Package org.openscience.cdk.stereo
Class TetrahedralChirality
java.lang.Object
org.openscience.cdk.stereo.TetrahedralChirality
- All Implemented Interfaces:
Cloneable
,ICDKObject
,IStereoElement<IAtom,
,IAtom> ITetrahedralChirality
Stereochemistry specification for tetravalent atoms. See
ITetrahedralChirality
for
further details.- See Also:
- Source code:
- main
- Belongs to CDK module:
- core
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.ITetrahedralChirality
ITetrahedralChirality.Stereo
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected static final int
protected static final int
protected static final int
protected static final int
protected static final int
protected static final int
Fields inherited from interface org.openscience.cdk.interfaces.IStereoElement
AL, Allenal, AT, Atropisomeric, CFG_MASK, CisTrans, CLS_MASK, CT, CU, Cumulene, GRP_ABS, GRP_MASK, GRP_NUM_MASK, GRP_NUM_SHIFT, GRP_RAC, GRP_RAC1, GRP_RAC2, GRP_RAC3, GRP_RAC4, GRP_RAC5, GRP_REL, GRP_REL1, GRP_REL2, GRP_REL3, GRP_REL4, GRP_REL5, GRP_TYPE_MASK, HBPY8, HBPY9, HeptagonalBipyramidal, HexagonalBipyramidal, LEFT, OC, Octahedral, OPPOSITE, PBPY, PentagonalBipyramidal, RIGHT, SP, SP4, SPU, SPY, SPZ, SquarePlanar, SquarePyramidal, TBPY, Tetrahedral, TH, TOGETHER, TrigonalBipyramidal
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Constructor Summary
ConstructorsConstructorDescriptionTetrahedralChirality
(IAtom chiralAtom, IAtom[] ligands, int config) TetrahedralChirality
(IAtom chiralAtom, IAtom[] ligands, ITetrahedralChirality.Stereo stereo) -
Method Summary
Modifier and TypeMethodDescriptionboolean
Does the stereo element contain the provided atom.protected IStereoElement<IAtom,
IAtom> Returns aIChemObjectBuilder
for the data classes that extend this class.The carriers of the stereochemistryAtom that is the chirality center.int
Access the configuration order and class of the stereochemistry.int
The configuration class of the stereochemistry.int
The configuration order of the stereochemistry.getFocus()
The focus atom or bond at the 'centre' of the stereo-configuration.int
Access the stereo group information - see class doc.IAtom[]
Returns an array of ligand atoms around the chiral atom.Defines the stereochemistry around the chiral atom.protected static <T> T[]
invapply
(T[] src, int[] perm) Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.map
(Map<IChemObject, IChemObject> chemobjs) Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.final IStereoElement<IAtom,
IAtom> mapStrict
(Map<IChemObject, IChemObject> chemobjs) Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.protected static int
numCarriers
(int cfg) void
setBuilder
(IChemObjectBuilder builder) void
setConfigOrder
(int cfg) Set the configuration order of the stereochemistry.void
setGroupInfo
(int grp) Set the stereo group information - see class doc.void
Set the stereochemistry of this tetrahedral centre.toString()
Returns aString
representation of this chiral element.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
Methods inherited from interface org.openscience.cdk.interfaces.IStereoElement
contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, mapStrict, setConfigOrder, setGroupInfo
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Field Details
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A
protected static final int A- See Also:
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B
protected static final int B- See Also:
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C
protected static final int C- See Also:
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D
protected static final int D- See Also:
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E
protected static final int E- See Also:
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F
protected static final int F- See Also:
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Constructor Details
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TetrahedralChirality
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TetrahedralChirality
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Method Details
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getLigands
Description copied from interface:ITetrahedralChirality
Returns an array of ligand atoms around the chiral atom. If the chiral centre has an implicit hydrogen or lone pair one of the ligands will be the chiral atom (ITetrahedralChirality.getChiralAtom()
).- Specified by:
getLigands
in interfaceITetrahedralChirality
- Returns:
- an array of four
IAtom
s.
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getChiralAtom
Description copied from interface:ITetrahedralChirality
Atom that is the chirality center.- Specified by:
getChiralAtom
in interfaceITetrahedralChirality
- Returns:
- the chiral
IAtom
.
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getStereo
Description copied from interface:ITetrahedralChirality
Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.- Specified by:
getStereo
in interfaceITetrahedralChirality
- Returns:
- the
ITetrahedralChirality.Stereo
for this stereo element.
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setStereo
Description copied from interface:ITetrahedralChirality
Set the stereochemistry of this tetrahedral centre.- Specified by:
setStereo
in interfaceITetrahedralChirality
- Parameters:
stereo
- the new stereo assignment
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create
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map
Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond it is left intact. However the provided atom and bonds maps must not be null.- Specified by:
map
in interfaceIStereoElement<IAtom,
IAtom> - Specified by:
map
in interfaceITetrahedralChirality
- Parameters:
atoms
- used to convert the original atoms to their mapped counterpartsbonds
- used to convert the original bonds to their mapped counterparts- Returns:
- a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
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map
Description copied from interface:IStereoElement
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond the existing atom/bond it is left intact. If you want to remove stereo in such cases please useIStereoElement.mapStrict(java.util.Map<org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObject>)
.- Specified by:
map
in interfaceIStereoElement<IAtom,
IAtom> - Parameters:
chemobjs
- chem object mapping- Returns:
- a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
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setBuilder
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toString
Returns aString
representation of this chiral element. -
numCarriers
protected static int numCarriers(int cfg) -
getFocus
The focus atom or bond at the 'centre' of the stereo-configuration.- Specified by:
getFocus
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- the focus
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getCarriers
The carriers of the stereochemistry- Specified by:
getCarriers
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- the carriers
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getConfigClass
public int getConfigClass()The configuration class of the stereochemistry.- Specified by:
getConfigClass
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- configuration class
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getConfigOrder
public int getConfigOrder()The configuration order of the stereochemistry.- Specified by:
getConfigOrder
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- configuration
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getConfig
public int getConfig()Access the configuration order and class of the stereochemistry.- Specified by:
getConfig
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- the configuration
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setConfigOrder
public void setConfigOrder(int cfg) Set the configuration order of the stereochemistry.- Specified by:
setConfigOrder
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Parameters:
cfg
- the new configuration
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getGroupInfo
public int getGroupInfo()Access the stereo group information - see class doc.- Specified by:
getGroupInfo
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Returns:
- the group info
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setGroupInfo
public void setGroupInfo(int grp) Set the stereo group information - see class doc.- Specified by:
setGroupInfo
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Parameters:
grp
- the group info
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contains
Does the stereo element contain the provided atom.- Specified by:
contains
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Parameters:
atom
- an atom to test membership- Returns:
- whether the atom is present
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mapStrict
Description copied from interface:IStereoElement
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond a new element is NOT created.- Specified by:
mapStrict
in interfaceIStereoElement<F extends IChemObject,
C extends IChemObject> - Parameters:
chemobjs
- chem object mapping- Returns:
- a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
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getBuilder
Returns aIChemObjectBuilder
for the data classes that extend this class.- Specified by:
getBuilder
in interfaceICDKObject
- Returns:
- The
IChemObjectBuilder
matching thisICDKObject
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invapply
protected static <T> T[] invapply(T[] src, int[] perm)
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