getAttachParentSgroup, getBicycloStereo, getBond, getBondCount, getBondTo, getCharge, getColumn, getEdge, getEdgeCount, getEdgeTo, getElectronProp, getExplicitHcount, getExtraLabel, getExtraLabelColor, getExtraLabelColor, getExtraLabelColor, getExtraLabelSetSeq, getFlags, getHybridizationState, getImplicitHcount, getLigand, getLigandIndex, getLigandOrder, getLigands, getLinkNodeOuterAtom, getList, getLocation, getLocation, getLock, getLonePairCount, getMass, getMassno, getMaxRepetitions, getMinRepetitions, getNonQueryImplicitHcount, getParent, getPreferredLabelDir, getProperty, getQProp, getQPropAsInt, getQPropMinMax, getQPropNames, getQPropNameSet, getQueryAromaticity, getQueryLabel, getQuerystr, getQueryString, getRadical, getRadicalCount, getReactionStereo, getRealBondCount, getRelativeNegativity, getResidueAtomId, getResidueSeq, getResidueType, getRgroup, getRgroupAttachmentPointOrder, getRow, getSetSeq, getStereoCare, getStereoGroupNumber, getStereoGroupType, getTemporaryObject, getValence, getValenceProp, getValencePropMinMax, getX, getY, getZ, hasAromaticBond, hasQProps, hasQueryBonds, hasSMARTSProps, hasSMARTSPropsExcluding, hasValenceError, hasWedgedBond, haveEqualProperties, haveSimilarBonds, haveSimilarEdges, incQProp, incQueryAromaticity, incValenceProp, indexOf, insideLabel, ionChargeOf, isAmbiguousStereo, isAromaticSMILESSubset, isArrowEnd, isBoundTo, isGeneric, isImplicitizableH, isLinkNode, isMappable, isNobleGas, isotopeType, isPseudo, isQProp, isQuery, isSameParityClass, isSelected, isSpecIsotopeSymbolPreferred, isSpecIsotopeSymbolUsed, isTerminalAtom, maxAbsOxStateOf, moveCorners, nameOf, naturalWeightOf, negOxOf, numOf, numoxstatesOf, oxstateOf, pack, paritySign, posOxOf, propertyCount, propertyKeySet, propertySet, putProperty, qpropCheck, removeBond, removeProperty, residueSymbolOf, residueTypeOf, setAliasstr, setAtno, setAtomMap, setAttach, setAttach, setBicycloStereo, setCharge, setCorners, setElectronProp, setExtraLabel, setExtraLabelColor, setExtraLabelColor, setExtraLabelSetSeq, setFlags, setFlags, setForSpecIsotopeSymbol, setHybridizationState, setImplicitHBasedOnValence, setImplicitHcount, setLigandOrder, setLinkNodeDefaultOuters, setLinkNodeOuterAtom, setList, setList, setLocation, setMassno, setMassnoIfKnown, setMaxRepetitions, setMinRepetitions, setNonQueryImplicitHcount, setQProp, setQProp, setQueryAromaticity, setQuerystr, setQuerystr, setQueryString, setRadical, setReactionStereo, setResidueAtomId, setResidueSeq, setResidueType, setRgroup, setRgroupAttachmentPointOrder, setSelected, setSetSeq, setSMARTS, setSpecIsotopeSymbolPreferred, setStereoGroupNumber, setStereoGroupType, setValenceError, setValenceProp, setX, setXY, setXYZ, setY, setZ, sringsize, storeTemporaryObject, symbolOf, symbolOf, toString, twicesumbonds, valenceCheck, valenceCheck

Methods inherited from class java.lang.Object

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

Field Detail

LABEL_DEFAULT

public static final int LABEL_DEFAULT

See Also:

Constant Field Values

LABEL_AUTO

public static final int LABEL_AUTO

See Also:

Constant Field Values

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 name with the numbers subscripted

See Also:

MolAtom.SYM_SQBRACKETS, MolAtom.SYM_IMPLH, MolAtom.SYM_EXPLH, MolAtom.SYM_NEUTRAL, MolAtom.SYM_SMARTS, MolAtom.SYM_MOLEX

clone

public java.lang.Object clone()

Clones the S-group superatom.

Overrides:

clone in class MolAtom

Returns:

the clone

set

public void set(MolAtom atom)

Set properties of this S-group superatom.

Overrides:

set in class MolAtom

Parameters:

atom - the target atom

Since:

Marvin 4.1, 01/01/2006

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

transform

public void transform(CTransform3D t,
                      boolean incg)

Apply a transformation matrix to the coordinates.

Overrides:

transform in class MolAtom

Parameters:

t - the transformation matrix

incg - graph invariants are changed (true) or not (false)

Since:

Marvin 4.0.2, 10/26/2005

getSymbol

public java.lang.String getSymbol()

Gets the abbreviated group symbol.

Overrides:

getSymbol in class MolAtom

Returns:

the symbol

getLeftName

public java.lang.String getLeftName()

Gets the string that will be shown at the left side of the molecule.

Returns:

the left name string

Since:

Marvin 4.1

setLeftName

public void setLeftName(java.lang.String s)

Set the string that will be shown at the left side of the molecule.

Parameters:

s -

Since:

Marvin 4.1

getRightName

public java.lang.String getRightName()

Set the string that will be shown at the right side of the molecule.

Since:

Marvin 4.1

setRightName

public void setRightName(java.lang.String s)

Set the string that will be shown at the right side of the molecule.

Parameters:

s -

Since:

Marvin 4.1

hasAlternativeName

public boolean hasAlternativeName()

Checks whether there is an alternative name at all.

Returns:

true if an alternative name is available for the (s)group

Since:

Marvin 4.1

getLabelCenter

public int getLabelCenter()

Gets the index of the character in the label the bonds should point to.

Returns:

character index + 1, or LABEL_DEFAULT for default behavior (geometrical center unless alternative name is specified), or LABEL_AUTO for automatic calculation

Since:

Marvin 4.1

setLabelCenter

public void setLabelCenter(int k)

Sets the index of the character in the label the bonds should point to.

Parameters:

k - character index + 1, or LABEL_DEFAULT for default behavior (geometrical center unless alternative name is specified), or LABEL_AUTO for automatic calculation

Since:

Marvin 4.1

setFromSgroupCopy

protected void setFromSgroupCopy(SgroupAtom sa)

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:

sa - the target atom

Since:

Marvin 4.1, 01/01/2006

add

protected boolean add(MolBond 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

Throws:

NoFreeAttachmentPointException - if there is no free attachment point for the given edge.

removeBond

protected void removeBond(int i)

Removes a bond.

Overrides:

removeBond in class MolAtom

Parameters:

i - bond index

setAtom1

protected static void setAtom1(MolBond edge,
                               MolAtom 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

setAtom2

protected static void setAtom2(MolBond edge,
                               MolAtom 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

removeAllBonds

protected void removeAllBonds()

Remove all edges.

Overrides:

removeAllBonds in class MolAtom

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