Open Babel: OBCisTransStereo::Config Struct Reference

Public Member Functions

# 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.

- OBStereo::Ref `begin:` The begin atom for the double bond.
- OBStereo::Ref `end:` The end atom for the double bond.
- OBStereo::Refs `refs:` The 4 atoms connected to the double bond.
- OBStereo::Shape `shape:` The shape formed by the `refs` by connecting them in the same order as they occur in `refs`.

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.

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

             else:

               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.

Returns:
  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==.

Returns:
  True if the two Config structs represent a different stereochemistry.

## Member Data Documentation

unsigned long begin

Referenced by OpenBabel::CanonicalLabels(), and OBBuilder::CorrectStereoBonds().

unsigned long end

Referenced by OpenBabel::CanonicalLabels(), and OBBuilder::CorrectStereoBonds().

OBStereo::Refs refs

The 4 reference ids.

Referenced by OBBuilder::CorrectStereoBonds().

OBStereo::Shape shape

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:

- cistrans.h

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