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; };
SmilesParser(const SmilesParser &parser)
const System & getSystem() const
void createBond(SPAtom *left, SPAtom *right, Index order)
void parse(const String &s)
std::pair< ChiralClass, Position > ChiralDef
void createBonds(SPAtom *atom, const ConnectionList *list)
std::vector< SPAtom * > all_atoms_
SPAtom * createAtom(const String &symbol, bool in_bracket=false)
std::list< Position > ConnectionList
std::vector< SPAtom * > connections_
void addMissingHydrogens()
static SmilesParser * current_parser_
SPBond(SPAtom *first, SPAtom *second, Index order=1)
ZEIsomerType getZEType() const
void setZEType(ZEIsomerType type)
bool isInBrackets() const
void setInBrackets(bool in_brackets)
void setIsotope(Size isotope)
SPAtom(const String &symbol, bool in_brackets)
const ChiralDef & getChirality() const
void setAromatic(bool is_aromatic)
Size getDefaultValence() const
Size countRealValences() const
void setChirality(const ChiralDef &chirality)
void setFormalCharge(Index charge)
Index getFormalCharge() const
SmilesParser * current_parser