SmilesWrite.h File Reference

#include <RDGeneral/export.h>
#include <string>
#include <vector>
#include <memory>
#include <cstdint>
#include <limits>
#include <RDGeneral/BetterEnums.h>
#include <boost/shared_ptr.hpp>

Go to the source code of this file.

Classes
struct	RDKit::SmilesWriteParams

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

Functions
	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_ALL=0x7fffffff, CX_ALL_BUT_COORDS=CX_ALL ^ CX_COORDS)
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 std::string	RDKit::SmilesWrite::getCXExtensions (const std::vector< ROMol * > &mols, std::uint32_t flags)
	returns the cxsmiles data for a vector of molecules
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::BETTER_ENUM (RestoreBondDirOption, unsigned int, RestoreBondDirOptionTrue=0, RestoreBondDirOptionClear=1)
RDKIT_SMILESPARSE_EXPORT std::string	RDKit::MolToCXSmiles (const ROMol &mol, const SmilesWriteParams &ps, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL, RestoreBondDirOption restoreBondDirs=RestoreBondDirOption::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