Stereochemical configuration for tetrahedral stereocenters. More...

#include <openbabel/stereo/tetrahedral.h>

Public Member Functions
	Config ()
	Config (unsigned long _center, unsigned long from_or_towards, const OBStereo::Refs &_refs, OBStereo::Winding _winding=OBStereo::Clockwise, OBStereo::View _view=OBStereo::ViewFrom)
bool	operator== (const Config &other) const
bool	operator!= (const Config &other) const
Public Attributes
unsigned long	from
unsigned long	towards
Data members defining stereochemistry.
unsigned long	center
union {
unsigned long from
unsigned long towards
};
OBStereo::Refs	refs
OBStereo::Winding	winding
OBStereo::View	view
bool	specified

Detailed Description

Stereochemical configuration for tetrahedral stereocenters.

The config struct represents the stereochemistry in a well defined way. For tetrahedral stereo centers, the following data members define the special orientation of the atoms:

OBStereo::Ref center: Atom id of the stereogenic center atom.
OBStereo::Ref from/towards: Atom id (or OBStereo::ImplicitRef) for the atom to view from/towards.
OBStereo::Refs refs: The three remaining atom ids (may also contain one OBStereo::NoRef element if from/towards is set to a real atom id).
OBStereo::View view: Specify the viewing from or towards the atom with from/towards id.
OBStereo::Winding winding: Clockwise or AntiClockwise (order in the Refs refs list)

Only center is specific for OBTetrahedralStereo::Config. The other data members occur in all OBTetraNonPlanarStereo derived classes.

Constructor & Destructor Documentation

Config ( ) [inline]

Default constructor. Initializes the from/torards and center to OBStereo::NoRef, the winding to OBStereo::Clockwise and view to OBStereo::ViewFrom.

Config	(	unsigned long	_center,
		unsigned long	from_or_towards,
		const OBStereo::Refs &	_refs,
		OBStereo::Winding	_winding = `OBStereo::Clockwise`,
		OBStereo::View	_view = `OBStereo::ViewFrom`
	)		`[inline]`

Constructor with all parameters.

Parameters:

_center	The center (chiral) atom id.
from_or_towards	The atom id from which to view or view towards (see `view`).
_refs	The 3 reference ids.
_winding	The winding for the 3 ids in `_refs`.
_view	Specify viewing from or towards the atom with `from_or_towards` id.

Member Function Documentation

bool operator== ( const Config & other ) const

Equal to operator. Comparing OBTetrahedralStereo::Config structs is done using the information stored in the struct's data members (i.e. view, winding, from/towards and refs).

There are a number of cases resuling in false being returned:

The centers don't match.
One of the Refs lists does not contain 3 elements.
2 or more OBStereo::ImplicitRef values in a single Config struct

When either Config struct is unspecified (i.e. the stereochemistry implied is accidental), true is returned.

It doesn't matter if the two Config structs use the same view, same from/towards Ref or the same winding. All needed conversions will be carried out automatically (see OBTetraNonPlanerStereo::ToConfig). These conversions ensure the spacial orientation of the 4 groups remains unchanged.

Another key feature is the ability to comapre Config structs regardless of implicit (OBStereo::ImplicitRef) or explicit hydrogens. This is best illustrated with some examples. In these examples the same ref has already been selected as from/towards atom and both use the same winding and view direction. We will focus on how the three remaining refs are interpreted.

         234 == 234 // true
         2H4 == 234 // 3 is missing, must be the implicit --> 234 == 234 // true
         2H4 == 243 // same as above, but now 234 == 243 // false
         234 == H34 // 2 is missing, must be implicit --> 234 == 234 // true

By comparing the second and third example above, it can be clearly seen that the value of 1 Ref can actually be ignored. It's position in the sequence (or the winding) is defined by the two explicit Ref values.