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|
%{
#include <BALL/STRUCTURE/smilesParser.h>
using namespace BALL;
using namespace std;
extern int yylex();
extern void yyerror(char const* s);
%}
%union {
char* text;
Index number;
SmilesParser::SPAtom* atom;
SmilesParser::ConnectionList* conns;
SmilesParser::ChiralDef* chiral;
}
%token <text> TK_ATOM
%token <text> TK_ORG_SUBSET_ATOM
%token <text> TK_HYDROGEN
%token <number> TK_DIGIT
%token <number> TK_ONE_TWO
%token <number> TK_ONE_TWO_THREE
%token <text> TK_CHIRAL_CLASS_TH
%token <text> TK_CHIRAL_CLASS_AL
%token <text> TK_CHIRAL_CLASS_SP
%token <text> TK_CHIRAL_CLASS_TB
%token <text> TK_CHIRAL_CLASS_OH
%type <atom> smiles
%type <atom> expression
%type <atom> node
%type <atom> atom
%type <atom> atom_symbol
%type <atom> org_subset_atom_symbol
%type <number> bond
%type <number> opt_charge
%type <number> pos_charge
%type <number> neg_charge
%type <conns> opt_connection_list
%type <conns> connection_list
%type <number> opt_isotope
%type <number> isotope
%type <number> opt_hydrogens
%type <chiral> opt_chirality
%start smiles
%%
smiles: expression
{
}
;
expression:
node { $$ = $1; }
| node bond expression { new SmilesParser::SPBond($1, $3, $2); $$ = $1; }
| node expression { new SmilesParser::SPBond($1, $2); $$ = $1; }
;
node:
atom { $$ = $1; }
| node '(' expression ')' { new SmilesParser::SPBond($3, $1, 1); $$ = $1; }
| node '(' bond expression ')' { new SmilesParser::SPBond($4, $1, $3); $$ = $1; }
;
atom:
org_subset_atom_symbol opt_connection_list
{
$$ = $1;
if ($2 != 0)
{
SmilesParser::state.current_parser->createBonds($1, $2);
delete ($2);
}
}
| '[' opt_isotope atom_symbol opt_chirality opt_hydrogens opt_charge ']' opt_connection_list
{
$3->setFormalCharge($6);
$3->setIsotope($2);
$3->setInBrackets(true);
if ($5 != 0)
{
for (int i = 0; i < $5; i++)
{
new SmilesParser::SPBond(SmilesParser::state.current_parser->createAtom("H"), $3);
}
}
if ($4 != 0)
{
$3->setChirality(*$4);
delete $4;
}
if ($8 != 0)
{
SmilesParser::state.current_parser->createBonds($3, $8);
delete $8;
}
$$ = $3;
}
| '[' opt_isotope TK_HYDROGEN opt_charge ']'
{
$$ = SmilesParser::state.current_parser->createAtom("H");
$$->setFormalCharge($4);
$$->setIsotope($2);
$$->setInBrackets(true);
}
;
opt_hydrogens:
{ $$ = 0; }
| TK_HYDROGEN
{
$$ = 1;
}
| TK_HYDROGEN TK_DIGIT
{
$$ = $2;
}
;
org_subset_atom_symbol:
TK_ORG_SUBSET_ATOM { $$ = SmilesParser::state.current_parser->createAtom(yylval.text); }
;
atom_symbol:
org_subset_atom_symbol { $$ = $1; }
| TK_ATOM { $$ = SmilesParser::state.current_parser->createAtom(yylval.text); }
;
opt_charge:
{
$$ = 0;
}
| pos_charge
{
$$ = $1;
}
| neg_charge
{
$$ = $1;
}
;
pos_charge:
'+' { $$ = 1; }
| '+' '+' { $$ = 2; }
| '+' '+' '+' { $$ = 3; }
| '+' TK_DIGIT { $$ = $2; }
;
neg_charge:
'-' { $$ = -1; }
| '-' '-' { $$ = -2; }
| '-' '-' '-' { $$ = -3; }
| '-' TK_DIGIT { $$ = -$2; }
;
opt_connection_list:
{ $$ = 0; }
| connection_list
{
$$ = $1;
}
;
connection_list:
TK_DIGIT
{
$$ = new SmilesParser::ConnectionList;
$$->push_back($1);
}
| connection_list TK_DIGIT
{
$$ = $1;
$$->push_back($2);
}
;
opt_isotope:
{ $$ = 0; }
| isotope { $$ = $1; }
;
isotope:
TK_DIGIT { $$ = $1; }
| isotope TK_DIGIT { $$ = 10 * $1 + $2; }
;
bond:
'.' { $$ = 0; }
| '-' { $$ = 1; }
| ':' { $$ = 1; }
| '=' { $$ = 2; }
| '#' { $$ = 3; }
| '/' { $$ = 1; }
| '\\' { $$ = 1; }
;
opt_chirality:
{ $$ = 0; }
| '@'
{
$$ = new SmilesParser::ChiralDef(SmilesParser::TH, 1);
}
| '@' '@'
{
$$ = new SmilesParser::ChiralDef(SmilesParser::TH, 1);
}
| TK_CHIRAL_CLASS_TH TK_ONE_TWO
{
$$ = new SmilesParser::ChiralDef(SmilesParser::TH, $2);
}
| TK_CHIRAL_CLASS_AL TK_ONE_TWO
{
$$ = new SmilesParser::ChiralDef(SmilesParser::AL, $2);
}
| TK_CHIRAL_CLASS_TB TK_DIGIT
{
$$ = new SmilesParser::ChiralDef(SmilesParser::TB, $2);
}
| TK_CHIRAL_CLASS_SP TK_DIGIT
{
$$ = new SmilesParser::ChiralDef(SmilesParser::TB, $2);
}
| TK_CHIRAL_CLASS_OH TK_DIGIT
{
$$ = new SmilesParser::ChiralDef(SmilesParser::OH, $2);
}
;
%%
void yyerror(char const* s)
{
throw Exception::ParseError(__FILE__, 0,
SmilesParser::state.buffer,
String(s) + String(" (at position ")
+ String(SmilesParser::state.char_count) + String(")"));
}
|
