Implementation of Daylight SMARTS parser. More...
#include <openbabel/babelconfig.h>#include <ctype.h>#include <iomanip>#include <openbabel/mol.h>#include <openbabel/parsmart.h>#include <openbabel/stereo/stereo.h>#include <openbabel/stereo/tetrahedral.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 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 void | MarkGrowBonds (Pattern *pat) |
| static int | GetChiralFlag (AtomExpr *expr) |
| 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 | GetExprOrder (BondExpr *expr) |
| void | SmartsLexReplace (std::string &s, std::vector< std::pair< std::string, std::string > > &vlex) |
Variables | |
| static int | N_parsed_bonds |
Implementation of Daylight SMARTS parser.
| #define ELEMMAX 104 |
Referenced by OBSmartsPattern::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 |
| #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 |
Referenced by OpenBabel::AndAtomExpr(), OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::BuildAtomLeaf(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EqualAtomExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::IsInvalidAtom(), OpenBabel::NotAtomExpr(), OpenBabel::OrAtomExpr(), and OpenBabel::OrderAtomExpr().
| #define AE_RECUR 0x02 |
| #define AE_NOT 0x03 |
Referenced by OpenBabel::AtomLeafConflict(), OpenBabel::AtomLeafImplies(), OpenBabel::BuildAtomNot(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EqualAtomExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::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(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OpenBabel::GenerateAromElem(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), and OBSmartsPattern::ParseAtomExpr().
| #define AE_OR 0x05 |
Referenced by OpenBabel::AndAtomExpr(), OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), OpenBabel::OrAtomExpr(), OpenBabel::OrAtomExprLeaf(), and OBSmartsPattern::ParseAtomExpr().
| #define AE_ANDLO 0x06 |
Referenced by OpenBabel::CopyAtomExpr(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OBSmartsPattern::GetAtomicNum(), OBSmartsPattern::GetCharge(), OpenBabel::GetChiralFlag(), OpenBabel::NotAtomExpr(), and OBSmartsPattern::ParseAtomExpr().
| #define AL_CONST 0x01 |
Referenced by OpenBabel::AndAtomExpr(), OpenBabel::AndAtomExprLeaf(), OpenBabel::ConstrainRecursion(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::IsBooleanAtomLeaf(), OpenBabel::IsInvalidAtom(), OpenBabel::OrAtomExpr(), OBSmartsPattern::ParseComplexAtomPrimitive(), and OBSmartsPattern::ParseSimpleAtomPrimitive().
| #define AL_MASS 0x02 |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_AROM 0x03 |
| #define AL_ELEM 0x04 |
| #define AL_HCOUNT 0x05 |
| #define AL_NEGATIVE 0x06 |
| #define AL_POSITIVE 0x07 |
| #define AL_CONNECT 0x08 |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_DEGREE 0x09 |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_IMPLICIT 0x0a |
| #define AL_RINGS 0x0b |
| #define AL_SIZE 0x0c |
| #define AL_VALENCE 0x0d |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_CHIRAL 0x0e |
| #define AL_HYB 0x0f |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_RINGCONNECT 0x10 |
Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_CLOCKWISE 1 |
Referenced by OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_ANTICLOCKWISE 2 |
Referenced by OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define AL_UNSPECIFIED 0 |
Referenced by OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().
| #define OB_EVAL_STACKSIZE 40 |
Referenced by OpenBabel::GetChiralFlag().
This file is part of the documentation for Open Babel, version 2.3.
1.7.2.