11 #ifndef RD_SMILESWRITE_H_012020
12 #define RD_SMILESWRITE_H_012020
22 namespace SmilesWrite {
41 bool doKekule =
false,
42 const Bond *bondIn =
nullptr,
43 bool allHsExplicit =
false,
44 bool isomericSmiles =
true);
56 const Bond *bond,
int atomToLeftIdx = -1,
bool doKekule =
false,
57 bool allBondsExplicit =
false);
75 const ROMol &mol,
bool doIsomericSmiles =
true,
bool doKekule =
false,
76 int rootedAtAtom = -1,
bool canonical =
true,
bool allBondsExplicit =
false,
77 bool allHsExplicit =
false,
bool doRandom =
false);
93 const ROMol &mol,
unsigned int numSmiles,
unsigned int randomSeed = 0,
94 bool doIsomericSmiles =
true,
bool doKekule =
false,
95 bool allBondsExplicit =
false,
bool allHsExplicit =
false);
123 const ROMol &mol,
const std::vector<int> &atomsToUse,
124 const std::vector<int> *bondsToUse =
nullptr,
125 const std::vector<std::string> *atomSymbols =
nullptr,
126 const std::vector<std::string> *bondSymbols =
nullptr,
127 bool doIsomericSmiles =
true,
bool doKekule =
false,
int rootedAtAtom = -1,
128 bool canonical =
true,
bool allBondsExplicit =
false,
129 bool allHsExplicit =
false);
146 const ROMol &mol,
bool doIsomericSmiles =
true,
bool doKekule =
false,
147 int rootedAtAtom = -1,
bool canonical =
true,
bool allBondsExplicit =
false,
148 bool allHsExplicit =
false,
bool doRandom =
false);
176 const ROMol &mol,
const std::vector<int> &atomsToUse,
177 const std::vector<int> *bondsToUse =
nullptr,
178 const std::vector<std::string> *atomSymbols =
nullptr,
179 const std::vector<std::string> *bondSymbols =
nullptr,
180 bool doIsomericSmiles =
true,
bool doKekule =
false,
int rootedAtAtom = -1,
181 bool canonical =
true,
bool allBondsExplicit =
false,
182 bool allHsExplicit =
false);
The class for representing atoms.
class for representing a bond
#define RDKIT_SMILESPARSE_EXPORT
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 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=nullptr, bool allHsExplicit=false, bool isomericSmiles=true)
returns the SMILES for an atom
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 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
RDKIT_SMILESPARSE_EXPORT std::vector< std::string > 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 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 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