CDPL.Chem.StereoDescriptor Class Reference

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

Inheritance diagram for CDPL.Chem.StereoDescriptor:

Classes
class	ReferenceAtomArray

Public Member Functions
None	__init__ (int config)
	Constructs a StereoDescriptor instance that specifies the configuration config but stores no reference atoms. More...
None	__init__ (StereoDescriptor descr)
	Constructs a copy of the StereoDescriptor instance descr. More...
None	__init__ (int config, Atom atom1, Atom atom2, Atom atom3)
	Constructs a StereoDescriptor instance that specifies a configuration of config for three reference atoms. More...
None	__init__ (int config, Atom atom1, Atom atom2, Atom atom3, Atom atom4)
	Constructs a StereoDescriptor instance that specifies a configuration of config for four reference atoms. More...
int	getConfiguration ()
	Returns the configuration of the reference atoms. More...
None	setConfiguration (int config)
	Sets the configuration of the reference atoms to config. More...
int	getNumReferenceAtoms ()
	Returns the number of specified reference atoms. More...
ReferenceAtomArray	getReferenceAtoms ()
	Returns an array of references to the stored reference atoms. More...
StereoDescriptor	assign (StereoDescriptor descr)
	Assignment operator. More...
int	getPermutationParity (Atom atom1, Atom atom2, Atom atom3, Atom atom4)
	Tells if an odd or even number of atom transpositions is required to achieve the same ordering of reference and argument atoms. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
bool	isValid (Atom atom)
	Tells wheter this StereoDescriptor instance is valid for the specified center atom. More...
str	__str__ ()
	Returns a string representation of the StereoDescriptor instance. More...

Properties
	objectID = property(getObjectID)
	configuration = property(getConfiguration, setConfiguration)
	numReferenceAtoms = property(getNumReferenceAtoms)
	referenceAtoms = property(getReferenceAtoms)

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

__init__() [1/4]

None CDPL.Chem.StereoDescriptor.__init__

(

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.

__init__() [2/4]

None CDPL.Chem.StereoDescriptor.__init__

(

StereoDescriptor

descr

)

Constructs a copy of the StereoDescriptor instance descr.

Parameters

descr

The StereoDescriptor instance to copy.

__init__() [3/4]

None CDPL.Chem.StereoDescriptor.__init__	(	int	config,
		Atom	atom1,
		Atom	atom2,
		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.

__init__() [4/4]

None CDPL.Chem.StereoDescriptor.__init__	(	int	config,
		Atom	atom1,
		Atom	atom2,
		Atom	atom3,
		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

getConfiguration()

int CDPL.Chem.StereoDescriptor.getConfiguration

(

)

Returns the configuration of the reference atoms.

Returns

A constant specifying the configuration of the reference atoms.

setConfiguration()

None CDPL.Chem.StereoDescriptor.setConfiguration

(

int

config

)

Sets the configuration of the reference atoms to config.

Parameters

config

A constant specifying the configuration of the reference atoms.

getNumReferenceAtoms()

int CDPL.Chem.StereoDescriptor.getNumReferenceAtoms

(

)

Returns the number of specified reference atoms.

Returns

The number of specified reference atoms.

getReferenceAtoms()

ReferenceAtomArray CDPL.Chem.StereoDescriptor.getReferenceAtoms

(

)

Returns an array of references to the stored reference atoms.

Returns

An array of references to the stored reference atoms.

assign()

StereoDescriptor CDPL.Chem.StereoDescriptor.assign

(

StereoDescriptor

descr

)

Assignment operator.

Parameters

descr

The StereoDescriptor instance to copy.

Returns

self

getPermutationParity()

int CDPL.Chem.StereoDescriptor.getPermutationParity	(	Atom	atom1,
		Atom	atom2,
		Atom	atom3,
		Atom	atom4
	)

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.

getObjectID()

int CDPL.Chem.StereoDescriptor.getObjectID

(

)

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python StereoDescriptor instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two StereoDescriptor instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns

The numeric ID of the internally referenced C++ class instance.

isValid()

bool CDPL.Chem.StereoDescriptor.isValid

(

Atom

atom

)

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.

__str__()

str CDPL.Chem.StereoDescriptor.__str__

(

)

Returns a string representation of the StereoDescriptor instance.

Returns

The generated string representation.