parsmart.h

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/**********************************************************************
parsmart.h - Daylight SMARTS parser.
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_PARSMART_H
#define OB_PARSMART_H

#include <string>
#include <vector>

#include "mol.h"

/*==========================*/
/*  SMARTS Data Structures  */
/*==========================*/

#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_CLOCKWISE     1
#define AL_ANTICLOCKWISE 2

namespace OpenBabel
{

  // mark this so that SWIG will not attempt to wrap for scripting languages

#ifndef SWIG

typedef union _AtomExpr {
    int type;
    struct
    {
        int type;
        int prop;
        int value;
    }
    leaf;
    struct
    {
        int type;
        void *recur;
    }
    recur;
    struct
    {
        int type;
        union _AtomExpr *arg;
    }
    mon;
    struct
    {
        int type;
        union _AtomExpr *lft;
        union _AtomExpr *rgt;
    }
    bin;
} AtomExpr;

#define BE_LEAF      0x01
#define BE_ANDHI     0x02
#define BE_ANDLO     0x03
#define BE_NOT       0x04
#define BE_OR        0x05

#define BL_CONST     0x01
#define BL_TYPE      0x02

#define BT_SINGLE     0x01
#define BT_DOUBLE     0x02
#define BT_TRIPLE     0x03
#define BT_AROM       0x04
#define BT_UP         0x05
#define BT_DOWN       0x06
#define BT_UPUNSPEC   0x07
#define BT_DOWNUNSPEC 0x08
#define BT_RING       0x09

typedef union _BondExpr {
    int type;
    struct
    {
        int type;
        int prop;
        int value;
    }
    leaf;
    struct
    {
        int type;
        union _BondExpr *arg;
    }
    mon;
    struct
    {
        int type;
        union _BondExpr *lft;
        union _BondExpr *rgt;
    }
    bin;
} BondExpr;

typedef struct
{
    BondExpr *expr;
    int src,dst;
    int visit;
    bool grow;
}
BondSpec;

typedef struct
{
    AtomExpr *expr;
    int visit;
    int part;
    int chiral_flag;
    int vb;
}
AtomSpec;

typedef struct
{
    int aalloc,acount;
    int balloc,bcount;
    bool ischiral;
    AtomSpec *atom;
    BondSpec *bond;
    int parts;
}
Pattern;
#else
// for SWIG, just forward declare that we have some Pattern struct
// (but this is private and not wrapped for scripting languages)
struct Pattern;
#endif

// class introduction in parsmart.cpp
class OBAPI OBSmartsPattern
{
protected:
    std::vector<bool>                   _growbond;
    std::vector<std::vector<int> >      _mlist;
    Pattern                             *_pat;
    std::string                         _str;

public:
    OBSmartsPattern()
    {
        _pat=NULL;
    }
    virtual ~OBSmartsPattern();

    OBSmartsPattern(const OBSmartsPattern& cp)
    {
        _pat = NULL;
        *this = cp;
    }
    OBSmartsPattern& operator=(const OBSmartsPattern& cp)
    {
        if (_pat)
            delete [] _pat;
        _pat = NULL;
        std::string s = cp._str;
        Init(s);
        return (*this);
    }

    unsigned int NumMatches() const
    {
        return (unsigned int)_mlist.size();
    }
    unsigned int NumAtoms()   const
    {
        return _pat ? _pat->acount : 0;
    }
    unsigned int NumBonds()   const
    {
        return _pat ? _pat->bcount : 0;
    }

    int          GetAtomicNum(int);
    void         GetBond(int&,int&,int&,int);
    int          GetCharge(int);
    const std::string &GetSMARTS() const
    {
        return _str;
    }
    std::string  &GetSMARTS()
    {
        return _str;
    }
    int          GetVectorBinding(int idx) const
    {
        return(_pat->atom[idx].vb);
    }
    bool         Empty()                   const
    {
        return(_pat == NULL);
    }
    bool         IsValid()                 const
    {
        return(_pat != NULL);
    }
    bool         Init(const char*);
    bool         Init(const std::string&);
    void         WriteMapList(std::ostream&);

    bool Match(OBMol &mol, bool single=false);
    bool RestrictedMatch(OBMol &mol, std::vector<std::pair<int,int> > &pairs, bool single=false);
    bool RestrictedMatch(OBMol &mol, OBBitVec &bv, bool single=false);

    std::vector<std::vector<int> > &GetMapList()
    {
        return(_mlist);
    }
    std::vector<std::vector<int> > &GetUMapList();
    std::vector<std::vector<int> >::iterator BeginMList()
    {
        return(_mlist.begin());
    }
    std::vector<std::vector<int> >::iterator EndMList()
    {
        return(_mlist.end());
    }
};

class OBAPI OBSSMatch //used for fast exhaustive matching
{
protected:
    bool        *_uatoms;
    OBMol       *_mol;
    Pattern     *_pat;
    std::vector<int>  _map;

public:
    OBSSMatch(OBMol&,Pattern*);
    ~OBSSMatch();
    void Match(std::vector<std::vector<int> > &v, int bidx=-1);
};

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

} // end namespace OpenBabel

#endif // OB_PARSMART_H

---

This file is part of the documentation for Open Babel, version 2.0.2.

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