OBTetrahedralStereo::Config Struct Reference
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 withfrom/towards
id. - OBStereo::Winding
winding:
Clockwise or AntiClockwise (order in the Refsrefs
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.
- Returns:
- True if both Config structs represent the same stereochemistry.
bool operator!= | ( | const Config & | other ) | const [inline] |
Not equal to operator. This is the inverse of the Equal to operator==.
- Returns:
- True if the two Config structs represent a different stereochemistry.
Member Data Documentation
unsigned long center |
Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), and OBSmartsMatcher::match().
unsigned long from |
Referenced by OBSmartsMatcher::match().
unsigned long towards |
union { ... } |
The 3 reference ids.
Referenced by OBSmartsMatcher::match().
Referenced by OBSmartsMatcher::match().
Specify viewing from or towards the atom with from/towards
id.
Referenced by OBSmartsMatcher::match().
bool specified |
True if the stereochemistry is specified. When false, the described special orientation is only accidental (i.e. unspecified).
Referenced by OpenBabel::CanonicalLabels(), and OBSmartsMatcher::match().
The documentation for this struct was generated from the following file: