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]

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Detailed Description

Implementation of Daylight SMARTS parser.

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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().