Package chemaxon.struc.sgroup

Class SgroupAtom

java.lang.Object

chemaxon.struc.MolAtom

chemaxon.struc.sgroup.SgroupAtom

All Implemented Interfaces:

StereoConstants, Serializable

@PublicAPI
public class SgroupAtom
extends MolAtom

S-group superatom.

Since:

Marvin 3.0, 11/05/2002

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static int	LABEL_AUTO
static int	LABEL_DEFAULT

Fields inherited from class chemaxon.struc.MolAtom

AAMAP_MASK, AAMAP_MAX, AAMAP_OFF, ALIPHATIC, ALL_H, ANGLE_STEP, ANY, AROMATIC, AROMATIC_OR_ALIPHATIC, ATOM_TYPE_COUNT, ATOM_TYPE_MAX, ATTACH_BOTH, ATTACH_NONE, ATTACH_UNKNOWN, ATTACH1, ATTACH2, bondCount, BRIDGEHEAD_H, CHARGED_H, CTSPECIFIC_H, ELEMENT_COUNT, EMPTY, FIX_CHARGE, HBONDED_H, 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, METALCONNECTED_H, MULTICENTER, NOTLIST, OMIT_POSTCLEAN, 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_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected boolean	add(MolBond edge)	Add an edge if it had not been already added.
protected boolean	add(MolBond edge, MolAtom atom)	Add an edge to the given atom of the sgroup, if it had not been already added.
SgroupAtom	clone()	Clones the S-group superatom and it's SuperatomSgroup as well.
SgroupAtom	cloneFromSgroupCopy()	Clones the S-group superatom partially.
protected int	countAllAtoms()	Counts all atoms represented by this atom.
String	getAtomSymbol(int style, int flags, int[] lcenter, CTransform3D preTransform)	Gets the string representation of the atom symbol.
int	getCharge()	Returns the sum of the charges in the corresponding superatom s-group.
int	getLabelCenter()	Gets the index of the character in the label the bonds should point to.
String	getLeftName()	Gets the string that will be shown at the left side of the molecule.
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.
String	getSymbol()	Gets the abbreviated group symbol.
boolean	hasAlternativeName()	Checks whether there is an alternative name at all.
boolean	hasValenceError()	Checks if any atom of the Sgroup has a valence error.
int	indexOf(MolBond bond)	Returns the index of the specified bond in this atom.
protected void	insertBond(int index, MolBond bond)	Inserts a bond at a specified index.
protected void	removeAllBonds()	Remove all edges.
protected void	removeAllBonds(boolean clearFromAttachmentPoints)	Removes all edges.
protected void	removeBond(int i, boolean clearFromAttachmentPoints)	Removes a bond.
protected void	removeBond(MolBond bond, boolean clearFromAttachmentPoints)	Removes a bond by reference.
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(String s)	Set the string that will be shown at the left side of the molecule.
void	setRightName(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, bonds, bondweights, checkAtno, clear, clearExtraLabel, clearProperties, clearQProps, containsPropertyKey, covalentRadiusOf, decQProp, decValenceProp, electronegOf, getAliasstr, getAtno, getAtomicNumber, getAtomMap, getAttach, getAttachFromExtraAtomProp, getAttachParentSgroup, getBicycloStereo, getBond, getBondArray, getBondCount, getBondTo, getChargeAngle, getColumn, getElectronProp, getExplicitHcount, getExtraLabel, getExtraLabelColor, getExtraLabelColor, getExtraLabelColor, getExtraLabelSetSeq, getFlags, getHybridizationState, getImplicitHcount, 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, getRadicalValue, getReactionStereo, getRealBondCount, getRelativeNegativity, getResidueAtomId, getResidueSeq, getResidueType, getRgroup, getRgroupAttachmentPointOrder, getRow, getSetSeq, getStereoCare, getStereoGroupNumber, getStereoGroupType, getTemporaryObject, getValence, getValenceProp, getValencePropMinMax, getX, getY, getZ, hasAromaticBond, hasCharge, hasQProps, hasQueryBonds, hasSameCharge, hasSMARTSProps, hasSMARTSPropsExcluding, hasWedgedBond, haveEqualProperties, haveSimilarBonds, incQProp, incQueryAromaticity, incValenceProp, indexOfReferenced, insideLabel, ionChargeOf, isAmbiguousStereo, isAromaticSMILESSubset, isBoundTo, isChargeAngleSet, isGeneric, isImplicitizableH, isLinkNode, isMappable, isotopeType, isPlainHydrogen, isPseudo, isQProp, isQuery, isSameParityClass, isSelected, isSpecIsotopeSymbolPreferred, isSpecIsotopeSymbolUsed, isTerminalAtom, ligands, maxAbsOxStateOf, moveCorners, nameOf, naturalWeightOf, negOxOf, numOf, numoxstatesOf, oxstateOf, pack, paritySign, posOxOf, propertyCount, propertyKeySet, propertySet, putProperty, qpropCheck, removeBond, removeBond, removeProperty, residueSymbolOf, residueTypeOf, setAliasstr, setAtno, setAtomMap, setAttach, setAttach, setAttachParentSgroup, setBicycloStereo, setCharge, setChargeAngle, setCorners, setElectronProp, setExtraLabel, setExtraLabelColor, setExtraLabelColor, setExtraLabelSetSeq, setFlags, setFlags, setForSpecIsotopeSymbol, setHybridizationState, setImplicitHBasedOnValence, setImplicitHcount, setIsValenceCheckNeeded, setLigandOrder, setLinkNodeDefaultOuters, setLinkNodeOuterAtom, setList, setList, setLocation, setMassno, setMaxRepetitions, setMinRepetitions, setNonQueryImplicitHcount, setQProp, setQProp, setQueryAromaticity, setQuerystr, setQuerystr, setQueryString, setRadical, setRadicalValue, 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

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 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 SgroupAtom clone()

Clones the S-group superatom and it's SuperatomSgroup as well.

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. Use it only for this purpose.

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 String getSymbol()

Gets the abbreviated group symbol.

Overrides:

getSymbol in class MolAtom

Returns:

the symbol

getLeftName

public 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(String s)

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

Parameters:

s -

Since:

Marvin 4.1

getRightName

public String getRightName()

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

Since:

Marvin 4.1

setRightName

public void setRightName(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

hasValenceError

public boolean hasValenceError()

Checks if any atom of the Sgroup has a valence error.

Overrides:

hasValenceError in class MolAtom

Returns:

true if at least one atom of this Sgroup has a valence error

See Also:

MolAtom.valenceCheck()

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

Returns:

true if valence check needed

Throws:

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

add

protected boolean add(MolBond edge,
                      MolAtom atom)

Add an edge to the given atom of the sgroup, if it had not been already added.

Parameters:

edge - the edge to add

Throws:

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

removeBond

protected void removeBond(int i,
                          boolean clearFromAttachmentPoints)

Removes a bond.

Overrides:

removeBond in class MolAtom

Parameters:

i - bond index

removeBond

protected void removeBond(MolBond bond,
                          boolean clearFromAttachmentPoints)

Removes a bond by reference.

Overrides:

removeBond in class MolAtom

Parameters:

bond - bond reference to remove

insertBond

protected void insertBond(int index,
                          MolBond bond)

Description copied from class: MolAtom

Inserts a bond at a specified index.

Overrides:

insertBond in class MolAtom

Parameters:

index - the index where to insert the bond

bond - the bond reference to insert

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

removeAllBonds

protected void removeAllBonds(boolean clearFromAttachmentPoints)

Removes all edges. If the parameter clearFromAttachmentPoints is true, then the bonds are cleared from the SgroupAtoms's s-group's attachment points

Overrides:

removeAllBonds in class MolAtom

Parameters:

clearFromAttachmentPoints -

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

getCharge

public int getCharge()

Returns the sum of the charges in the corresponding superatom s-group.

Overrides:

getCharge in class MolAtom

Returns:

the charge

Since:

Marvin 6.1, 2013.05.21.

indexOf

public int indexOf(MolBond bond)

Returns the index of the specified bond in this atom. This method uses == for the bond comparison.

Overrides:

indexOf in class MolAtom

Parameters:

bond - bond reference

Returns:

the bond index, or -1 if it not found

Since:

Marvin 6.1, 2013.06.23.

See Also:

Object.equals(Object)