11 #ifndef _RD_SMILESWRITE_H 12 #define _RD_SMILESWRITE_H 22 namespace SmilesWrite {
43 bool doKekule =
false,
44 const Bond *bondIn = 0,
45 bool allHsExplicit =
false,
46 bool isomericSmiles =
true);
58 const Bond *bond,
int atomToLeftIdx = -1,
bool doKekule =
false,
59 bool allBondsExplicit =
false);
77 const ROMol &mol,
bool doIsomericSmiles =
true,
bool doKekule =
false,
78 int rootedAtAtom = -1,
bool canonical =
true,
bool allBondsExplicit =
false,
79 bool allHsExplicit =
false,
bool doRandom =
false);
105 const ROMol &mol,
const std::vector<int> &atomsToUse,
106 const std::vector<int> *bondsToUse = 0,
107 const std::vector<std::string> *atomSymbols = 0,
108 const std::vector<std::string> *bondSymbols = 0,
109 bool doIsomericSmiles =
true,
bool doKekule =
false,
int rootedAtAtom = -1,
110 bool canonical =
true,
bool allBondsExplicit =
false,
111 bool allHsExplicit =
false);
129 const ROMol &mol,
bool doIsomericSmiles =
true,
bool doKekule =
false,
130 int rootedAtAtom = -1,
bool canonical =
true,
bool allBondsExplicit =
false,
131 bool allHsExplicit =
false,
bool doRandom =
false);
157 const ROMol &mol,
const std::vector<int> &atomsToUse,
158 const std::vector<int> *bondsToUse = 0,
159 const std::vector<std::string> *atomSymbols = 0,
160 const std::vector<std::string> *bondSymbols = 0,
161 bool doIsomericSmiles =
true,
bool doKekule =
false,
int rootedAtAtom = -1,
162 bool canonical =
true,
bool allBondsExplicit =
false,
163 bool allHsExplicit =
false);
RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToCXSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=0, const std::vector< std::string > *atomSymbols=0, const std::vector< std::string > *bondSymbols=0, 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
RDKIT_SMILESPARSE_EXPORT bool inOrganicSubset(int atomicNumber)
returns true if the atom number is in the SMILES organic subset
RDKIT_SMILESPARSE_EXPORT std::string getCXExtensions(const ROMol &mol)
returns the cxsmiles data for a molecule
RDKIT_SMILESPARSE_EXPORT std::string 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::string GetBondSmiles(const Bond *bond, int atomToLeftIdx=-1, bool doKekule=false, bool allBondsExplicit=false)
returns the SMILES for a bond
RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmiles(const Atom *atom, bool doKekule=false, const Bond *bondIn=0, bool allHsExplicit=false, bool isomericSmiles=true)
returns the SMILES for an atom
RDKIT_SMILESPARSE_EXPORT std::string 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
#define RDKIT_SMILESPARSE_EXPORT
class for representing a bond
RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=0, const std::vector< std::string > *atomSymbols=0, const std::vector< std::string > *bondSymbols=0, 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
The class for representing atoms.