Open Babel: OBSquarePlanarStereo::Config Struct Reference

Public Member Functions

# OBSquarePlanarStereo::Config Struct Reference

Stereochemical configuration for square planar stereocenters. More...

`#include <openbabel/stereo/squareplanar.h>`

List of all members.

## Public Member Functions
| Config ()
| 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
## Public Attributes
Data members defining stereochemistry.
unsigned long | center
OBStereo::Refs | refs
OBStereo::Shape | shape
bool | specified

## Detailed Description

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.

- OBStereo::Ref `center:` The central atom.
- 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 `center` are specific for OBSquarePlanarStereo::Config. The other data members occur in all OBTetraPlanarStereo derived classes.

## Constructor & Destructor Documentation

Config | ( | ) | `[inline]`

Default constructor. Initializes `center` to OBStereo::NoRef and `shape` to OBStereo::ShapeU.

Config | ( | unsigned long | _center,
|  | const OBStereo::Refs & | _refs,
|  | OBStereo::Shape | _shape = `OBStereo::ShapeU`
| ) |  | `[inline]`

Constructor with all parameters.

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:

- `center` atom 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 `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      |      |           |
              / \     |      |           |
             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 center

OBStereo::Refs refs

The 4 reference ids.

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).

The documentation for this struct was generated from the following file:

- squareplanar.h

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