Package org.openscience.cdk.stereo
Class ExtendedTetrahedral
java.lang.Object
org.openscience.cdk.stereo.ExtendedTetrahedral
- All Implemented Interfaces:
Cloneable
,ICDKObject
,IStereoElement<IAtom,
IAtom>
Extended tetrahedral configuration. Defines the winding configuration in
a system with an even number of cumulated pi bonds. Examples include,
(R)-laballenic acid (CHEBI:38401) and (S)-laballenic acid (CHEBI:38402).
The extended tetrahedral stereochemistry can be represented and handled the
same as normal tetrahedral stereochemistry. However the handling of the
neighbours is subtly different. To assist in the description here are how
atoms are referred to.
p0 p2 p<i>: periphals
\ / t<i>: terminals
t0 = f = t1 f: focus
/ \
p1 p3
The data structure stores, the central 'focus' atom and the four peripheral
atoms. The peripheral atoms are stored in a single array, {p0, p1,
p2, p3}
, the first two and last two entries should be attached to the same
terminal atom (t0 or t1). For convenience the terminal atoms can be found with
findTerminalAtoms(IAtomContainer)
.
p0 p2 p0 p2
\ / \ /
t0 = f = t1 --> c c: t0/f/t1
/ \ / \
p1 p3 p1 p3
The configuration treats the focus and terminal atoms as a single atom, the
neighbours {p1, p2, p3}
then proceeded either clockwise or
anti-clockwise when the centre (t0/f/t1) is viewed from the first peripheral
atom p0
.
If any of the peripherals are implicit hydrogen atoms, then the terminal atom
to which the hydrogen is attached can be used as a placeholder.- Author:
- John May
- Keywords:
- extended tetrahedral, allene, axial chirality
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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
ConstructorsConstructorDescriptionExtendedTetrahedral
(IAtom focus, IAtom[] peripherals, int config) ExtendedTetrahedral
(IAtom focus, IAtom[] peripherals, ITetrahedralChirality.Stereo winding) Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'. -
Method Summary
Modifier and TypeMethodDescriptionboolean
Does the stereo element contain the provided atom.protected IStereoElement<IAtom,
IAtom> IAtom[]
findTerminalAtoms
(IAtomContainer container) Helper method to locate two terminal atoms in a container for this extended tetrahedral element.static IAtom[]
findTerminalAtoms
(IAtomContainer container, IAtom focus) Helper method to locate two terminal atoms in a container for a given focus.focus()
The central atom in the cumulated system.Returns aIChemObjectBuilder
for the data classes that extend this class.The carriers of the stereochemistryint
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.static int
getLength
(IAtomContainer container, IAtom focus) 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) IAtom[]
The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.protected 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.winding()
The winding of the peripherals, when viewed from the first atom.
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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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ExtendedTetrahedral
Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'. See class documentation an annotated storage description.- Parameters:
focus
- the central cumulated atomperipherals
- atoms attached to the terminal atomswinding
- the configuration
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ExtendedTetrahedral
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Method Details
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focus
The central atom in the cumulated system.- Returns:
- the focus
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peripherals
The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.- Returns:
- the peripheral atoms
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winding
The winding of the peripherals, when viewed from the first atom.- Returns:
- winding configuration
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findTerminalAtoms
Helper method to locate two terminal atoms in a container for a given focus.- Parameters:
container
- structure representationfocus
- cumulated atom- Returns:
- the terminal atoms (unordered)
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findTerminalAtoms
Helper method to locate two terminal atoms in a container for this extended tetrahedral element. The atoms are ordered such that the first index is attached to the first two peripheral atoms and the second index is attached to the second two peripheral atoms.- Parameters:
container
- structure representation- Returns:
- the terminal atoms (ordered)
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getLength
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create
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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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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<F extends IChemObject,
C extends IChemObject> - 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<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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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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setBuilder
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invapply
protected static <T> T[] invapply(T[] src, int[] perm)
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