OBCisTransStereo::Config Struct Reference

Stereochemical configuration for double-bond cis/trans stereochemistry. More...

#include <openbabel/stereo/cistrans.h>

List of all members.

Public Member Functions

 Config ()
 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

Public Attributes

Data members defining stereochemistry.

unsigned long begin
unsigned long end
OBStereo::Refs refs
OBStereo::Shape shape
bool specified

Detailed Description

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.


Only begin and end are specific for OBCisTransStereo::Config. The other data members occur in all OBTetraPlanarStereo derived classes.

Constructor & Destructor Documentation

Config (  )  [inline]

Default constructor. Initializes begin and end to OBStereo::NoRef and shape to OBStereo::ShapeU.

Config ( unsigned long  _begin,
unsigned long  _end,
const OBStereo::Refs _refs,
OBStereo::Shape  _shape = OBStereo::ShapeU 
) [inline]

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:

  • begin and end don'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 refs don'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[2] 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[0] & refs[2] 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[2] != OBStereo::ImplicitId:

           (analog to the case above where they contained the same elements )

           1 2 3 4
           |   |      <- refs[0] & refs[2] remain unchanged
           1 H 3 H


           1 2 3 4
           |     |    <- refs[0] & refs[3] remain unchanged
           1 H H 4

           1 2 3 4
           | |        <- refs[0] & refs[1] 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 [inline]

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

The 4 reference ids.

Referenced by OBBuilder::CorrectStereoBonds().

The shape of the 4 reference ids.

bool specified

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:
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