SquarePlanar (cdk 2.5 API)

java.lang.Object
- org.openscience.cdk.stereo.SquarePlanar

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IAtom,IAtom>
```
public final class SquarePlanar
extends Object
```
Describes square planar configuration. The configuration around a square planar is described by 3 possible values (1:U, 2:4, or 3:Z) based on the ordering of the planar carries around the focus:
```
 Configurations:

     a                a                a
     |                |                |
  d--f--b = U      c--f--d = 4      b--f--c = Z
     |                |                |
     c                b                d

    SP1              SP2              SP3
 
```
cis-platin can be represented as any of the following:
```
 [NH3][Pt@SP1]([NH3])(Cl)Cl
 [NH3][Pt@SP3]([NH3])(Cl)Cl
 [NH3][Pt@SP2](Cl)([NH3])Cl
 [NH3][Pt@SP1](Cl)(Cl)[NH3]
 
```
trans-platin can be represented as any of the following:
```
 [NH3][Pt@SP2]([NH3])(Cl)Cl
 [NH3][Pt@SP1](Cl)([NH3])Cl
 [NH3][Pt@SP1](Cl)([NH3])Cl
 [NH3][Pt@SP3](Cl)(Cl)[NH3]
 
```
The normalize function (normalize()) create a new
```
IStereoElement
```
where the carriers have been reorder such that the configuration is in a U shape (order=1).
See Also:

Square Planar Centers, OpenSMILES, TrigonalBipyramidal, Octahedral

Field Summary

Fields
Modifier and Type	Field and Description
`protected static int`	`A`
`protected static int`	`B`
`protected static int`	`C`
`protected static int`	`D`
`protected static int`	`E`
`protected static int`	`F`

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

Constructor Summary

Constructors
Constructor and Description

SquarePlanar(IAtom focus, IAtom[] carriers, int order)
Create a square-planar configuration around a provided focus atom.

Constructors
Constructor and Description
`SquarePlanar(IAtom focus, IAtom[] carriers, int order)` Create a square-planar configuration around a provided focus atom.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`contains(IAtom atom)` Does the stereo element contain the provided atom.
`protected SquarePlanar`	`create(IAtom focus, List<IAtom> carriers, int cfg)`
`IChemObjectBuilder`	`getBuilder()` Returns a `IChemObjectBuilder` for the data classes that extend this class.
`List<C>`	`getCarriers()` The carriers of the stereochemistry
`int`	`getConfig()` Access the configuration order and class of the stereochemistry.
`int`	`getConfigClass()` The configuration class of the stereochemistry.
`int`	`getConfigOrder()` The configuration order of the stereochemistry.
`F`	`getFocus()` The focus atom or bond at the 'centre' of the stereo-configuration.
`int`	`getGroupInfo()` Access the stereo group information - see class doc.
`protected static <T> T[]`	`invapply(T[] src, int[] perm)`
`IStereoElement<F,C>`	`map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)` Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
`IStereoElement<F,C>`	`map(Map<IChemObject,IChemObject> chemobjs)`
`SquarePlanar`	`normalize()` Normalize the configuration to the lowest configuration order (1) - U-shaped.
`protected static int`	`numCarriers(int cfg)`
`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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - A
```
protected static final int A
```
    See Also:
    
    Constant Field Values
  - B
```
protected static final int B
```
    See Also:
    
    Constant Field Values
  - C
```
protected static final int C
```
    See Also:
    
    Constant Field Values
  - D
```
protected static final int D
```
    See Also:
    
    Constant Field Values
  - E
```
protected static final int E
```
    See Also:
    
    Constant Field Values
  - F
```
protected static final int F
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SquarePlanar
```
public SquarePlanar(IAtom focus,
                    IAtom[] carriers,
                    int order)
```
    Create a square-planar configuration around a provided focus atom. The carriers are flat in the plane and their arrangement is either, U-shape, 4-shape, or Z-shape.
    
    Parameters:
    
    focus - the focus
    
    carriers - the carriers
    
    order - the configuration order, 1-3
- Method Detail
  - normalize
```
public SquarePlanar normalize()
```
    Normalize the configuration to the lowest configuration order (1) - U-shaped.
    
    Returns:
    
    the normalized configuration
  - create
```
protected SquarePlanar create(IAtom focus,
                              List<IAtom> carriers,
                              int cfg)
```
  - numCarriers
```
protected static int numCarriers(int cfg)
```
  - getFocus
```
public F getFocus()
```
    The focus atom or bond at the 'centre' of the stereo-configuration.
    
    Specified by:
    
    getFocus in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the focus
  - getCarriers
```
public List<C> getCarriers()
```
    The carriers of the stereochemistry
    
    Specified by:
    
    getCarriers in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the carriers
  - getConfigClass
```
public int getConfigClass()
```
    The configuration class of the stereochemistry.
    
    Specified by:
    
    getConfigClass in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    configuration class
  - getConfigOrder
```
public int getConfigOrder()
```
    The configuration order of the stereochemistry.
    
    Specified by:
    
    getConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    configuration
  - getConfig
```
public int getConfig()
```
    Access the configuration order and class of the stereochemistry.
    
    Specified by:
    
    getConfig in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the configuration
  - setConfigOrder
```
public void setConfigOrder(int cfg)
```
    Set the configuration order of the stereochemistry.
    
    Specified by:
    
    setConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    cfg - the new configuration
  - getGroupInfo
```
public int getGroupInfo()
```
    Access the stereo group information - see class doc.
    
    Specified by:
    
    getGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the group info
  - setGroupInfo
```
public void setGroupInfo(int grp)
```
    Set the stereo group information - see class doc.
    
    Specified by:
    
    setGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    grp - the group info
  - contains
```
public boolean contains(IAtom atom)
```
    Does the stereo element contain the provided atom.
    
    Specified by:
    
    contains in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    atom - an atom to test membership
    
    Returns:
    
    whether the atom is present
  - map
```
public IStereoElement<F,C> map(Map<IAtom,IAtom> atoms,
                               Map<IBond,IBond> bonds)
```
    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 interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    atoms - nullable atom mapping, used to convert the original atoms to their mapped counterparts
    
    bonds - nullable bond mapping, 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.
  - map
```
public IStereoElement<F,C> map(Map<IChemObject,IChemObject> chemobjs)
```
    Specified by:
    
    map in interface IStereoElement<F extends IChemObject,C extends IChemObject>
  - getBuilder
```
public IChemObjectBuilder getBuilder()
```
    Returns a IChemObjectBuilder for the data classes that extend this class.
    
    Specified by:
    
    getBuilder in interface ICDKObject
    
    Returns:
    
    The IChemObjectBuilder matching this ICDKObject
  - setBuilder
```
protected void setBuilder(IChemObjectBuilder builder)
```
  - invapply
```
protected static <T> T[] invapply(T[] src,
                                  int[] perm)
```

Class SquarePlanar

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IStereoElement

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

A

B

C

D

E

F

Constructor Detail

SquarePlanar

Method Detail

normalize

create

numCarriers

getFocus

getCarriers

getConfigClass

getConfigOrder

getConfig

setConfigOrder

getGroupInfo

setGroupInfo

contains

map

map

getBuilder

setBuilder

invapply