RDKit::SmilesWrite Namespace Reference

Namespaces
namespace	detail

Functions
	BETTER_ENUM (CXSmilesFields, uint32_t, CX_NONE=0, CX_ATOM_LABELS=1<< 0, CX_MOLFILE_VALUES=1<< 1, CX_COORDS=1<< 2, CX_RADICALS=1<< 3, CX_ATOM_PROPS=1<< 4, CX_LINKNODES=1<< 5, CX_ENHANCEDSTEREO=1<< 6, CX_SGROUPS=1<< 7, CX_POLYMER=1<< 8, CX_BOND_CFG=1<< 9, CX_BOND_ATROPISOMER=1<< 10, CX_COORDINATE_BONDS=1<< 11, CX_HYDROGEN_BONDS=1<< 12, CX_ZERO_BONDS=1<< 13, CX_ALL=0x7fffffff, CX_ALL_BUT_COORDS=CX_ALL ^ CX_COORDS)
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

Function Documentation

BETTER_ENUM()

RDKit::SmilesWrite::BETTER_ENUM	(	CXSmilesFields	,
		uint32_t	,
		CX_NONE	= 0,
		CX_ATOM_LABELS	= 1<< 0,
		CX_MOLFILE_VALUES	= 1<< 1,
		CX_COORDS	= 1<< 2,
		CX_RADICALS	= 1<< 3,
		CX_ATOM_PROPS	= 1<< 4,
		CX_LINKNODES	= 1<< 5,
		CX_ENHANCEDSTEREO	= 1<< 6,
		CX_SGROUPS	= 1<< 7,
		CX_POLYMER	= 1<< 8,
		CX_BOND_CFG	= 1<< 9,
		CX_BOND_ATROPISOMER	= 1<< 10,
		CX_COORDINATE_BONDS	= 1<< 11,
		CX_HYDROGEN_BONDS	= 1<< 12,
		CX_ZERO_BONDS	= 1<< 13,
		CX_ALL	= 0x7fffffff,
		CX_ALL_BUT_COORDS	= CX_ALL ^ CX_COORDS )

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 106 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allHsExplicit, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, and GetAtomSmiles().

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

References RDKIT_SMILESPARSE_EXPORT.

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

References RDKIT_SMILESPARSE_EXPORT.

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 137 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allBondsExplicit, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, and GetBondSmiles().

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

References RDKIT_SMILESPARSE_EXPORT.

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

References RDKIT_SMILESPARSE_EXPORT.

inOrganicSubset()

RDKIT_SMILESPARSE_EXPORT bool RDKit::SmilesWrite::inOrganicSubset

(

int

atomicNumber

)

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

References RDKIT_SMILESPARSE_EXPORT.