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RDKit
Open-source cheminformatics and machine learning.
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11 #ifndef RD_SMILESWRITE_H_012020
12 #define RD_SMILESWRITE_H_012020
22 namespace SmilesWrite {
41 bool doKekule =
false,
42 const Bond *bondIn = 0,
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 = 0,
125 const std::vector<std::string> *atomSymbols = 0,
126 const std::vector<std::string> *bondSymbols = 0,
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 = 0,
178 const std::vector<std::string> *atomSymbols = 0,
179 const std::vector<std::string> *bondSymbols = 0,
180 bool doIsomericSmiles =
true,
bool doKekule =
false,
int rootedAtAtom = -1,
181 bool canonical =
true,
bool allBondsExplicit =
false,
182 bool allHsExplicit =
false);
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
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
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
RDKIT_SMILESPARSE_EXPORT std::string GetBondSmiles(const Bond *bond, int atomToLeftIdx=-1, bool doKekule=false, bool allBondsExplicit=false)
returns the SMILES for a bond
The class for representing atoms.
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 getCXExtensions(const ROMol &mol)
returns the cxsmiles data for a molecule
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
#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::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)