SmilesWrite.h File Reference

#include <RDGeneral/export.h>
#include <string>
#include <vector>
#include <memory>
#include <cstdint>
#include <limits>

Go to the source code of this file.

Classes
struct	RDKit::SmilesWriteParams

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDKit::SmilesWrite
namespace	RDKit::SmilesWrite::detail

Macros
#define	CXSMILESFIELDS_ENUM_ITEMS
#define	CXSMILESFIELDS_ENUM_ITEM(k, v)   k = (v),
#define	CXSMILESFIELDS_STD_MAP_ITEM(k)   {#k, SmilesWrite::CXSmilesFields::k},
#define	CXSMILESFIELDS_ENUM_ITEM(k, v)   CXSMILESFIELDS_STD_MAP_ITEM(k)
#define	CXSMILESFIELDS_ITEMS_MAP
#define	RESTOREBONDDIROPTION_ENUM_ITEMS
#define	RESTOREBONDDIROPTION_ENUM_ITEM(k, v)   k = v,
#define	RESTOREBONDDIROPTION_STD_MAP_ITEM(k)   {#k, k},
#define	RESTOREBONDDIROPTION_ENUM_ITEM(k, v)    RESTOREBONDDIROPTION_STD_MAP_ITEM(k)
#define	RESTOREBONDDIROPTION_ITEMS_MAP

Enumerations
enum	RDKit::SmilesWrite::CXSmilesFields : uint32_t { RDKit::SmilesWrite::CXSMILESFIELDS_ENUM_ITEMS }
enum	RDKit::RestoreBondDirOption { RDKit::RESTOREBONDDIROPTION_ENUM_ITEMS }

Functions
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
RDKIT_SMILESPARSE_EXPORT bool	RDKit::SmilesWrite::inOrganicSubset (int atomicNumber)
	returns true if the atom number is in the SMILES organic subset
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::SmilesWrite::GetAtomSmiles (const Atom *atom, const SmilesWriteParams &ps)
	returns the SMILES for an atom
std::string	RDKit::SmilesWrite::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	RDKit::SmilesWrite::GetBondSmiles (const Bond *bond, const SmilesWriteParams &ps, int atomToLeftIdx=-1)
	returns the SMILES for a bond
std::string	RDKit::SmilesWrite::GetBondSmiles (const Bond *bond, int atomToLeftIdx=-1, bool doKekule=false, bool allBondsExplicit=false)
	returns the SMILES for a bond
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::SmilesWrite::detail::MolToSmiles (const ROMol &mol, const SmilesWriteParams &params, bool doingCXSmiles)
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::MolToSmiles (const ROMol &mol, const SmilesWriteParams &params)
	returns canonical SMILES for a molecule
std::string	RDKit::MolToSmiles (const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false, bool ignoreAtomMapNumbers=false)
	returns SMILES for a molecule, canonical by default
RDKIT_SMILESPARSE_EXPORT std::vector< std::string >	RDKit::MolToRandomSmilesVect (const ROMol &mol, unsigned int numSmiles, unsigned int randomSeed=0, bool doIsomericSmiles=true, bool doKekule=false, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns a vector of random SMILES for a molecule (may contain duplicates)
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::MolFragmentToSmiles (const ROMol &mol, const SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr)
	returns canonical SMILES for part of a molecule
std::string	RDKit::MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns canonical SMILES for part of a molecule
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::MolToCXSmiles (const ROMol &mol, const SmilesWriteParams &ps, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL, RestoreBondDirOption restoreBondDirs=RestoreBondDirOptionClear)
	returns canonical CXSMILES for a molecule
std::string	RDKit::MolToCXSmiles (const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false)
	returns canonical CXSMILES for a molecule
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::MolFragmentToCXSmiles (const ROMol &mol, const SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr)
	returns canonical CXSMILES for part of a molecule
std::string	RDKit::MolFragmentToCXSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns canonical CXSMILES for part of a molecule
void	RDKit::updateSmilesWriteParamsFromJSON (SmilesWriteParams &params, const std::string &details_json)
void	RDKit::updateSmilesWriteParamsFromJSON (SmilesWriteParams &params, const char *details_json)
void	RDKit::updateCXSmilesFieldsFromJSON (SmilesWrite::CXSmilesFields &cxSmilesFields, RestoreBondDirOption &restoreBondDirs, const std::string &details_json)
void	RDKit::updateCXSmilesFieldsFromJSON (SmilesWrite::CXSmilesFields &cxSmilesFields, RestoreBondDirOption &restoreBondDirs, const char *details_json)

Macro Definition Documentation

CXSMILESFIELDS_ENUM_ITEM [1/2]

#define CXSMILESFIELDS_ENUM_ITEM	(		k,
			v
	)		k = (v),

Definition at line 65 of file SmilesWrite.h.

CXSMILESFIELDS_ENUM_ITEM [2/2]

#define CXSMILESFIELDS_ENUM_ITEM	(		k,
			v
	)		CXSMILESFIELDS_STD_MAP_ITEM(k)

Definition at line 65 of file SmilesWrite.h.

CXSMILESFIELDS_ENUM_ITEMS

#define CXSMILESFIELDS_ENUM_ITEMS

Value:

  CXSMILESFIELDS_ENUM_ITEM(CX_NONE, 0)                   \
  CXSMILESFIELDS_ENUM_ITEM(CX_ATOM_LABELS, 1 << 0)       \
  CXSMILESFIELDS_ENUM_ITEM(CX_MOLFILE_VALUES, 1 << 1)    \
  CXSMILESFIELDS_ENUM_ITEM(CX_COORDS, 1 << 2)            \
  CXSMILESFIELDS_ENUM_ITEM(CX_RADICALS, 1 << 3)          \
  CXSMILESFIELDS_ENUM_ITEM(CX_ATOM_PROPS, 1 << 4)        \
  CXSMILESFIELDS_ENUM_ITEM(CX_LINKNODES, 1 << 5)         \
  CXSMILESFIELDS_ENUM_ITEM(CX_ENHANCEDSTEREO, 1 << 6)    \
  CXSMILESFIELDS_ENUM_ITEM(CX_SGROUPS, 1 << 7)           \
  CXSMILESFIELDS_ENUM_ITEM(CX_POLYMER, 1 << 8)           \
  CXSMILESFIELDS_ENUM_ITEM(CX_BOND_CFG, 1 << 9)          \
  CXSMILESFIELDS_ENUM_ITEM(CX_BOND_ATROPISOMER, 1 << 10) \
  CXSMILESFIELDS_ENUM_ITEM(CX_COORDINATE_BONDS, 1 << 11) \
  CXSMILESFIELDS_ENUM_ITEM(CX_ALL, 0x7fffffff)           \
  CXSMILESFIELDS_ENUM_ITEM(CX_ALL_BUT_COORDS, CX_ALL ^ CX_COORDS)

Definition at line 48 of file SmilesWrite.h.

CXSMILESFIELDS_ITEMS_MAP

#define CXSMILESFIELDS_ITEMS_MAP

Value:

  std::map<std::string, SmilesWrite::CXSmilesFields> { \
    CXSMILESFIELDS_ENUM_ITEMS                          \
  }

Definition at line 70 of file SmilesWrite.h.

CXSMILESFIELDS_STD_MAP_ITEM

#define CXSMILESFIELDS_STD_MAP_ITEM

(

k

)

{#k, SmilesWrite::CXSmilesFields::k},

Definition at line 68 of file SmilesWrite.h.

RESTOREBONDDIROPTION_ENUM_ITEM [1/2]

#define RESTOREBONDDIROPTION_ENUM_ITEM	(		k,
			v
	)		k = v,

Definition at line 268 of file SmilesWrite.h.

RESTOREBONDDIROPTION_ENUM_ITEM [2/2]

#define RESTOREBONDDIROPTION_ENUM_ITEM	(		k,
			v
	)		RESTOREBONDDIROPTION_STD_MAP_ITEM(k)

Definition at line 268 of file SmilesWrite.h.

RESTOREBONDDIROPTION_ENUM_ITEMS

#define RESTOREBONDDIROPTION_ENUM_ITEMS

Value:

  RESTOREBONDDIROPTION_ENUM_ITEM(RestoreBondDirOptionTrue,       \
                                 0) /*!< DO restore bond dirs */ \
  RESTOREBONDDIROPTION_ENUM_ITEM(RestoreBondDirOptionClear,      \
                                 1)

clear all bond dir information

Definition at line 266 of file SmilesWrite.h.

RESTOREBONDDIROPTION_ITEMS_MAP

#define RESTOREBONDDIROPTION_ITEMS_MAP

Value:

  std::map<std::string, RestoreBondDirOption> { \
    RESTOREBONDDIROPTION_ENUM_ITEMS             \
  }

Definition at line 274 of file SmilesWrite.h.

RESTOREBONDDIROPTION_STD_MAP_ITEM

#define RESTOREBONDDIROPTION_STD_MAP_ITEM

(

k

)

{#k, k},

Definition at line 271 of file SmilesWrite.h.