OBSquarePlanarStereo::Config Struct Reference
Stereochemical configuration for square planar stereocenters. More...
|Config (unsigned long _center, const OBStereo::Refs &_refs, OBStereo::Shape _shape=OBStereo::ShapeU)|
|bool||operator== (const Config &other) const|
|bool||operator!= (const Config &other) const|
Data members defining stereochemistry.
Stereochemical configuration for square planar stereocenters.
The config struct represents the stereochemistry in a well defined way. For squareplanar stereocenters, the following data members define the spacial arrengement of the atoms.
center:The central atom.
refs:The 4 atoms connected to the double bond.
shape:The shape formed by the
refsby connecting them in the same order as they occur in
Constructor & Destructor Documentation
|const OBStereo::Refs &||_refs,|
|OBStereo::Shape|| _shape = |
Constructor with all parameters.
_center The atom id for the central atom. _refs The 4 reference ids. _shape The shape for the 4 reference ids.
Member Function Documentation
|bool operator==||(||const Config &||other||)||const|
Equal to operator. Comparing OBSquarePlanarStereo::Config structs is done using the information stored in the struct's data members (i.e. center, refs and shape).
There are a number of cases resuling in false being returned:
centeratom ids don't match
- One of the Refs lists does not contain 4 elements.
- 2 or more OBStereo::ImplicitRef values in a single Config struct
- (The two
refsdon't share a single common element)
In the simplest case where both
refs contain exactly the same elements (OBStereo::ContainsSameRefs()), coould include OBStereo::ImplicitRef), both Config struct are normalized to OBStereo::ShapeU starting with the same element. After this normalization, there are two possible orientations to overlay the shape on the double bond. From the illustration below, it can be seen only
refs has to be checked in order to conclude both Config structs have the same stereochemistry.
1 4 1 4 1------4 \ / | | | C | | | / \ | | | 2 3 2------3 2------3 1 2 3 4 1 2 3 4 | | | | <- in any case, refs & refs remain unchanged 1 2 3 4 1 4 3 2
When comparing a Config struct with explicit hydrogen(s) to one with implicit hydrogen(s), both
refs are also normalized to OBStereo::ShapeU starting with the same common element. This shared element cannot be OBStereo::ImplicitRef. Depending on the position of the OBStereo::ImplicitRef element(s) in the
refs, 3 cases are possible:
refs != OBStereo::ImplicitId: (analog to the case above where they contained the same elements ) 1 2 3 4 | | <- refs & refs remain unchanged 1 H 3 H else: 1 2 3 4 | | <- refs & refs remain unchanged 1 H H 4 1 2 3 4 | | <- refs & refs remain unchanged 1 2 H H
In each case, the orientation of the U shape is also defined since there can be only one OBStereo::ImplicitRef for each side of the double bond.
- True if both Config structs represent the stereochemistry.
|bool operator!=||(||const Config &||other||)|| const
Not equal to operator. This is the inverse of the Equal to operator==.
- True if the two Config structs represent a different stereochemistry.
Member Data Documentation
|unsigned long center|
True if the stereochemistry is specified. When false, the described special orientation is only accidental (i.e. unspecified).
The documentation for this struct was generated from the following file: