OBCisTransStereo::Config Struct Reference
Stereochemical configuration for double-bond cis/trans stereochemistry. More...
|Config (unsigned long _begin, unsigned long _end, 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 double-bond cis/trans stereochemistry.
The config struct represents the stereochemistry in a well defined way. For cis/trans stereo bonds, the following data members define the spacial arrengement of the atoms.
begin:The begin atom for the double bond.
end:The end atom for the double bond.
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.
_begin The double bond begin atom id. _end The double bond end atom id. _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 OBCisTransStereo::Config structs is done using the information stored in the struct's data members (i.e. begin, end, refs and shape).
There are a number of cases resuling in false being returned:
enddon't match (is checked using the 2 combinations)
- 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==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 begin|
True if the stereochemistry is specified. When false, the described special orientation is only accidental (i.e. unspecified).
Referenced by OpenBabel::CanonicalLabels().
The documentation for this struct was generated from the following file: