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|
%{
// $Id: esmiles.flex 4974 2006-02-18 00:49:21Z glandrum $
//
// Copyright (C) 2002-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#pragma warning(disable:4786)
#include <stdio.h>
#undef yywrap
#undef YY_INPUT
#include "InputFiller.h"
extern INPUT_FUNC_TYPE gp_myInput;
#define YY_INPUT( b, r, ms) (r = gp_myInput( b, ms ))
#include <GraphMol/GraphMol.h>
#include <GraphMol/Atom.h>
#include <GraphMol/Bond.h>
#include <GraphMol/PeriodicTable.h>
#ifdef WIN32
#include <io.h>
#endif
#include <string>
#include "smiles.tab.h"
#ifdef WIN32
int
isatty( int fd )
{
return _isatty( fd );
}
#endif
using namespace RDKit;
static PeriodicTable * gl_ptab = PeriodicTable::getTable();
%}
%s IN_ATOM_STATE
%%
@[' ']*TH |
@[' ']*AL |
@[' ']*SQ |
@[' ']*BP |
@[' ']*OH { return CHI_CLASS; }
@+ { return AT; }
<IN_ATOM_STATE>He |
<IN_ATOM_STATE>Li |
<IN_ATOM_STATE>Be |
<IN_ATOM_STATE>Ne |
<IN_ATOM_STATE>Na |
<IN_ATOM_STATE>Mg |
<IN_ATOM_STATE>Al |
<IN_ATOM_STATE>Si |
<IN_ATOM_STATE>Ar |
<IN_ATOM_STATE>K |
<IN_ATOM_STATE>Ca |
<IN_ATOM_STATE>Sc |
<IN_ATOM_STATE>Ti |
<IN_ATOM_STATE>V |
<IN_ATOM_STATE>Cr |
<IN_ATOM_STATE>Mn |
<IN_ATOM_STATE>Co |
<IN_ATOM_STATE>Fe |
<IN_ATOM_STATE>Ni |
<IN_ATOM_STATE>Cu |
<IN_ATOM_STATE>Zn |
<IN_ATOM_STATE>Ga |
<IN_ATOM_STATE>Ge |
<IN_ATOM_STATE>As |
<IN_ATOM_STATE>Se |
<IN_ATOM_STATE>Kr |
<IN_ATOM_STATE>Rb |
<IN_ATOM_STATE>Sr |
<IN_ATOM_STATE>Y |
<IN_ATOM_STATE>Zr |
<IN_ATOM_STATE>Nb |
<IN_ATOM_STATE>Mo |
<IN_ATOM_STATE>Tc |
<IN_ATOM_STATE>Ru |
<IN_ATOM_STATE>Rh |
<IN_ATOM_STATE>Pd |
<IN_ATOM_STATE>Ag |
<IN_ATOM_STATE>Cd |
<IN_ATOM_STATE>In |
<IN_ATOM_STATE>Sn |
<IN_ATOM_STATE>Sb |
<IN_ATOM_STATE>Te |
<IN_ATOM_STATE>Xe |
<IN_ATOM_STATE>Cs |
<IN_ATOM_STATE>Ba |
<IN_ATOM_STATE>La |
<IN_ATOM_STATE>Ce |
<IN_ATOM_STATE>Pr |
<IN_ATOM_STATE>Nd |
<IN_ATOM_STATE>Pm |
<IN_ATOM_STATE>Sm |
<IN_ATOM_STATE>Eu |
<IN_ATOM_STATE>Gd |
<IN_ATOM_STATE>Tb |
<IN_ATOM_STATE>Dy |
<IN_ATOM_STATE>Ho |
<IN_ATOM_STATE>Er |
<IN_ATOM_STATE>Tm |
<IN_ATOM_STATE>Yb |
<IN_ATOM_STATE>Lu |
<IN_ATOM_STATE>Hf |
<IN_ATOM_STATE>Ta |
<IN_ATOM_STATE>W |
<IN_ATOM_STATE>Re |
<IN_ATOM_STATE>Os |
<IN_ATOM_STATE>Ir |
<IN_ATOM_STATE>Pt |
<IN_ATOM_STATE>Au |
<IN_ATOM_STATE>Hg |
<IN_ATOM_STATE>Tl |
<IN_ATOM_STATE>Pb |
<IN_ATOM_STATE>Bi |
<IN_ATOM_STATE>Po |
<IN_ATOM_STATE>At |
<IN_ATOM_STATE>Rn |
<IN_ATOM_STATE>Fr |
<IN_ATOM_STATE>Ra |
<IN_ATOM_STATE>Ac |
<IN_ATOM_STATE>Th |
<IN_ATOM_STATE>Pa |
<IN_ATOM_STATE>U |
<IN_ATOM_STATE>Np |
<IN_ATOM_STATE>Pu |
<IN_ATOM_STATE>Am |
<IN_ATOM_STATE>Cm |
<IN_ATOM_STATE>Bk |
<IN_ATOM_STATE>Cf |
<IN_ATOM_STATE>Es |
<IN_ATOM_STATE>Fm |
<IN_ATOM_STATE>Md |
<IN_ATOM_STATE>No |
<IN_ATOM_STATE>Lr { yylval.atom = new Atom( gl_ptab->getAtomicNumber( yytext ) );
return ATOM;
}
B |
C |
N |
O |
P |
S |
F |
Cl |
Br |
I { yylval.atom = new Atom( gl_ptab->getAtomicNumber( yytext ) );
return ORGANIC_ATOM;
}
H {
return H;
}
c { yylval.atom = new Atom ( 6 );
yylval.atom->setIsAromatic(true);
return AROMATIC_ATOM;
}
n { yylval.atom = new Atom( 7 );
yylval.atom->setIsAromatic(true);
return AROMATIC_ATOM;
}
o { yylval.atom = new Atom( 8 );
yylval.atom->setIsAromatic(true);
return AROMATIC_ATOM;
}
p { yylval.atom = new Atom( 15 );
yylval.atom->setIsAromatic(true);
return AROMATIC_ATOM;
}
s { yylval.atom = new Atom( 16 );
yylval.atom->setIsAromatic(true);
return AROMATIC_ATOM;
}
\- { return MINUS; }
\+ { return PLUS; }
\< { return LT; }
\> { return GT; }
[\=\#\:] { yylval.bond = new Bond();
Bond::BondType bt;
switch(yytext[0]){
case '=':
bt = Bond::DOUBLE;
break;
case '#':
bt = Bond::TRIPLE;
break;
case ':':
bt = Bond::AROMATIC;
break;
}
yylval.bond->setBondType(bt);
return BOND; }
[\\] { yylval.bond = new Bond(Bond::SINGLE);
yylval.bond->setBondDir(Bond::ENDDOWNRIGHT);
return BOND; }
[\/] { yylval.bond = new Bond(Bond::SINGLE);
yylval.bond->setBondDir(Bond::ENDUPRIGHT);
return BOND; }
\( { return GROUP_OPEN; }
\) { return GROUP_CLOSE; }
\[ { BEGIN IN_ATOM_STATE; return ATOM_OPEN; }
<IN_ATOM_STATE>\] { BEGIN INITIAL; return ATOM_CLOSE; }
\. { return SEPARATOR; }
\_ { return DATIVE_MARK; }
\% { return PERCENT; }
[0-9] { yylval.ival = atoi( yytext ); return DIGIT; }
\n return 0;
. return yytext[0];
%%
int yywrap( void ) { return 1; }
|
