parsmart.cpp File Reference

Implementation of Daylight SMARTS parser. More...

#include <openbabel/babelconfig.h>
#include <ctype.h>
#include <iomanip>
#include <openbabel/mol.h>
#include <openbabel/parsmart.h>

Namespaces

namespace OpenBabel

Defines

#define ELEMMAX   104

#define ATOMEXPRPOOL   1

#define BONDEXPRPOOL   1

#define ATOMPOOL   1

#define BONDPOOL   1

#define BF_NONRINGUNSPEC   0x0001

#define BF_NONRINGDOWN   0x0002

#define BF_NONRINGUP   0x0004

#define BF_NONRINGDOUBLE   0x0008

#define BF_NONRINGTRIPLE   0x0010

#define BF_RINGUNSPEC   0x0020

#define BF_RINGDOWN   0x0040

#define BF_RINGUP   0x0080

#define BF_RINGAROM   0x0100

#define BF_RINGDOUBLE   0x0200

#define BF_RINGTRIPLE   0x0400

#define BS_ALL   0x07FF

#define BS_SINGLE   0x00E7

#define BS_DOUBLE   0x0208

#define BS_TRIPLE   0x0410

#define BS_AROM   0x0100

#define BS_UP   0x0084

#define BS_DOWN   0x0042

#define BS_UPUNSPEC   0x00A5

#define BS_DOWNUNSPEC   0x0063

#define BS_RING   0x07E0

#define BS_DEFAULT   0x01E7

#define AE_LEAF   0x01

#define AE_RECUR   0x02

#define AE_NOT   0x03

#define AE_ANDHI   0x04

#define AE_OR   0x05

#define AE_ANDLO   0x06

#define AL_CONST   0x01

#define AL_MASS   0x02

#define AL_AROM   0x03

#define AL_ELEM   0x04

#define AL_HCOUNT   0x05

#define AL_NEGATIVE   0x06

#define AL_POSITIVE   0x07

#define AL_CONNECT   0x08

#define AL_DEGREE   0x09

#define AL_IMPLICIT   0x0a

#define AL_RINGS   0x0b

#define AL_SIZE   0x0c

#define AL_VALENCE   0x0d

#define AL_CHIRAL   0x0e

#define AL_HYB   0x0f

#define AL_RINGCONNECT   0x10

#define AL_CLOCKWISE   1

#define AL_ANTICLOCKWISE   2

#define AL_UNSPECIFIED   0

#define OB_EVAL_STACKSIZE   40

Functions

static bool match (OBMol &mol, Pattern *pat, std::vector< std::vector< int > > &mlist, bool single=false)

static bool EvalAtomExpr (AtomExpr *expr, OBAtom *atom)

static bool EvalBondExpr (BondExpr *expr, OBBond *bond)

static int GetVectorBinding ()

static int CreateAtom (Pattern *, AtomExpr *, int, int vb=0)

static void FatalAllocationError (const char *ptr)

static void FreePattern (Pattern *)

static Pattern * CopyPattern (Pattern *)

static AtomExpr * AllocAtomExpr (void)

static AtomExpr * CopyAtomExpr (AtomExpr *expr)

static void FreeAtomExpr (AtomExpr *expr)

static AtomExpr * BuildAtomLeaf (int prop, int val)

static AtomExpr * BuildAtomNot (AtomExpr *expr)

static AtomExpr * BuildAtomBin (int op, AtomExpr *lft, AtomExpr *rgt)

static AtomExpr * BuildAtomRecurs (Pattern *pat)

static AtomExpr * GenerateElement (int elem)

static AtomExpr * GenerateAromElem (int elem, int flag)

static int IsInvalidAtom (AtomExpr *expr)

static BondExpr * AllocBondExpr (void)

static BondExpr * CopyBondExpr (BondExpr *expr)

static bool EquivalentBondExpr (BondExpr *expr1, BondExpr *expr2)

static void FreeBondExpr (BondExpr *expr)

static BondExpr * BuildBondLeaf (int prop, int val)

static BondExpr * BuildBondNot (BondExpr *expr)

static BondExpr * BuildBondBin (int op, BondExpr *lft, BondExpr *rgt)

static BondExpr * GenerateDefaultBond (void)

static Pattern * AllocPattern (void)

static int CreateBond (Pattern *pat, BondExpr *expr, int src, int dst)

static Pattern * ParseSMARTSPattern (void)

static Pattern * ParseSMARTSPart (Pattern *, int)

static Pattern * SMARTSError (Pattern *pat)

static AtomExpr * ParseSimpleAtomPrimitive (void)

static AtomExpr * ParseComplexAtomPrimitive (void)

static AtomExpr * ParseAtomExpr (int level)

static BondExpr * ParseBondPrimitive (void)

static BondExpr * ParseBondExpr (int level)

static Pattern * ParseSMARTSError (Pattern *pat, BondExpr *expr)

static Pattern * SMARTSParser (Pattern *pat, ParseState *stat, int prev, int part)

static void MarkGrowBonds (Pattern *pat)

static int GetChiralFlag (AtomExpr *expr)

static Pattern * ParseSMARTSString (char *ptr)

Pattern * ParseSMARTSRecord (char *ptr)

static void TraverseSMARTS (Pattern *pat, int i)

static AtomExpr * NotAtomExpr (AtomExpr *)

static AtomExpr * AndAtomExpr (AtomExpr *, AtomExpr *)

static AtomExpr * OrAtomExpr (AtomExpr *, AtomExpr *)

static int IsBooleanAtomLeaf (AtomExpr *expr)

static int IsNegatingAtomLeaf (AtomExpr *expr)

static int EqualAtomExpr (AtomExpr *lft, AtomExpr *rgt)

static int OrderAtomExpr (AtomExpr *lft, AtomExpr *rgt)

static int AtomLeafConflict (AtomExpr *lft, AtomExpr *rgt)

static int AtomExprConflict (AtomExpr *lft, AtomExpr *rgt)

static int AtomLeafImplies (AtomExpr *lft, AtomExpr *rgt)

static int AtomExprImplied (AtomExpr *lft, AtomExpr *rgt)

static AtomExpr * AtomExprImplies (AtomExpr *lft, AtomExpr *rgt)

static AtomExpr * AndAtomExprLeaf (AtomExpr *lft, AtomExpr *rgt)

static AtomExpr * ConstrainRecursion (AtomExpr *recur, AtomExpr *expr)

static AtomExpr * OrAtomExprLeaf (AtomExpr *lft, AtomExpr *rgt)

static int GetBondLeafIndex (BondExpr *expr)

static int GetBondExprIndex (BondExpr *expr)

void SetupAtomMatchTable (std::vector< std::vector< bool > > &ttab, Pattern *pat, OBMol &mol)

static void FastSingleMatch (OBMol &mol, Pattern *pat, std::vector< std::vector< int > > &mlist)

static int GetExprOrder (BondExpr *expr)

void SmartsLexReplace (std::string &s, std::vector< std::pair< std::string, std::string > > &vlex)

Variables

std::vector< std::pair
< Pattern *, std::vector< bool > > > RSCACHE

static char * MainPtr

static char * LexPtr

static char Buffer [BUFF_SIZE]

static char Descr [BUFF_SIZE]

Detailed Description

Implementation of Daylight SMARTS parser.

Define Documentation

#define ELEMMAX 104

Referenced by OpenBabel::ParseComplexAtomPrimitive().

#define ATOMEXPRPOOL 1

#define BONDEXPRPOOL 1

#define ATOMPOOL 1

Referenced by OpenBabel::CreateAtom().

#define BONDPOOL 1

Referenced by OpenBabel::CreateBond().

#define BF_NONRINGUNSPEC 0x0001

#define BF_NONRINGDOWN 0x0002

#define BF_NONRINGUP 0x0004

#define BF_NONRINGDOUBLE 0x0008

#define BF_NONRINGTRIPLE 0x0010

#define BF_RINGUNSPEC 0x0020

#define BF_RINGDOWN 0x0040

#define BF_RINGUP 0x0080

#define BF_RINGAROM 0x0100

#define BF_RINGDOUBLE 0x0200

#define BF_RINGTRIPLE 0x0400

#define BS_ALL 0x07FF

Referenced by OpenBabel::GetBondExprIndex(), and OpenBabel::GetBondLeafIndex().

#define BS_SINGLE 0x00E7

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_DOUBLE 0x0208

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_TRIPLE 0x0410

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_AROM 0x0100

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_UP 0x0084

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_DOWN 0x0042

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_UPUNSPEC 0x00A5

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_DOWNUNSPEC 0x0063

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_RING 0x07E0

Referenced by OpenBabel::GetBondLeafIndex().

#define BS_DEFAULT 0x01E7

#define AE_LEAF 0x01

Referenced by OpenBabel::AndAtomExpr(), OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::BuildAtomLeaf(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EqualAtomExpr(), OpenBabel::EquivalentBondExpr(), OpenBabel::EvalAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::IsInvalidAtom(), OpenBabel::NotAtomExpr(), OpenBabel::OrAtomExpr(), and OpenBabel::OrderAtomExpr().

#define AE_RECUR 0x02

Referenced by OpenBabel::AndAtomExpr(), OpenBabel::BuildAtomRecurs(), OpenBabel::CopyAtomExpr(), OpenBabel::EqualAtomExpr(), OpenBabel::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), and OpenBabel::GetChiralFlag().

#define AE_NOT 0x03

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::BuildAtomNot(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EqualAtomExpr(), OpenBabel::EquivalentBondExpr(), OpenBabel::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), and OpenBabel::OrderAtomExpr().

#define AE_ANDHI 0x04

Referenced by OpenBabel::AndAtomExpr(), OpenBabel::AndAtomExprLeaf(), OpenBabel::AtomExprConflict(), OpenBabel::AtomExprImplied(), OpenBabel::AtomExprImplies(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OpenBabel::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OpenBabel::GenerateAromElem(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), and OpenBabel::ParseAtomExpr().

#define AE_OR 0x05

Referenced by OpenBabel::AndAtomExpr(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OpenBabel::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), OpenBabel::OrAtomExpr(), OpenBabel::OrAtomExprLeaf(), and OpenBabel::ParseAtomExpr().

#define AE_ANDLO 0x06

Referenced by OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OpenBabel::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), and OpenBabel::ParseAtomExpr().

#define AL_CONST 0x01

Referenced by OpenBabel::AndAtomExpr(), OpenBabel::AndAtomExprLeaf(), OpenBabel::ConstrainRecursion(), OpenBabel::EvalAtomExpr(), OpenBabel::IsBooleanAtomLeaf(), OpenBabel::IsInvalidAtom(), OpenBabel::OrAtomExpr(), OpenBabel::ParseComplexAtomPrimitive(), and OpenBabel::ParseSimpleAtomPrimitive().

#define AL_MASS 0x02

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_AROM 0x03

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::EvalAtomExpr(), OpenBabel::GenerateAromElem(), OpenBabel::IsBooleanAtomLeaf(), OpenBabel::ParseComplexAtomPrimitive(), and OpenBabel::ParseSimpleAtomPrimitive().

#define AL_ELEM 0x04

Referenced by OpenBabel::EvalAtomExpr(), OpenBabel::GenerateAromElem(), OpenBabel::GenerateElement(), and OBSmartsPattern::GetAtomicNum().

#define AL_HCOUNT 0x05

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_NEGATIVE 0x06

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::EvalAtomExpr(), OBSmartsPattern::GetCharge(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_POSITIVE 0x07

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::EvalAtomExpr(), OBSmartsPattern::GetCharge(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_CONNECT 0x08

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_DEGREE 0x09

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_IMPLICIT 0x0a

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_RINGS 0x0b

Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::EvalAtomExpr(), OpenBabel::IsNegatingAtomLeaf(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_SIZE 0x0c

Referenced by OpenBabel::AtomLeafImplies(), OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_VALENCE 0x0d

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_CHIRAL 0x0e

Referenced by OpenBabel::EvalAtomExpr(), OpenBabel::GetChiralFlag(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_HYB 0x0f

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_RINGCONNECT 0x10

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_CLOCKWISE 1

Referenced by OpenBabel::EvalAtomExpr(), OpenBabel::match(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_ANTICLOCKWISE 2

Referenced by OpenBabel::EvalAtomExpr(), OpenBabel::match(), and OpenBabel::ParseComplexAtomPrimitive().

#define AL_UNSPECIFIED 0

Referenced by OpenBabel::EvalAtomExpr(), and OpenBabel::ParseComplexAtomPrimitive().

#define OB_EVAL_STACKSIZE 40

Referenced by OpenBabel::GetChiralFlag().


Namespaces
namespace	OpenBabel
Defines
#define	ELEMMAX 104
#define	ATOMEXPRPOOL 1
#define	BONDEXPRPOOL 1
#define	ATOMPOOL 1
#define	BONDPOOL 1
#define	BF_NONRINGUNSPEC 0x0001
#define	BF_NONRINGDOWN 0x0002
#define	BF_NONRINGUP 0x0004
#define	BF_NONRINGDOUBLE 0x0008
#define	BF_NONRINGTRIPLE 0x0010
#define	BF_RINGUNSPEC 0x0020
#define	BF_RINGDOWN 0x0040
#define	BF_RINGUP 0x0080
#define	BF_RINGAROM 0x0100
#define	BF_RINGDOUBLE 0x0200
#define	BF_RINGTRIPLE 0x0400
#define	BS_ALL 0x07FF
#define	BS_SINGLE 0x00E7
#define	BS_DOUBLE 0x0208
#define	BS_TRIPLE 0x0410
#define	BS_AROM 0x0100
#define	BS_UP 0x0084
#define	BS_DOWN 0x0042
#define	BS_UPUNSPEC 0x00A5
#define	BS_DOWNUNSPEC 0x0063
#define	BS_RING 0x07E0
#define	BS_DEFAULT 0x01E7
#define	AE_LEAF 0x01
#define	AE_RECUR 0x02
#define	AE_NOT 0x03
#define	AE_ANDHI 0x04
#define	AE_OR 0x05
#define	AE_ANDLO 0x06
#define	AL_CONST 0x01
#define	AL_MASS 0x02
#define	AL_AROM 0x03
#define	AL_ELEM 0x04
#define	AL_HCOUNT 0x05
#define	AL_NEGATIVE 0x06
#define	AL_POSITIVE 0x07
#define	AL_CONNECT 0x08
#define	AL_DEGREE 0x09
#define	AL_IMPLICIT 0x0a
#define	AL_RINGS 0x0b
#define	AL_SIZE 0x0c
#define	AL_VALENCE 0x0d
#define	AL_CHIRAL 0x0e
#define	AL_HYB 0x0f
#define	AL_RINGCONNECT 0x10
#define	AL_CLOCKWISE 1
#define	AL_ANTICLOCKWISE 2
#define	AL_UNSPECIFIED 0
#define	OB_EVAL_STACKSIZE 40
Functions
static bool	match (OBMol &mol, Pattern *pat, std::vector< std::vector< int > > &mlist, bool single=false)
static bool	EvalAtomExpr (AtomExpr expr, OBAtom atom)
static bool	EvalBondExpr (BondExpr expr, OBBond bond)
static int	GetVectorBinding ()
static int	CreateAtom (Pattern , AtomExpr , int, int vb=0)
static void	FatalAllocationError (const char *ptr)
static void	FreePattern (Pattern *)
static Pattern *	CopyPattern (Pattern *)
static AtomExpr *	AllocAtomExpr (void)
static AtomExpr *	CopyAtomExpr (AtomExpr *expr)
static void	FreeAtomExpr (AtomExpr *expr)
static AtomExpr *	BuildAtomLeaf (int prop, int val)
static AtomExpr *	BuildAtomNot (AtomExpr *expr)
static AtomExpr *	BuildAtomBin (int op, AtomExpr lft, AtomExpr rgt)
static AtomExpr *	BuildAtomRecurs (Pattern *pat)
static AtomExpr *	GenerateElement (int elem)
static AtomExpr *	GenerateAromElem (int elem, int flag)
static int	IsInvalidAtom (AtomExpr *expr)
static BondExpr *	AllocBondExpr (void)
static BondExpr *	CopyBondExpr (BondExpr *expr)
static bool	EquivalentBondExpr (BondExpr expr1, BondExpr expr2)
static void	FreeBondExpr (BondExpr *expr)
static BondExpr *	BuildBondLeaf (int prop, int val)
static BondExpr *	BuildBondNot (BondExpr *expr)
static BondExpr *	BuildBondBin (int op, BondExpr lft, BondExpr rgt)
static BondExpr *	GenerateDefaultBond (void)
static Pattern *	AllocPattern (void)
static int	CreateBond (Pattern pat, BondExpr expr, int src, int dst)
static Pattern *	ParseSMARTSPattern (void)
static Pattern *	ParseSMARTSPart (Pattern *, int)
static Pattern *	SMARTSError (Pattern *pat)
static AtomExpr *	ParseSimpleAtomPrimitive (void)
static AtomExpr *	ParseComplexAtomPrimitive (void)
static AtomExpr *	ParseAtomExpr (int level)
static BondExpr *	ParseBondPrimitive (void)
static BondExpr *	ParseBondExpr (int level)
static Pattern *	ParseSMARTSError (Pattern pat, BondExpr expr)
static Pattern *	SMARTSParser (Pattern pat, ParseState stat, int prev, int part)
static void	MarkGrowBonds (Pattern *pat)
static int	GetChiralFlag (AtomExpr *expr)
static Pattern *	ParseSMARTSString (char *ptr)
Pattern *	ParseSMARTSRecord (char *ptr)
static void	TraverseSMARTS (Pattern *pat, int i)
static AtomExpr *	NotAtomExpr (AtomExpr *)
static AtomExpr *	AndAtomExpr (AtomExpr , AtomExpr )
static AtomExpr *	OrAtomExpr (AtomExpr , AtomExpr )
static int	IsBooleanAtomLeaf (AtomExpr *expr)
static int	IsNegatingAtomLeaf (AtomExpr *expr)
static int	EqualAtomExpr (AtomExpr lft, AtomExpr rgt)
static int	OrderAtomExpr (AtomExpr lft, AtomExpr rgt)
static int	AtomLeafConflict (AtomExpr lft, AtomExpr rgt)
static int	AtomExprConflict (AtomExpr lft, AtomExpr rgt)
static int	AtomLeafImplies (AtomExpr lft, AtomExpr rgt)
static int	AtomExprImplied (AtomExpr lft, AtomExpr rgt)
static AtomExpr *	AtomExprImplies (AtomExpr lft, AtomExpr rgt)
static AtomExpr *	AndAtomExprLeaf (AtomExpr lft, AtomExpr rgt)
static AtomExpr *	ConstrainRecursion (AtomExpr recur, AtomExpr expr)
static AtomExpr *	OrAtomExprLeaf (AtomExpr lft, AtomExpr rgt)
static int	GetBondLeafIndex (BondExpr *expr)
static int	GetBondExprIndex (BondExpr *expr)
void	SetupAtomMatchTable (std::vector< std::vector< bool > > &ttab, Pattern *pat, OBMol &mol)
static void	FastSingleMatch (OBMol &mol, Pattern *pat, std::vector< std::vector< int > > &mlist)
static int	GetExprOrder (BondExpr *expr)
void	SmartsLexReplace (std::string &s, std::vector< std::pair< std::string, std::string > > &vlex)
Variables
std::vector< std::pair < Pattern *, std::vector< bool > > >	RSCACHE
static char *	MainPtr
static char *	LexPtr
static char	Buffer [BUFF_SIZE]
static char	Descr [BUFF_SIZE]