RDKit::CIPLabeler Namespace Reference

Classes
class	MaxIterationsExceeded
class	CIPMolSpan
class	CIPMol
class	AtropisomerBond
class	Configuration
class	Sp2Bond
class	Tetrahedral
class	Digraph
class	Edge
class	FractionalAtomicNum
class	Node
class	Priority
class	PairList
class	Rule1a
class	Rule1b
class	Rule2
class	Rule3
class	Rule4a
class	Rule4b
class	Rule4c
class	Rule5
class	Rule5New
class	Rule6
class	Rules
class	SequenceRule
class	Sort
class	TooManyNodesException

Functions
RDKIT_CIPLABELER_EXPORT void	assignCIPLabels (ROMol &mol, unsigned int maxRecursiveIterations=0)
RDKIT_CIPLABELER_EXPORT void	assignCIPLabels (ROMol &mol, const boost::dynamic_bitset<> &atoms, const boost::dynamic_bitset<> &bonds, unsigned int maxRecursiveIterations=0)
std::vector< FractionalAtomicNum >	calcFracAtomNums (const CIPMol &mol)

Variables
constexpr unsigned int	IMPLICITH
enum class	Descriptor : uint8_t {   NONE , UNKNOWN , ns , R ,   S , r , s , seqTrans ,   seqCis , E , Z , M ,   P , m , p , SP_4 ,   TBPY_5 , OC_6 }
static std::string	to_string (const Descriptor &desc)

Enumeration Type Documentation

Descriptor

enum class RDKit::CIPLabeler::Descriptor : uint8_t

strong

Defines a descriptor which can be assigned to an atom to indicate the type of chirality (if there is any). Each descriptor defines its generallink Type} which can be useful when comparing centres of different geometry.

Enumerator
NONE
UNKNOWN
ns
R	Tetrahedral
S
r
s
seqTrans	Cis/Trans
seqCis
E
Z
M
P
m
p
SP_4
TBPY_5
OC_6

Definition at line 26 of file Descriptor.h.

Function Documentation

assignCIPLabels() [1/2]

RDKIT_CIPLABELER_EXPORT void RDKit::CIPLabeler::assignCIPLabels	(	ROMol &	mol,
		const boost::dynamic_bitset<> &	atoms,
		const boost::dynamic_bitset<> &	bonds,
		unsigned int	maxRecursiveIterations = 0 )

Overload that allows selecting which atoms and/or bonds will be labeled.

Parameters

mol	- the molecule to be labelled.
atoms	- bitset with the atom indexes to be labeled. The bitset must have mol.getNumAtoms() bits. Unselected atom configurations may still be used as auxiliary stereochemical dependencies, but their primary labels are not written.
bonds	- bitset with the bond indexes to be labeled. The bitset must have mol.getNumBonds() bits. Unselected bond configurations may still be used as auxiliary stereochemical dependencies, but their primary labels are not written.
maxRecursiveIterations	- maximum total number of recursive comparisons across the preliminary and full labeling passes. A value of zero means no caller-specified limit. A value of 1,250,000 takes about 1 second. Most structures require fewer than 10,000 comparisons. A peptide with MW~3000 took about 100 comparisons, and a 20,000 MW protein took about 600 comparisons.

Note

Partial labeling does not set common_properties::_CIPComputed, which denotes a complete molecule-wide calculation.

References RDKIT_CIPLABELER_EXPORT.

assignCIPLabels() [2/2]

RDKIT_CIPLABELER_EXPORT void RDKit::CIPLabeler::assignCIPLabels	(	ROMol &	mol,
		unsigned int	maxRecursiveIterations = 0 )

Calculate Stereochemical labels based on an accurate implementation of the CIP rules.

This is a C++ port of https://github.com/SiMolecule/centres, which was originally written by John Mayfield in Java. The original algorithm was described in:

Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, A., Redkin, D. Algorithmic Analysis of Cahn–Ingold–Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. J. Chem. Inf. Model. 2018, 58, 1755-1765.

Parameters

mol	- the molecule to be labelled.

Note

only atoms with chiral tags and double bonds with proper bond directions will be labelled.

Labels will be stored under the common_properties::_CIPCode property of the relevant atoms/bonds.

Parameters

maxRecursiveIterations

- maximum total number of recursive comparisons across all labeling passes; zero means no caller-specified limit.

References RDKIT_CIPLABELER_EXPORT.

calcFracAtomNums()

std::vector< FractionalAtomicNum > RDKit::CIPLabeler::calcFracAtomNums

(

const CIPMol &

mol

)

Calculate fractional atomic numbers for all atoms in the mol. Using fractional atomic numbers makes sure that atoms in rings that have resonant structures are always considered with the same priority.

to_string()

std::string RDKit::CIPLabeler::to_string ( const Descriptor & desc )

static

Definition at line 55 of file Descriptor.h.

References E, M, m, NONE, ns, OC_6, P, p, R, r, S, s, seqCis, seqTrans, SP_4, TBPY_5, UNKNOWN, and Z.

Referenced by RDKit::CIPLabeler::PairList::toString().

Variable Documentation

IMPLICITH

unsigned int RDKit::CIPLabeler::IMPLICITH

inlineconstexpr

Initial value:

=
    std::numeric_limits<unsigned int>::max()

Definition at line 28 of file Configuration.h.