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

Enumerations
enum	RDKit::SmilesWrite::CXSmilesFields : uint32_t {   RDKit::SmilesWrite::CX_NONE = 0 , RDKit::SmilesWrite::CX_ATOM_LABELS = 1 << 0 , RDKit::SmilesWrite::CX_MOLFILE_VALUES = 1 << 1 , RDKit::SmilesWrite::CX_COORDS = 1 << 2 ,   RDKit::SmilesWrite::CX_RADICALS = 1 << 3 , RDKit::SmilesWrite::CX_ATOM_PROPS = 1 << 4 , RDKit::SmilesWrite::CX_LINKNODES = 1 << 5 , RDKit::SmilesWrite::CX_ENHANCEDSTEREO = 1 << 6 ,   RDKit::SmilesWrite::CX_SGROUPS = 1 << 7 , RDKit::SmilesWrite::CX_POLYMER = 1 << 8 , RDKit::SmilesWrite::CX_BOND_CFG = 1 << 9 , RDKit::SmilesWrite::CX_BOND_ATROPISOMER = 1 << 10 ,   RDKit::SmilesWrite::CX_ALL = 0x7fffffff , RDKit::SmilesWrite::CX_ALL_BUT_COORDS = CX_ALL ^ CX_COORDS }
enum	RDKit::RestoreBondDirOption { RDKit::RestoreBondDirOptionTrue = 0 , RDKit::RestoreBondDirOptionClear = 1 }

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, bool doKekule=false, const Bond *bondIn=nullptr, bool allHsExplicit=false, bool isomericSmiles=true)
	returns the SMILES for an atom
RDKIT_SMILESPARSE_EXPORT 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)
	returns canonical SMILES for a molecule
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