Config Struct Reference

#include <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
	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
	Config ()
	Config (unsigned long _center, unsigned long from_or_towards, const OBStereo::Refs &_refs, OBStereo::Winding _winding=OBStereo::Clockwise, OBStereo::View _view=OBStereo::ViewFrom)
bool	operator== (const Config &other) const
bool	operator!= (const Config &other) const
Public Attributes
unsigned long	from
unsigned long	towards
Data members defining stereochemistry.
unsigned long	begin
unsigned long	end
OBStereo::Refs	refs
OBStereo::Shape	shape
bool	specified
unsigned long	center
union {
unsigned long   from
unsigned long   towards
};
OBStereo::Winding	winding
OBStereo::View	view

---

Detailed Description

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.

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.

The config struct represents the stereochemistry in a well defined way. For tetrahedral stereo centers, the following data members define the special orientation of the atoms:

• OBStereo::Ref center: Atom id of the stereogenic center atom.
• OBStereo::Ref from/towards: Atom id (or OBStereo::ImplicitRef) for the atom to view from/towards.
• OBStereo::Refs refs: The three remaining atom ids (may also contain one OBStereo::NoRef element if from/towards is set to a real atom id).
• OBStereo::View view: Specify the viewing from or towards the atom with from/towards id.
• OBStereo::Winding winding: Clockwise or AntiClockwise (order in the Refs refs list)

Only center is specific for OBTetrahedralStereo::Config. The other data members occur in all OBTetraNonPlanarStereo 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.

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.

Config

(

)

[inline]

Default constructor. Initializes the from/torards and center to OBStereo::NoRef, the winding to OBStereo::Clockwise and view to OBStereo::ViewFrom.

Config	(	unsigned long	_center,
		unsigned long	from_or_towards,
		const OBStereo::Refs &	_refs,
		OBStereo::Winding	_winding = OBStereo::Clockwise,
		OBStereo::View	_view = OBStereo::ViewFrom
	)			[inline]

Constructor with all parameters.

Parameters:

	_center	The center (chiral) atom id.
	from_or_towards	The atom id from which to view or view towards (see view).
	_refs	The 3 reference ids.
	_winding	The winding for the 3 ids in _refs.
	_view	Specify viewing from or towards the atom with from_or_towards id.

---

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.

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.

bool operator==

(

const Config &

other

)

const

Equal to operator. Comparing OBTetrahedralStereo::Config structs is done using the information stored in the struct's data members (i.e. view, winding, from/towards and refs).

There are a number of cases resuling in false being returned:

• The centers don't match.
• One of the Refs lists does not contain 3 elements.
• 2 or more OBStereo::ImplicitRef values in a single Config struct

When either Config struct is unspecified (i.e. the stereochemistry implied is accidental), true is returned.

It doesn't matter if the two Config structs use the same view, same from/towards Ref or the same winding. All needed conversions will be carried out automatically (see OBTetraNonPlanerStereo::ToConfig). These conversions ensure the spacial orientation of the 4 groups remains unchanged.

Another key feature is the ability to comapre Config structs regardless of implicit (OBStereo::ImplicitRef) or explicit hydrogens. This is best illustrated with some examples. In these examples the same ref has already been selected as from/towards atom and both use the same winding and view direction. We will focus on how the three remaining refs are interpreted.

         234 == 234 // true
         2H4 == 234 // 3 is missing, must be the implicit --> 234 == 234 // true
         2H4 == 243 // same as above, but now 234 == 243 // false
         234 == H34 // 2 is missing, must be implicit --> 234 == 234 // true
       

By comparing the second and third example above, it can be clearly seen that the value of 1 Ref can actually be ignored. It's position in the sequence (or the winding) is defined by the two explicit Ref values.

Returns:

True if both Config structs represent the same 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

unsigned long end

OBStereo::Refs refs

The 4 reference ids.

The 3 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).

Referenced by OpenBabel::CanonicalLabels().

unsigned long center

unsigned long from

unsigned long towards

union { ... }

This anonymous union helps to keep code clean. Both the from and towards data members contain the same OBStereo::Ref (same memory address) but can be used interchangeably to match the context of the code. The real viewing direction is specified by the view data member.

OBStereo::Winding winding

OBStereo::View view

Specify viewing from or towards the atom with from/towards id.

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

• cistrans.h
• squareplanar.h
• tetrahedral.h