OBStereo Class Reference [Stereochemistry]

Placeholder for enums & Ref/Refs related functions. More...

#include <openbabel/stereo/stereo.h>

List of all members.

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

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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

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Member Typedef Documentation

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

typedef std::vector<Ref> Refs

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

typedef Refs::iterator RefIter

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

typedef Refs::const_iterator ConstRefIter

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

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Member Enumeration Documentation

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.

enum BondDirection

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

Enumerator:

NotStereo
UpBond
DownBond
UnknownDir

enum Shape

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

See also:

OBTetraPlanarStereo

Enumerator:

ShapeU
ShapeZ
Shape4

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)

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

Special case Ref values.

Enumerator:

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

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Member Function Documentation

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

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.

Referenced by OBSmartsMatcher::match().

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.

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

Returns:

True if refs contains ref.

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

static void Permutate	(	Refs &	refs,
		int	i,
		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().

static Refs Permutated	(	const Refs &	refs,
		int	i,
		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.

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

• stereo.h