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|
%{
// $Id$
//
// Copyright (C) 2001-2010 Randal Henne, Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <cstring>
#include <iostream>
#include <vector>
#include <list>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesParseOps.h>
#include <RDGeneral/RDLog.h>
#include "smiles.tab.hpp"
extern int yysmiles_lex(YYSTYPE *,void *);
#define YYDEBUG 1
void
yysmiles_error( const char *input,
std::vector<RDKit::RWMol *> *ms,
std::list<unsigned int> *branchPoints,
void *scanner,const char * msg )
{
throw RDKit::SmilesParseException(msg);
}
using namespace RDKit;
namespace {
void yyErrorCleanup(std::vector<RDKit::RWMol *> *molList){
for(std::vector<RDKit::RWMol *>::iterator iter=molList->begin();
iter != molList->end(); ++iter){
delete *iter;
}
molList->clear();
molList->resize(0);
}
}
%}
%define api.pure
%lex-param {yyscan_t *scanner}
%parse-param {const char *input}
%parse-param {std::vector<RDKit::RWMol *> *molList}
%parse-param {std::list<unsigned int> *branchPoints}
%parse-param {void *scanner}
%union {
int moli;
RDKit::Atom * atom;
RDKit::Bond * bond;
int ival;
}
%token <atom> AROMATIC_ATOM_TOKEN ATOM_TOKEN ORGANIC_ATOM_TOKEN
%token <ival> NONZERO_DIGIT_TOKEN ZERO_TOKEN
%token GROUP_OPEN_TOKEN GROUP_CLOSE_TOKEN SEPARATOR_TOKEN LOOP_CONNECTOR_TOKEN
%token MINUS_TOKEN PLUS_TOKEN CHIRAL_MARKER_TOKEN CHI_CLASS_TOKEN CHI_CLASS_OH_TOKEN
%token H_TOKEN AT_TOKEN PERCENT_TOKEN COLON_TOKEN
%token <bond> BOND_TOKEN
%type <moli> cmpd mol
%type <atom> atomd element chiral_element h_element charge_element simple_atom
%type <ival> nonzero_number number ring_number digit
%token ATOM_OPEN_TOKEN ATOM_CLOSE_TOKEN
%token EOS_TOKEN
%%
/* --------------------------------------------------------------- */
cmpd: mol
| cmpd SEPARATOR_TOKEN mol {
RWMol *m1_p = (*molList)[$1],*m2_p=(*molList)[$3];
SmilesParseOps::AddFragToMol(m1_p,m2_p,Bond::IONIC,Bond::NONE,true);
delete m2_p;
int sz = molList->size();
if ( sz==$3+1) {
molList->resize( sz-1 );
}
}
| cmpd error EOS_TOKEN{
yyclearin;
yyerrok;
yyErrorCleanup(molList);
YYABORT;
}
| cmpd EOS_TOKEN {
YYACCEPT;
}
| error EOS_TOKEN {
yyclearin;
yyerrok;
yyErrorCleanup(molList);
YYABORT;
}
;
/* --------------------------------------------------------------- */
// FIX: mol MINUS DIGIT
mol: atomd {
int sz = molList->size();
molList->resize( sz + 1);
(*molList)[ sz ] = new RWMol();
RDKit::RWMol *curMol = (*molList)[ sz ];
$1->setProp("_SmilesStart",1);
curMol->addAtom($1);
delete $1;
$$ = sz;
}
| mol atomd {
RWMol *mp = (*molList)[$$];
Atom *a1 = mp->getActiveAtom();
int atomIdx1=a1->getIdx();
int atomIdx2=mp->addAtom($2,true,true);
mp->addBond(atomIdx1,atomIdx2,
SmilesParseOps::GetUnspecifiedBondType(mp,a1,mp->getAtomWithIdx(atomIdx2)));
//delete $2;
}
| mol BOND_TOKEN atomd {
RWMol *mp = (*molList)[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3,true,true);
if( $2->getBondType() == Bond::DATIVER ){
$2->setBeginAtomIdx(atomIdx1);
$2->setEndAtomIdx(atomIdx2);
$2->setBondType(Bond::DATIVE);
}else if ( $2->getBondType() == Bond::DATIVEL ){
$2->setBeginAtomIdx(atomIdx2);
$2->setEndAtomIdx(atomIdx1);
$2->setBondType(Bond::DATIVE);
} else {
$2->setBeginAtomIdx(atomIdx1);
$2->setEndAtomIdx(atomIdx2);
}
mp->addBond($2,true);
//delete $3;
}
| mol MINUS_TOKEN atomd {
RWMol *mp = (*molList)[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3,true,true);
mp->addBond(atomIdx1,atomIdx2,Bond::SINGLE);
//delete $3;
}
| mol ring_number {
RWMol * mp = (*molList)[$$];
Atom *atom=mp->getActiveAtom();
mp->setAtomBookmark(atom,$2);
Bond *newB = mp->createPartialBond(atom->getIdx(),
Bond::UNSPECIFIED);
mp->setBondBookmark(newB,$2);
newB->setProp("_unspecifiedOrder",1);
INT_VECT tmp;
if(atom->hasProp("_RingClosures")){
atom->getProp("_RingClosures",tmp);
}
tmp.push_back(-($2+1));
atom->setProp("_RingClosures",tmp);
}
| mol BOND_TOKEN ring_number {
RWMol * mp = (*molList)[$$];
Atom *atom=mp->getActiveAtom();
Bond *newB = mp->createPartialBond(atom->getIdx(),
$2->getBondType());
newB->setBondDir($2->getBondDir());
mp->setAtomBookmark(atom,$3);
mp->setBondBookmark(newB,$3);
INT_VECT tmp;
if(atom->hasProp("_RingClosures")){
atom->getProp("_RingClosures",tmp);
}
tmp.push_back(-($3+1));
atom->setProp("_RingClosures",tmp);
delete $2;
}
| mol MINUS_TOKEN ring_number {
RWMol * mp = (*molList)[$$];
Atom *atom=mp->getActiveAtom();
Bond *newB = mp->createPartialBond(atom->getIdx(),
Bond::SINGLE);
mp->setAtomBookmark(atom,$3);
mp->setBondBookmark(newB,$3);
INT_VECT tmp;
if(atom->hasProp("_RingClosures")){
atom->getProp("_RingClosures",tmp);
}
tmp.push_back(-($3+1));
atom->setProp("_RingClosures",tmp);
}
| mol GROUP_OPEN_TOKEN atomd {
RWMol *mp = (*molList)[$$];
Atom *a1 = mp->getActiveAtom();
int atomIdx1=a1->getIdx();
int atomIdx2=mp->addAtom($3,true,true);
mp->addBond(atomIdx1,atomIdx2,
SmilesParseOps::GetUnspecifiedBondType(mp,a1,mp->getAtomWithIdx(atomIdx2)));
//delete $3;
branchPoints->push_back(atomIdx1);
}
| mol GROUP_OPEN_TOKEN BOND_TOKEN atomd {
RWMol *mp = (*molList)[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($4,true,true);
if( $3->getBondType() == Bond::DATIVER ){
$3->setBeginAtomIdx(atomIdx1);
$3->setEndAtomIdx(atomIdx2);
$3->setBondType(Bond::DATIVE);
}else if ( $3->getBondType() == Bond::DATIVEL ){
$3->setBeginAtomIdx(atomIdx2);
$3->setEndAtomIdx(atomIdx1);
$3->setBondType(Bond::DATIVE);
} else {
$3->setBeginAtomIdx(atomIdx1);
$3->setEndAtomIdx(atomIdx2);
}
mp->addBond($3,true);
//delete $4;
branchPoints->push_back(atomIdx1);
}
| mol GROUP_OPEN_TOKEN MINUS_TOKEN atomd {
RWMol *mp = (*molList)[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($4,true,true);
mp->addBond(atomIdx1,atomIdx2,Bond::SINGLE);
//delete $4;
branchPoints->push_back(atomIdx1);
}
| mol GROUP_CLOSE_TOKEN {
if(branchPoints->empty()) yyerror(input,molList,branchPoints,scanner,"extra close parentheses");
RWMol *mp = (*molList)[$$];
mp->setActiveAtom(branchPoints->back());
branchPoints->pop_back();
}
;
/* --------------------------------------------------------------- */
atomd: simple_atom
| ATOM_OPEN_TOKEN charge_element COLON_TOKEN number ATOM_CLOSE_TOKEN
{
$$ = $2;
$$->setNoImplicit(true);
$$->setProp("molAtomMapNumber",$4);
}
| ATOM_OPEN_TOKEN charge_element ATOM_CLOSE_TOKEN
{
$$ = $2;
$2->setNoImplicit(true);
}
;
/* --------------------------------------------------------------- */
charge_element: h_element
| h_element PLUS_TOKEN { $1->setFormalCharge(1); }
| h_element PLUS_TOKEN PLUS_TOKEN { $1->setFormalCharge(2); }
| h_element PLUS_TOKEN number { $1->setFormalCharge($3); }
| h_element MINUS_TOKEN { $1->setFormalCharge(-1); }
| h_element MINUS_TOKEN MINUS_TOKEN { $1->setFormalCharge(-2); }
| h_element MINUS_TOKEN number { $1->setFormalCharge(-$3); }
;
/* --------------------------------------------------------------- */
h_element: H_TOKEN { $$ = new Atom(1); }
| number H_TOKEN { $$ = new Atom(1); $$->setIsotope($1); }
| H_TOKEN H_TOKEN { $$ = new Atom(1); $$->setNumExplicitHs(1); }
| number H_TOKEN H_TOKEN { $$ = new Atom(1); $$->setIsotope($1); $$->setNumExplicitHs(1);}
| H_TOKEN H_TOKEN number { $$ = new Atom(1); $$->setNumExplicitHs($3); }
| number H_TOKEN H_TOKEN number { $$ = new Atom(1); $$->setIsotope($1); $$->setNumExplicitHs($4);}
| chiral_element
| chiral_element H_TOKEN { $$ = $1; $1->setNumExplicitHs(1);}
| chiral_element H_TOKEN number { $$ = $1; $1->setNumExplicitHs($3);}
;
/* --------------------------------------------------------------- */
chiral_element: element
| element AT_TOKEN { $1->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW); }
| element AT_TOKEN AT_TOKEN { $1->setChiralTag(Atom::CHI_TETRAHEDRAL_CW); }
;
/* --------------------------------------------------------------- */
element: simple_atom
| number simple_atom { $2->setIsotope( $1 ); $$ = $2; }
| ATOM_TOKEN
| number ATOM_TOKEN { $2->setIsotope( $1 ); $$ = $2; }
;
/* --------------------------------------------------------------- */
simple_atom: ORGANIC_ATOM_TOKEN
| AROMATIC_ATOM_TOKEN
;
/* --------------------------------------------------------------- */
ring_number: digit
| PERCENT_TOKEN NONZERO_DIGIT_TOKEN digit { $$ = $2*10+$3; }
;
/* --------------------------------------------------------------- */
number: ZERO_TOKEN
| nonzero_number
;
/* --------------------------------------------------------------- */
nonzero_number: NONZERO_DIGIT_TOKEN
| nonzero_number digit { $$ = $1*10 + $2; }
;
digit: NONZERO_DIGIT_TOKEN
| ZERO_TOKEN
;
/*
chival: CHI_CLASS_TOKEN DIGIT_TOKEN
| AT_TOKEN
;
*/
%%
|
