RDKit::SmilesWrite Namespace Reference

Namespaces
namespace	detail

Enumerations
enum	CXSmilesFields : uint32_t { CXSMILESFIELDS_ENUM_ITEMS }

Functions
RDKIT_SMILESPARSE_EXPORT std::string	getCXExtensions (const ROMol &mol, std::uint32_t flags=CXSmilesFields::CX_ALL)
	returns the cxsmiles data for a molecule
RDKIT_SMILESPARSE_EXPORT std::string	getCXExtensions (const std::vector< ROMol * > &mols, std::uint32_t flags)
	returns the cxsmiles data for a vector of molecules
RDKIT_SMILESPARSE_EXPORT bool	inOrganicSubset (int atomicNumber)
	returns true if the atom number is in the SMILES organic subset
RDKIT_SMILESPARSE_EXPORT std::string	GetAtomSmiles (const Atom *atom, const SmilesWriteParams &ps)
	returns the SMILES for an atom
std::string	GetAtomSmiles (const Atom *atom, bool doKekule=false, const Bond *=nullptr, bool allHsExplicit=false, bool isomericSmiles=true)
	returns the SMILES for an atom
RDKIT_SMILESPARSE_EXPORT std::string	GetBondSmiles (const Bond *bond, const SmilesWriteParams &ps, int atomToLeftIdx=-1)
	returns the SMILES for a bond
std::string	GetBondSmiles (const Bond *bond, int atomToLeftIdx=-1, bool doKekule=false, bool allBondsExplicit=false)
	returns the SMILES for a bond

Enumeration Type Documentation

CXSmilesFields

enum RDKit::SmilesWrite::CXSmilesFields : uint32_t

Enumerator
CXSMILESFIELDS_ENUM_ITEMS

Definition at line 74 of file SmilesWrite.h.

Function Documentation

GetAtomSmiles() [1/2]

std::string RDKit::SmilesWrite::GetAtomSmiles ( const Atom *  atom, bool  doKekule = false, const Bond *  = nullptr, bool  allHsExplicit = false, bool  isomericSmiles = true  )

inline

returns the SMILES for an atom

Parameters

atom	: the atom to work with
doKekule	: we're doing kekulized smiles (e.g. don't use lower case for the atom label)
bondIn	: the bond we came into the atom on (unused)
allHsExplicit	: if true, hydrogen counts will be provided for every atom.
isomericSmiles	: if true, isomeric SMILES will be generated

Definition at line 112 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, GetAtomSmiles(), and RDKit::rdvalue_is().

GetAtomSmiles() [2/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::SmilesWrite::GetAtomSmiles	(	const Atom *	atom,
		const SmilesWriteParams &	ps
	)

returns the SMILES for an atom

Parameters

atom	: the atom to work with
ps	: the parameters controlling the SMILES generation

Referenced by GetAtomSmiles().

GetBondSmiles() [1/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::SmilesWrite::GetBondSmiles	(	const Bond *	bond,
		const SmilesWriteParams &	ps,
		int	atomToLeftIdx = -1
	)

returns the SMILES for a bond

Parameters

bond	: the bond to work with
ps	: the parameters controlling the SMILES generation
atomToLeftIdx	: the index of the atom preceding bond in the SMILES

Referenced by GetBondSmiles().

GetBondSmiles() [2/2]

std::string RDKit::SmilesWrite::GetBondSmiles ( const Bond *  bond, int  atomToLeftIdx = -1, bool  doKekule = false, bool  allBondsExplicit = false  )

inline

returns the SMILES for a bond

Parameters

bond	: the bond to work with
atomToLeftIdx	: the index of the atom preceding bond in the SMILES
doKekule	: we're doing kekulized smiles (e.g. write out bond orders for aromatic bonds)
allBondsExplicit	: if true, symbols will be included for all bonds.

Definition at line 143 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::doKekule, GetBondSmiles(), and RDKit::rdvalue_is().

getCXExtensions() [1/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::SmilesWrite::getCXExtensions	(	const ROMol &	mol,
		std::uint32_t	flags = CXSmilesFields::CX_ALL
	)

returns the cxsmiles data for a molecule

getCXExtensions() [2/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::SmilesWrite::getCXExtensions	(	const std::vector< ROMol * > &	mols,
		std::uint32_t	flags
	)

returns the cxsmiles data for a vector of molecules

inOrganicSubset()

RDKIT_SMILESPARSE_EXPORT bool RDKit::SmilesWrite::inOrganicSubset

(

int

atomicNumber

)

returns true if the atom number is in the SMILES organic subset