OBStereo Class Reference

#include <openbabel/stereo/stereo.h>

Public Types
enum	Type {   CisTrans = (1<<0), ExtendedCisTrans = (1<<1), SquarePlanar = (1<<2), Tetrahedral = (1<<3),   ExtendedTetrahedral = (1<<4), TrigonalBipyramidal = (1<<5), Octahedral = (1<<6) }
enum	BondDirection { NotStereo = 0, UpBond = 1, DownBond = 6, UnknownDir = 4 }
enum	Shape { ShapeU = 1, ShapeZ = 2, Shape4 = 3 }
enum	View { ViewFrom = 1, ViewTowards = 2 }
enum	Winding { Clockwise = 1, AntiClockwise = 2, UnknownWinding = 3 }
Ref & Refs types
enum	{ NoRef = UINT_MAX, ImplicitRef = UINT_MAX - 1 }
typedef unsigned long	Ref
typedef std::vector< Ref >	Refs
typedef Refs::iterator	RefIter
typedef Refs::const_iterator	ConstRefIter

Static Public Member Functions
Refs utility functions
static Refs	MakeRefs (Ref ref1, Ref ref2, Ref ref3, Ref ref4=NoRef)
static bool	ContainsSameRefs (const Refs &refs1, const Refs &refs2)
static bool	ContainsRef (const Refs &refs, unsigned long ref)
Low-level functions used by implementation.
static int	NumInversions (const Refs &refs)
static void	Permutate (Refs &refs, unsigned int i, unsigned int j)
static Refs	Permutated (const Refs &refs, unsigned int i, unsigned int j)

Detailed Description

Placeholder for enums & Ref/Refs related functions.

The OBStereo struct contains a number of enums with predefined values. These are OBStereo::BondDirection, OBStereo::Type, OBStereo::Shape, OBStereo::View, OBStereo::Winding. There are enums which only apply to certain types of stereochemistry but having them in 1 place makes it easier to remember.

The OBStereo struct also contains typedefs and functions which are crucial to fully understand how to use the OBStereoBase derived classes (i.e. OBTetrahedralStereo, OBCisTransStereo, ...). Ref variables and Refs lists are a way to uniquely reference atoms in the molecule. In most cases these Ref variables are the same as the unique atom ids (OBAtom::GetId). However, 2 special cases are provided:

• OBStereo::NoRef: An initial value for Ref variables. The constructors of the various Config structs set all refs to NoRef (Refs lists will remain empty). This value is considered invalid when comparing stereochemistry.
• OBStereo::ImplicitRef: Can be used to replace implicit hydrogen ids. Even with explicit hydrogens, it is still valid to replace the Ref of the hydrogen with ImplicitRef. This flexibility also applies to comparing stereochemistry. It is possible to compare stereochemistry (e.g. OBTetrahedral::Config::operator==) between a Config struct with an ImplicitRef and a Config struct where the Ref is the atom id of the explicit hydrogen. See actual documentation for details about operator==.

There are utility functions which make it easier to handle Refs. The most frequently used one is OBStereo::MakeRefs to create lists containing 3 or 4 Ref values. Formats and library use normally doesn't need the other functions.

See also

OBStereoBase OBStereoFacade

Since

version 2.3

Member Typedef Documentation

Ref

typedef unsigned long Ref

All stereo classes work with variables of the type Ref to uniquely identify atoms. In most cases these Ref variables are the same as the unique atom ids.

See also

OBAtom::GetId() OBStereo

Refs

typedef std::vector<Ref> Refs

A list (std::vector) of Ref variables.

RefIter

typedef Refs::iterator RefIter

Iterator (std::iterator) for a Refs list.

ConstRefIter

typedef Refs::const_iterator ConstRefIter

Iterator (std::iterator) for a const Refs list.

Member Enumeration Documentation

Type

enum Type

The various types of stereochemistry

Enumerator
CisTrans	cis/trans double bond
ExtendedCisTrans	allene, biphenyl, ...
SquarePlanar	Square-planar stereochemistry.
Tetrahedral	tetrahedral
ExtendedTetrahedral	extended tetrahedral
TrigonalBipyramidal	Trigonal-bipyramidal stereochemistry.
Octahedral	Octahedral stereochemistry.

BondDirection

enum BondDirection

Bond directions used by StereoFrom0D() to translate to internal CisTransStereo representation.

Enumerator
NotStereo
UpBond
DownBond
UnknownDir

Shape

enum Shape

Shapes used by OBTetraPlanarStereo subclasses for setting/getting reference ids.

See also

OBTetraPlanarStereo

Enumerator
ShapeU
ShapeZ
Shape4

View

enum View

Views used by OBTetraNonPlanarStereo subclasses for setting/getting reference ids.

See also

OBTetraNonPlanarStereo

Enumerator
ViewFrom	view from the atom (id parameter) towards the center atom
ViewTowards	view from center atom towards the atom (id paramater)

Winding

enum Winding

Windings used by OBTetraNonPlanar subclasses for setting/getting reference ids.

See also

OBTetraNonPlanar

Enumerator
Clockwise	Clockwise winding.
AntiClockwise	AntiClockwise winding (or CounterClockwise)
UnknownWinding	The configuration is specified as unknown (squiggly line in depiction)

anonymous enum

anonymous enum

Special case Ref values.

Enumerator
NoRef	No Ref set (invalid Ref)
ImplicitRef	Implicit Ref (i.e. hydrogen, N lone pair, ...).

Member Function Documentation

MakeRefs()

static Refs MakeRefs ( Ref  ref1, Ref  ref2, Ref  ref3, Ref  ref4 = NoRef  )

inlinestatic

Create a Refs list filled with ref1, ref2, ref3 & ref4. ref4 is not added to the returned Refs if it is equal to NoRef.

Returns

A Refs list containing the specified Ref values.

ContainsSameRefs()

static bool ContainsSameRefs ( const Refs &  refs1, const Refs &  refs2  )

static

Check if refs1 and refs2 contain the same Ref values regardless of their order.

OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3), OBStereo::MakeRefs(2, 3, 1)) // true
OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3), OBStereo::MakeRefs(3, 2, 1)) // true
OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3), OBStereo::MakeRefs(3, 4, 1)) // false

Returns

True if refs1 and refs2 contain the same Ref values.

Referenced by OBTetrahedralConfig::operator==(), OBCisTransConfig::operator==(), and OBSquarePlanarConfig::operator==().

ContainsRef()

static bool ContainsRef ( const Refs &  refs, unsigned long  ref  )

static

Returns

True if refs contains ref.

Referenced by OBTetrahedralConfig::operator==(), OBCisTransConfig::operator==(), and OBSquarePlanarConfig::operator==().

NumInversions()

static int NumInversions ( const Refs &  refs )

static

Compute the inversion vector for refs and return the sum of it's elements. The ith element in the inversion vector is the number of element to the right of element i with a lower value.

The number of inversions is the same as the number of interchanges of consecutive elements.

When working with 3 refs from a tetrahedral configuration:

permutation inversion vector sum
-------------------------------------
123 0 0 0 0 (even) -> clockwise
132 0 1 0 1 (odd) -> anti-clockwise
213 1 0 0 1 (odd) -> anti-clockwise
231 1 1 0 2 (even) -> clockwise
312 2 0 0 2 (even) -> clockwise
321 2 1 0 3 (odd) -> anti-clockwise

Referenced by OBTetrahedralConfig::operator==().

Permutate()

static void Permutate ( Refs &  refs, unsigned int  i, unsigned int  j  )

static

Permutate element i with j in refs.

Parameters

refs	The sequence with N elements to permutate.
i	Element i (0...N-1) will be mutated to j and vice versa.
j	Element j (0...N-1) will be mutated to i and vice versa.

Note

This method does nothing if i equals j.

Referenced by OBTetraNonPlanarStereo::ChangeView(), OBTetraNonPlanarStereo::ChangeWinding(), OBTetraNonPlanarStereo::Invert(), OBTetraPlanarStereo::ToConfig(), and OBTetraNonPlanarStereo::ToConfig().

Permutated()

static Refs Permutated ( const Refs &  refs, unsigned int  i, unsigned int  j  )

static

Get refs with element i and j permutated.

Parameters

refs	The sequence with N elements to permutate.
i	Element i (0...N-1) will be mutated to j and vice versa.
j	Element j (0...N-1) will be mutated to i and vice versa.

Returns

refs with elements i and j permutated.

Note

This method does nothing if i equals j.

---

The documentation for this class was generated from the following file:

• stereo.h