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RDKit
Open-source cheminformatics and machine learning.
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Classes | |
class | CIPMolSpan |
class | CIPMol |
class | Configuration |
class | Sp2Bond |
class | Tetrahedral |
class | Digraph |
class | Edge |
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 |
Enumerations | |
enum class | Type { Cv4D3 , Nv3D2 , Nv4D3Plus , Nv2D2Minus , Cv3D3Minus , Ov3D2Plus , Other } |
Functions | |
RDKIT_CIPLABELER_EXPORT void | assignCIPLabels (ROMol &mol) |
RDKIT_CIPLABELER_EXPORT void | assignCIPLabels (ROMol &mol, const boost::dynamic_bitset<> &atoms, const boost::dynamic_bitset<> &bonds) |
std::vector< boost::rational< int > > | calcFracAtomNums (const CIPMol &mol) |
enum class | Descriptor { 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) |
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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 | |
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NONE | |
UNKNOWN | |
ns | |
R | |
S | |
r | |
s | |
seqTrans | Cis/Trans |
seqCis | |
E | |
Z | |
M | |
P | |
m | |
p | |
SP_4 | |
TBPY_5 | |
OC_6 |
Definition at line 25 of file Descriptor.h.
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RDKIT_CIPLABELER_EXPORT void RDKit::CIPLabeler::assignCIPLabels | ( | ROMol & | mol | ) |
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.
mol | - the molecule to be labelled. |
RDKIT_CIPLABELER_EXPORT void RDKit::CIPLabeler::assignCIPLabels | ( | ROMol & | mol, |
const boost::dynamic_bitset<> & | atoms, | ||
const boost::dynamic_bitset<> & | bonds | ||
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Overload that allows selecting which atoms and/or bonds will be labeled.
mol | - the molecule to be labelled. |
atoms | - bitset with the atom indexes to be labeled. |
bonds | - bitset with the bond indexes to be labeled. |
std::vector<boost::rational<int> > 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.
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Definition at line 54 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::MolDraw2D_detail::addAtomIndices(), RDKit::MolDraw2D_detail::addBondIndices(), RDKit::RGroupDecompData::setRlabel(), and RDKit::CIPLabeler::PairList::toString().