5 #ifndef BALL_STRUCTURE_SMILES_PARSER_H 6 #define BALL_STRUCTURE_SMILES_PARSER_H 12 #ifndef BALL_KERNEL_ATOM_H 16 #ifndef BALL_KERNEL_BOND_H 20 #ifndef BALL_KERNEL_SYSTEM_H 87 Size getDefaultValence()
const;
88 Size countRealValences()
const;
97 void setChirality(
const ChiralDef& chirality) { chirality_ = chirality; }
100 void setAromatic(
bool is_aromatic) { is_aromatic_ = is_aromatic; };
134 void parse(
const String& s);
138 const System& getSystem()
const;
144 SPAtom* createAtom(
const String& symbol,
bool in_bracket =
false);
148 void createBonds(
SPAtom* atom,
const ConnectionList* list);
154 void addMissingHydrogens();
176 #endif // BALL_STRUCTURE_SMILES_PARSER_H
void setIsotope(Size isotope)
std::pair< ChiralClass, Position > ChiralDef
std::vector< SPAtom * > connections_
bool isInBrackets() const
void setInBrackets(bool in_brackets)
BALL_EXTERN_VARIABLE const double E
Euler's number - base of the natural logarithm.
void setFormalCharge(Index charge)
void setAromatic(bool is_aromatic)
void setChirality(const ChiralDef &chirality)
const ChiralDef & getChirality() const
std::vector< SPAtom * > all_atoms_
static SmilesParser * current_parser_
std::list< Position > ConnectionList
Index getFormalCharge() const
SmilesParser * current_parser