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|
%{
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#pragma warning(disable:4786)
#include <iostream>
#include <string>
#include <GraphMol/GraphMol.h>
#include <GraphMol/Atom.h>
#include <GraphMol/Bond.h>
#include <RDGeneral/Invariant.h>
#include "SmilesParseOps.h"
#include <vector>
using namespace std;
extern int yylex();
#define YYDEBUG 1
void
yyerror( const char * msg )
{
std::cerr << msg << "\n";
}
using namespace RDKit;
extern vector<Mol *> molList_g;
static Mol * curMol_gps = 0;
int label_gs = -1;
%}
%union {
int moli;
RDKit::Atom * atom;
RDKit::Bond * bond;
int ival;
}
%token <atom> AROMATIC_ATOM ATOM ORGANIC_ATOM
%token <ival> DIGIT
%token GROUP_OPEN GROUP_CLOSE SEPARATOR LOOP_CONNECTOR
%token MINUS PLUS CHIRAL_MARKER CHI_CLASS CHI_CLASS_OH
%token H AT PERCENT
%token <bond> BOND
#if 0
%type <moli> mol branch hapto_branch dbl_hapto_branch
%type <atom> atomd general_atom element chiral_element h_element charge_element
%type <ival> number
#else
%type <moli> mol branch hapto_branch dbl_hapto_branch
%type <atom> atomd general_atom element chiral_element h_element charge_element
%type <ival> number
#endif
%token ATOM_OPEN ATOM_CLOSE
%token LT GT DATIVE_MARK
//%left SEPARATOR GROUP_CLOSE DIGIT
//%right GROUP_OPEN
%%
// FIX: mol MINUS DIGIT, mol LT DIGIT, mol GT DIGIT
mol: general_atom {
int sz = molList_g.size();
molList_g.resize( sz + 1);
molList_g[ sz ] = new Mol();
curMol_gps = molList_g[ sz ];
curMol_gps->addAtom($1);
delete $1;
$$ = sz;
}
| mol general_atom {
Mol *mp = molList_g[$$];
Mol::GRAPH_NODE_TYPE a1 = mp->getActiveAtom();
int atomIdx1=a1->getIdx();
int atomIdx2=mp->addAtom($2);
if(a1->getIsAromatic() && $2->getIsAromatic())
mp->addBond(atomIdx1,atomIdx2,Bond::AROMATIC);
else
mp->addBond(atomIdx1,atomIdx2,Bond::SINGLE);
delete $2;
}
| mol BOND general_atom {
Mol *mp = molList_g[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3);
if( $2->getBondType() == Bond::DATIVER ){
$2->setBeginAtomIdx(atomIdx1);
$2->setEndAtomIdx(atomIdx2);
$2->setBondType(Bond::DATIVE);
}else if ( $2->getBondType() == Bond::DATIVEL ){
$2->setBeginAtomIdx(atomIdx2);
$2->setEndAtomIdx(atomIdx1);
$2->setBondType(Bond::DATIVE);
} else {
$2->setBeginAtomIdx(atomIdx1);
$2->setEndAtomIdx(atomIdx2);
}
mp->addBond($2);
delete $2;
delete $3;
}
| mol MINUS general_atom {
Mol *mp = molList_g[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3);
mp->addBond(atomIdx1,atomIdx2,Bond::SINGLE);
delete $3;
}
| mol LT general_atom {
Mol *mp = molList_g[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3);
mp->addBond(atomIdx2,atomIdx1,Bond::DATIVE);
delete $3;
}
| mol GT general_atom {
Mol *mp = molList_g[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
int atomIdx2 = mp->addAtom($3);
mp->addBond(atomIdx1,atomIdx2,Bond::DATIVE);
delete $3;
}
| mol number {
Mol * mp = molList_g[$$];
mp->setAtomBookmark(mp->getActiveAtom(),$2);
}
| mol BOND number {
Mol * mp = molList_g[$$];
int atomIdx1 = mp->getActiveAtom()->getIdx();
Bond *newB_sp = mp->createPartialBond(atomIdx1,
$2->getBondType());
newB_sp->setBondDir($2->getBondDir());
mp->setAtomBookmark(mp->getActiveAtom(),$3);
mp->setBondBookmark(newB_sp,$3);
delete $2;
}
| mol branch {
Mol *m1_p = molList_g[$$],*m2_p=molList_g[$2];
AddFragToMol(m1_p,m2_p,Bond::UNSPECIFIED);
delete m2_p;
int sz = molList_g.size();
if ( sz==$2+1) {
molList_g.resize( sz-1 );
}
}
| mol BOND branch {
// FIX: should check that there's no partial bond already formed
// in the branch!
Mol *m1_p = molList_g[$$],*m2_p=molList_g[$3];
AddFragToMol(m1_p,m2_p,$2->getBondType(),$2->getBondDir());
delete m2_p;
delete $2;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| mol MINUS branch {
// FIX: should check that there's no partial bond already formed
// in the branch!
Mol *m1_p = molList_g[$$],*m2_p=molList_g[$3];
AddFragToMol(m1_p,m2_p,Bond::SINGLE);
delete m2_p;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| mol LT branch {
// FIX: should check that there's no partial bond already formed
// in the branch!
Mol *m1_p = molList_g[$$],*m2_p=molList_g[$3];
AddFragToMol(m1_p,m2_p,Bond::DATIVEL);
delete m2_p;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| mol GT branch {
// FIX: should check that there's no partial bond already formed
// in the branch!
Mol *m1_p = molList_g[$$],*m2_p=molList_g[$3];
AddFragToMol(m1_p,m2_p,Bond::DATIVER);
delete m2_p;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| mol SEPARATOR mol {
Mol *m1_p = molList_g[$1],*m2_p=molList_g[$3];
m1_p->insertMol(m2_p);
delete m2_p;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| mol LT dbl_hapto_branch GT mol {
Mol *m1_p = molList_g[$1],*m2_p=molList_g[$3],*m3_p=molList_g[$5];
AddDblHaptoBranch(m1_p,m2_p,m3_p,true,true,1,1);
delete m2_p;
molList_g.erase(molList_g.begin()+$3);
}
| mol LT hapto_branch {
Mol *m1_p = molList_g[$1],*m2_p=molList_g[$3];
AddHaptoBranch(m1_p,m2_p,true,true,1);
delete m2_p;
int sz = molList_g.size();
if ( sz==$3+1) {
molList_g.resize( sz-1 );
}
}
| hapto_branch GT mol {
Mol *m1_p = molList_g[$3],*m2_p=molList_g[$1];
AddHaptoBranch(m1_p,m2_p,false,true,1);
delete m2_p;
int sz = molList_g.size();
molList_g.erase(molList_g.begin()+$1);
}
| mol GROUP_OPEN LT hapto_branch GROUP_CLOSE {
Mol *m1_p = molList_g[$1],*m2_p=molList_g[$4];
AddHaptoBranch(m1_p,m2_p,false,true,1);
delete m2_p;
int sz = molList_g.size();
if ( sz==$4+1) {
molList_g.resize( sz-1 );
}
}
| error {
yyclearin;
std::cerr << "SMILES Parse Error" << std::endl;
molList_g.clear();
molList_g.resize(0);
YYABORT;
}
;
number: DIGIT
| PERCENT DIGIT DIGIT { $$ = $2*10 + $3; }
;
element: ORGANIC_ATOM
| AROMATIC_ATOM
| DIGIT ORGANIC_ATOM { $2->setMass( $1 ); $$ = $2; }
| ATOM
| DIGIT ATOM { $2->setMass( $1 ); $$ = $2; }
| H { $$ = new Atom(1); }
| DIGIT H { $$ = new Atom(1); $$->setMass( $1 ); }
;
chiral_element: element
| element chival
;
h_element: chiral_element
| chiral_element H { $$ = $1; $1->setNumExplicitHs(1);}
| chiral_element H DIGIT { $$ = $1; $1->setNumExplicitHs($3);}
;
/*sign: PLUS
| MINUS
;
*/
charge_element: h_element
| h_element PLUS { $1->setFormalCharge(1); }
| h_element PLUS PLUS { $1->setFormalCharge(2); }
| h_element MINUS { $1->setFormalCharge(-1); }
| h_element MINUS MINUS { $1->setFormalCharge(-2); }
| h_element PLUS DIGIT { $1->setFormalCharge($3); }
| h_element MINUS DIGIT { $1->setFormalCharge(-$3); }
/*| h_element sign DIGIT*/
;
general_atom: atomd
{
$$ = $1;
}
| atomd DATIVE_MARK
{
$$ = $1;
$1->setDativeFlag(1);
}
;
atomd: ORGANIC_ATOM
{
$$ = $1;
label_gs = -1;
}
| AROMATIC_ATOM
{
$$ = $1;
label_gs = -1;
}
| ATOM_OPEN charge_element ATOM_CLOSE
{
$$ = $2;
label_gs = -1;
$2->setNoImplicit(true);
}
;
chival: CHI_CLASS DIGIT
| AT
;
dbl_hapto_branch: hapto_branch DATIVE_MARK {
$$ = $1;
}
| dbl_hapto_branch GROUP_OPEN GT mol GROUP_CLOSE{
Mol *branch = molList_g[$1],*mol=molList_g[$4];
Atom *origActive = mol->getActiveAtom();
mol->setActiveAtom(0);
AddHaptoBranch(mol,branch,true,false,1);
$$ = $4-1;
molList_g.erase(molList_g.begin()+$1);
}
;
hapto_branch: DATIVE_MARK GROUP_OPEN mol GROUP_CLOSE {
$$ = $3;
}
| GROUP_OPEN mol GROUP_CLOSE DATIVE_MARK {
$$ = $2;
}
;
branch: GROUP_OPEN mol GROUP_CLOSE { $$ = $2; }
| GROUP_OPEN BOND mol GROUP_CLOSE {
$$ = $3;
int sz = molList_g.size();
curMol_gps = molList_g[ sz-1 ];
Bond *partialBond = curMol_gps->createPartialBond(0,$2->getBondType());
partialBond->setBondDir($2->getBondDir());
curMol_gps->setBondBookmark(partialBond,
ci_LEADING_BOND);
delete $2;
}
| GROUP_OPEN MINUS mol GROUP_CLOSE {
$$ = $3;
int sz = molList_g.size();
curMol_gps = molList_g[ sz-1 ];
Bond *partialBond = curMol_gps->createPartialBond(0,Bond::SINGLE);
curMol_gps->setBondBookmark(partialBond,
ci_LEADING_BOND);
}
| GROUP_OPEN GT mol GROUP_CLOSE {
$$ = $3;
int sz = molList_g.size();
curMol_gps = molList_g[ sz-1 ];
Bond *partialBond = curMol_gps->createPartialBond(0,Bond::DATIVER);
curMol_gps->setBondBookmark(partialBond,
ci_LEADING_BOND);
}
| GROUP_OPEN LT mol GROUP_CLOSE {
$$ = $3;
int sz = molList_g.size();
curMol_gps = molList_g[ sz-1 ];
Bond *partialBond = curMol_gps->createPartialBond(0,Bond::DATIVEL);
curMol_gps->setBondBookmark(partialBond,
ci_LEADING_BOND);
}
;
%%
|