CDPL::Chem::StereoDescriptor Class Reference

A data structure for the storage and retrieval of stereochemical information about atoms and bonds. More...

#include <StereoDescriptor.hpp>

Public Member Functions
	StereoDescriptor (unsigned int config)
	Constructs a StereoDescriptor instance that specifies the configuration config but stores no reference atoms. More...
	StereoDescriptor (const StereoDescriptor &descr)
	Constructs a copy of the StereoDescriptor instance descr. More...
	StereoDescriptor (unsigned int config, const Atom &atom1, const Atom &atom2, const Atom &atom3)
	Constructs a StereoDescriptor instance that specifies a configuration of config for three reference atoms. More...
	StereoDescriptor (unsigned int config, const Atom &atom1, const Atom &atom2, const Atom &atom3, const Atom &atom4)
	Constructs a StereoDescriptor instance that specifies a configuration of config for four reference atoms. More...
std::size_t	getNumReferenceAtoms () const
	Returns the number of specified reference atoms. More...
unsigned int	getConfiguration () const
	Returns the configuration of the reference atoms. More...
void	setConfiguration (unsigned int config)
	Sets the configuration of the reference atoms to config. More...
const Atom *const *	getReferenceAtoms () const
	Returns an array of pointers to the stored reference atoms. More...
StereoDescriptor &	operator= (const StereoDescriptor &descr)
	Assignment operator. More...
bool	isValid (const Atom &atom) const
	Tells wheter this StereoDescriptor instance is valid for the specified center atom. More...
bool	isValid (const Bond &bond) const
	Tells wheter this StereoDescriptor instance is valid for the specified center bond. More...
unsigned int	getPermutationParity (const Atom &atom1, const Atom &atom2, const Atom &atom3) const
	Tells if an odd or even number of atom transpositions is required to achieve the same ordering of reference and argument atoms. More...
unsigned int	getPermutationParity (const Atom &atom1, const Atom &atom2, const Atom &atom3, const Atom &atom4) const
	Tells if an odd or even number of atom transpositions is required to achieve the same ordering of reference and argument atoms. More...

Detailed Description

A data structure for the storage and retrieval of stereochemical information about atoms and bonds.

The stereochemistry of atoms and bonds is definded by an ordered list of reference atoms and an integer constant that describes the spatial configuration of the reference atoms. Requirements on the specification of the reference atom list and the way the associated steric configuration has to be interpreted both depend on the primary type of the stereocenter (if atom or bond) and, for atom centers, also on the number and geometric arrangement of the reference atoms. The following basic types of atom and bond stereocenters are currently supported:

• Atoms with four neighbors in tetrahedral arrangement:
  
  The four neighbor atoms serve as reference atoms. Their steric configuration is determined by looking along the bond from the center atom (stereocenter) to the 4th reference atom. If the direction of travel from reference atom 1 over atom 2 to atom 3 is clockwise (see Fig. 1a), the configuration flag is assigned the value AtomConfiguration::R, and AtomConfiguration::S, if the reference atoms 1, 2 and 3 are arranged in counterclockwise direction (Fig. 1b).

Fig. 1a: R-Configuration

Fig. 1b: S-Configuration

• Atoms with three neighbors in pyramidal arrangement:
  
  The neighbor atoms correspond to the first three atoms in the reference atom list. The 4th reference atom denotes the central atom. The configuration is determined by looking along the line from the center atom to a projected point (represented by a blue sphere in figure 2a and 2b) which is obtained by adding the bond vectors from each neighbor atom to the central atom. Like before, if the direction of travel from reference atom 1 over atom 2 to atom 3 is clockwise (see Fig. 2a), the configuration flag is assigned the value AtomConfiguration::R, and AtomConfiguration::S, if the reference atoms 1, 2 and 3 are arranged in a counterclockwise fashion (Fig. 2b).

Fig. 2a: R-Configuration

Fig. 2b: S-Configuration

• Non-terminal double bonds:
  As shown in figure 3a and 3b, the four reference atoms form a path with three consecutive bonds where atoms 2 and 3 are part of the central double bond. Atom 1 is the connected atom of the first double bond ligand, and atom 4 the connected atom of the second ligand. If reference atoms 1 and 4 lie on the same side of the double bond (see Fig. 3a), the configuration flag is assigned the value BondConfiguration::CIS, and BondConfiguration::TRANS, if they are on opposite sides f the bond (Fig. 3b).

Fig. 3a: Cis-Configuration

Fig. 3b: Trans-Configuration

Constructor & Destructor Documentation

StereoDescriptor() [1/4]

CDPL::Chem::StereoDescriptor::StereoDescriptor

(

unsigned int

config

)

Constructs a StereoDescriptor instance that specifies the configuration config but stores no reference atoms.

Parameters

config

A constant specifying the configuration of the central atoms.

StereoDescriptor() [2/4]

CDPL::Chem::StereoDescriptor::StereoDescriptor

(

const StereoDescriptor &

descr

)

Constructs a copy of the StereoDescriptor instance descr.

Parameters

descr

The StereoDescriptor instance to copy.

StereoDescriptor() [3/4]

CDPL::Chem::StereoDescriptor::StereoDescriptor	(	unsigned int	config,
		const Atom &	atom1,
		const Atom &	atom2,
		const Atom &	atom3
	)

Constructs a StereoDescriptor instance that specifies a configuration of config for three reference atoms.

Parameters

config	A constant specifying the configuration of the reference atoms.
atom1	The first reference atom.
atom2	The second reference atom.
atom3	The third reference atom.

StereoDescriptor() [4/4]

CDPL::Chem::StereoDescriptor::StereoDescriptor	(	unsigned int	config,
		const Atom &	atom1,
		const Atom &	atom2,
		const Atom &	atom3,
		const Atom &	atom4
	)

Constructs a StereoDescriptor instance that specifies a configuration of config for four reference atoms.

Parameters

config	A flag specifying the configuration of the reference atoms.
atom1	The first reference atom.
atom2	The second reference atom.
atom3	The third reference atom.
atom4	The fourth reference atom.

Member Function Documentation

getNumReferenceAtoms()

std::size_t CDPL::Chem::StereoDescriptor::getNumReferenceAtoms

(

)

const

Returns the number of specified reference atoms.

Returns

The number of specified reference atoms.

getConfiguration()

unsigned int CDPL::Chem::StereoDescriptor::getConfiguration

(

)

const

Returns the configuration of the reference atoms.

Returns

A constant specifying the configuration of the reference atoms.

setConfiguration()

void CDPL::Chem::StereoDescriptor::setConfiguration

(

unsigned int

config

)

Sets the configuration of the reference atoms to config.

Parameters

config

A constant specifying the configuration of the reference atoms.

getReferenceAtoms()

const Atom* const* CDPL::Chem::StereoDescriptor::getReferenceAtoms

(

)

const

Returns an array of pointers to the stored reference atoms.

Returns

An array of pointers to the stored reference atoms.

operator=()

StereoDescriptor& CDPL::Chem::StereoDescriptor::operator=

(

const StereoDescriptor &

descr

)

Assignment operator.

Parameters

descr

The StereoDescriptor instance to copy.

Returns

A reference to itself.

isValid() [1/2]

bool CDPL::Chem::StereoDescriptor::isValid

(

const Atom &

atom

)

const

Tells wheter this StereoDescriptor instance is valid for the specified center atom.

The method checks if the number of reference atoms is at least 3, the reference atoms are distinct and if every reference atom is connected to the argument atom.

Parameters

atom	The stereogenic center atom.

Returns

true if valid, false otherwise.

isValid() [2/2]

bool CDPL::Chem::StereoDescriptor::isValid

(

const Bond &

bond

)

const

Tells wheter this StereoDescriptor instance is valid for the specified center bond.

The method checks if the number of reference atoms is 4, the reference atoms are distinct, the specified bond connects reference atoms 2 and 3 and if reference atoms 1 and 4 are connected to reference atom 2 and 3, respectively.

Parameters

bond	The stereogenic center bond.

Returns

true if valid, false otherwise.

getPermutationParity() [1/2]

unsigned int CDPL::Chem::StereoDescriptor::getPermutationParity	(	const Atom &	atom1,
		const Atom &	atom2,
		const Atom &	atom3
	)		const

Tells if an odd or even number of atom transpositions is required to achieve the same ordering of reference and argument atoms.

Parameters

atom1	The first atom.
atom2	The second atom.
atom3	The third atom.

Returns

1 if an odd number of transpositions is required, 2 if an even number of transpositions is required and 0 if the argument atoms do not match the stored reference atoms.

getPermutationParity() [2/2]

unsigned int CDPL::Chem::StereoDescriptor::getPermutationParity	(	const Atom &	atom1,
		const Atom &	atom2,
		const Atom &	atom3,
		const Atom &	atom4
	)		const

Tells if an odd or even number of atom transpositions is required to achieve the same ordering of reference and argument atoms.

Parameters

atom1	The first atom.
atom2	The second atom.
atom3	The third atom.
atom4	The fourth atom.

Returns

1 if an odd number of transpositions is required, 2 if an even number of transpositions is required and 0 if the argument atoms do not match the stored reference atoms.

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

• StereoDescriptor.hpp