Go to the documentation of this file.
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
100 void setAromatic(
bool is_aromatic) { is_aromatic_ = is_aromatic; };
144 SPAtom* createAtom(
const String& symbol,
bool in_bracket =
false);
176 #endif // BALL_STRUCTURE_SMILES_PARSER_H
std::list< Position > ConnectionList
void parse(const String &s)
const System & getSystem() const
std::vector< SPAtom * > connections_
void setIsotope(Size isotope)
Index getFormalCharge() const
Size getDefaultValence() const
void setZEType(ZEIsomerType type)
ZEIsomerType getZEType() const
std::pair< ChiralClass, Position > ChiralDef
void setFormalCharge(Index charge)
SmilesParser * current_parser
Size countRealValences() const
void addMissingHydrogens()
std::vector< SPAtom * > all_atoms_
void createBonds(SPAtom *atom, const ConnectionList *list)
void setChirality(const ChiralDef &chirality)
SPAtom(const String &symbol, bool in_brackets)
const ChiralDef & getChirality() const
SPBond(SPAtom *first, SPAtom *second, Index order=1)
void setInBrackets(bool in_brackets)
static SmilesParser * current_parser_
BALL_EXTERN_VARIABLE const double E
Euler's number - base of the natural logarithm.
void createBond(SPAtom *left, SPAtom *right, Index order)
SmilesParser(const SmilesParser &parser)
void setAromatic(bool is_aromatic)
bool isInBrackets() const