Package chemaxon.struc.sgroup
Class SgroupAtom
java.lang.Object
chemaxon.struc.MolAtom
chemaxon.struc.sgroup.SgroupAtom
- All Implemented Interfaces:
StereoConstants
,Serializable
S-group superatom.
- Since:
- Marvin 3.0, 11/05/2002
- See Also:
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Field Summary
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
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Constructor Summary
ConstructorDescriptionConstructs a superatom for a superatom type S-group. -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
Add an edge if it had not been already added.protected boolean
Add an edge to the given atom of the sgroup, if it had not been already added.clone()
Clones the S-group superatom and it'sSuperatomSgroup
as well.Clones the S-group superatom partially.protected int
Counts all atoms represented by this atom.getAtomSymbol
(int style, int flags, int[] lcenter, CTransform3D preTransform) Gets the string representation of the atom symbol.int
Returns the sum of the charges in the corresponding superatom s-group.int
Gets the index of the character in the label the bonds should point to.Gets the string that will be shown at the left side of the molecule.Set the string that will be shown at the right side of the molecule.Gets the S-group corresponding to this superatom.Gets the abbreviated group symbol.boolean
Checks whether there is an alternative name at all.boolean
Checks if any atom of the Sgroup has a valence error.int
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
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 properties of this S-group superatom.protected static void
Sets the first node of an edge.protected static void
Sets the second node of an edge.protected void
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
Set the string that will be shown at the left side of the molecule.void
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
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Field Details
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LABEL_DEFAULT
public static final int LABEL_DEFAULT- See Also:
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LABEL_AUTO
public static final int LABEL_AUTO- See Also:
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Constructor Details
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SgroupAtom
Constructs a superatom for a superatom type S-group.- Parameters:
sg
- the S-group
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Method Details
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getSgroup
Gets the S-group corresponding to this superatom.- Returns:
- the S-group
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getAtomSymbol
Gets the string representation of the atom symbol.- Overrides:
getAtomSymbol
in classMolAtom
- Parameters:
style
- neglectedflags
- neglectedpreTransform
- neglectedlcenter
- neglected- Returns:
- the S-group name with the numbers subscripted
- See Also:
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clone
Clones the S-group superatom and it'sSuperatomSgroup
as well. -
set
Set properties of this S-group superatom. -
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
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transform
Apply a transformation matrix to the coordinates. -
getSymbol
Gets the abbreviated group symbol. -
getLeftName
Gets the string that will be shown at the left side of the molecule.- Returns:
- the left name string
- Since:
- Marvin 4.1
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setLeftName
Set the string that will be shown at the left side of the molecule.- Since:
- Marvin 4.1
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getRightName
Set the string that will be shown at the right side of the molecule.- Since:
- Marvin 4.1
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setRightName
Set the string that will be shown at the right side of the molecule.- Since:
- Marvin 4.1
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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
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hasValenceError
public boolean hasValenceError()Checks if any atom of the Sgroup has a valence error.- Overrides:
hasValenceError
in classMolAtom
- Returns:
- true if at least one atom of this Sgroup has a valence error
- See Also:
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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), orLABEL_AUTO
for automatic calculation - Since:
- Marvin 4.1
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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, orLABEL_DEFAULT
for default behavior (geometrical center unless alternative name is specified), orLABEL_AUTO
for automatic calculation- Since:
- Marvin 4.1
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setFromSgroupCopy
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
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add
Add an edge if it had not been already added. Overridden to enable access from other classes of this package. -
add
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.
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removeBond
protected void removeBond(int i, boolean clearFromAttachmentPoints) Removes a bond.- Overrides:
removeBond
in classMolAtom
- Parameters:
i
- bond index
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removeBond
Removes a bond by reference.- Overrides:
removeBond
in classMolAtom
- Parameters:
bond
- bond reference to remove
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insertBond
Description copied from class:MolAtom
Inserts a bond at a specified index.- Overrides:
insertBond
in classMolAtom
- Parameters:
index
- the index where to insert the bondbond
- the bond reference to insert
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setAtom1
Sets the first node of an edge. Overridden to enable access from other classes of this package.- Parameters:
edge
- the edgenewnode
- the new node value
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setAtom2
Sets the second node of an edge. Overridden to enable access from other classes of this package.- Parameters:
edge
- the edgenewnode
- the new node value
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removeAllBonds
protected void removeAllBonds()Remove all edges.- Overrides:
removeAllBonds
in classMolAtom
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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 classMolAtom
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countAllAtoms
protected int countAllAtoms()Counts all atoms represented by this atom.- Overrides:
countAllAtoms
in classMolAtom
- Returns:
- the number of atoms in the S-group
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getCharge
public int getCharge()Returns the sum of the charges in the corresponding superatom s-group. -
indexOf
Returns the index of the specified bond in this atom. This method uses==
for the bond comparison.
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