src/openbabel/parsmart.hpp

/**********************************************************************
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.hpp"

/*==========================*/
/*  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

//! \brief A SMARTS parser internal atomic expression
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

//! \brief A SMARTS parser internal bond expression
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;

//! \brief A SMARTS parser internal bond specification
typedef struct
{
    BondExpr *expr;
    int src,dst;
    int visit;
    bool grow;
}
BondSpec;

//! \brief A SMARTS parser internal bond specification
typedef struct
{
    AtomExpr *expr;
    int visit;
    int part;
    int chiral_flag;
    int vb;
}
AtomSpec;

//! \brief A SMARTS parser internal pattern
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
//! \brief SMARTS (SMiles ARbitrary Target Specification) substructure searching
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());
    }
};

//! Performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling.
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

//! \file parsmart.h
//! \brief Daylight SMARTS parser.
Revision:	3057
Committed:	Thu Oct 19 20:49:05 2006 UTC (17 years, 11 months ago) by gezelter
File size:	6538 byte(s)
Log Message:	updated OpenBabel to version 2.0.2
#	User	Rev	Content
1	tim	2440	/**********************************************************************
2			parsmart.h - Daylight SMARTS parser.
3
4			Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5			Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
6
7			This file is part of the Open Babel project.
8			For more information, see <http://openbabel.sourceforge.net/>
9
10			This program is free software; you can redistribute it and/or modify
11			it under the terms of the GNU General Public License as published by
12			the Free Software Foundation version 2 of the License.
13
14			This program is distributed in the hope that it will be useful,
15			but WITHOUT ANY WARRANTY; without even the implied warranty of
16			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17			GNU General Public License for more details.
18			***********************************************************************/
19
20			#ifndef OB_PARSMART_H
21			#define OB_PARSMART_H
22
23			#include <string>
24			#include <vector>
25
26			#include "mol.hpp"
27
28			/==========================/
29			/* SMARTS Data Structures */
30			/==========================/
31
32			#define AE_LEAF 0x01
33			#define AE_RECUR 0x02
34			#define AE_NOT 0x03
35			#define AE_ANDHI 0x04
36			#define AE_OR 0x05
37			#define AE_ANDLO 0x06
38
39			#define AL_CONST 0x01
40			#define AL_MASS 0x02
41			#define AL_AROM 0x03
42			#define AL_ELEM 0x04
43			#define AL_HCOUNT 0x05
44			#define AL_NEGATIVE 0x06
45			#define AL_POSITIVE 0x07
46			#define AL_CONNECT 0x08
47			#define AL_DEGREE 0x09
48			#define AL_IMPLICIT 0x0a
49			#define AL_RINGS 0x0b
50			#define AL_SIZE 0x0c
51			#define AL_VALENCE 0x0d
52			#define AL_CHIRAL 0x0e
53			#define AL_HYB 0x0f
54			#define AL_CLOCKWISE 1
55			#define AL_ANTICLOCKWISE 2
56
57			namespace OpenBabel
58			{
59
60	gezelter	3057	// mark this so that SWIG will not attempt to wrap for scripting languages
61
62			#ifndef SWIG
63
64	tim	2440	//! \brief A SMARTS parser internal atomic expression
65			typedef union _AtomExpr {
66			int type;
67			struct
68			{
69			int type;
70			int prop;
71			int value;
72			}
73			leaf;
74			struct
75			{
76			int type;
77			void *recur;
78			}
79			recur;
80			struct
81			{
82			int type;
83			union _AtomExpr *arg;
84			}
85			mon;
86			struct
87			{
88			int type;
89			union _AtomExpr *lft;
90			union _AtomExpr *rgt;
91			}
92			bin;
93			} AtomExpr;
94
95			#define BE_LEAF 0x01
96			#define BE_ANDHI 0x02
97			#define BE_ANDLO 0x03
98			#define BE_NOT 0x04
99			#define BE_OR 0x05
100
101			#define BL_CONST 0x01
102			#define BL_TYPE 0x02
103
104			#define BT_SINGLE 0x01
105			#define BT_DOUBLE 0x02
106			#define BT_TRIPLE 0x03
107			#define BT_AROM 0x04
108			#define BT_UP 0x05
109			#define BT_DOWN 0x06
110			#define BT_UPUNSPEC 0x07
111			#define BT_DOWNUNSPEC 0x08
112			#define BT_RING 0x09
113
114			//! \brief A SMARTS parser internal bond expression
115			typedef union _BondExpr {
116			int type;
117			struct
118			{
119			int type;
120			int prop;
121			int value;
122			}
123			leaf;
124			struct
125			{
126			int type;
127			union _BondExpr *arg;
128			}
129			mon;
130			struct
131			{
132			int type;
133			union _BondExpr *lft;
134			union _BondExpr *rgt;
135			}
136			bin;
137			} BondExpr;
138
139			//! \brief A SMARTS parser internal bond specification
140			typedef struct
141			{
142			BondExpr *expr;
143			int src,dst;
144			int visit;
145			bool grow;
146			}
147			BondSpec;
148
149			//! \brief A SMARTS parser internal bond specification
150			typedef struct
151			{
152			AtomExpr *expr;
153			int visit;
154			int part;
155			int chiral_flag;
156			int vb;
157			}
158			AtomSpec;
159
160			//! \brief A SMARTS parser internal pattern
161			typedef struct
162			{
163			int aalloc,acount;
164			int balloc,bcount;
165			bool ischiral;
166			AtomSpec *atom;
167			BondSpec *bond;
168			int parts;
169			}
170			Pattern;
171	gezelter	3057	#else
172			// for SWIG, just forward declare that we have some Pattern struct
173			// (but this is private and not wrapped for scripting languages)
174			struct Pattern;
175			#endif
176	tim	2440
177			// class introduction in parsmart.cpp
178			//! \brief SMARTS (SMiles ARbitrary Target Specification) substructure searching
179			class OBAPI OBSmartsPattern
180			{
181			protected:
182			std::vector<bool> _growbond;
183			std::vector<std::vector<int> > _mlist;
184			Pattern *_pat;
185			std::string _str;
186
187			public:
188			OBSmartsPattern()
189			{
190			_pat=NULL;
191			}
192			virtual ~OBSmartsPattern();
193
194			OBSmartsPattern(const OBSmartsPattern& cp)
195			{
196			_pat = NULL;
197			*this = cp;
198			}
199			OBSmartsPattern& operator=(const OBSmartsPattern& cp)
200			{
201			if (_pat)
202			delete [] _pat;
203			_pat = NULL;
204			std::string s = cp._str;
205			Init(s);
206			return (*this);
207			}
208
209			unsigned int NumMatches() const
210			{
211			return (unsigned int)_mlist.size();
212			}
213			unsigned int NumAtoms() const
214			{
215			return _pat ? _pat->acount : 0;
216			}
217			unsigned int NumBonds() const
218			{
219			return _pat ? _pat->bcount : 0;
220			}
221
222			int GetAtomicNum(int);
223			void GetBond(int&,int&,int&,int);
224			int GetCharge(int);
225			const std::string &GetSMARTS() const
226			{
227			return _str;
228			}
229			std::string &GetSMARTS()
230			{
231			return _str;
232			}
233			int GetVectorBinding(int idx) const
234			{
235			return(_pat->atom[idx].vb);
236			}
237			bool Empty() const
238			{
239			return(_pat == NULL);
240			}
241			bool IsValid() const
242			{
243			return(_pat != NULL);
244			}
245			bool Init(const char*);
246			bool Init(const std::string&);
247			void WriteMapList(std::ostream&);
248
249			bool Match(OBMol &mol, bool single=false);
250			bool RestrictedMatch(OBMol &mol, std::vector<std::pair<int,int> > &pairs, bool single=false);
251			bool RestrictedMatch(OBMol &mol, OBBitVec &bv, bool single=false);
252
253			std::vector<std::vector<int> > &GetMapList()
254			{
255			return(_mlist);
256			}
257			std::vector<std::vector<int> > &GetUMapList();
258			std::vector<std::vector<int> >::iterator BeginMList()
259			{
260			return(_mlist.begin());
261			}
262			std::vector<std::vector<int> >::iterator EndMList()
263			{
264			return(_mlist.end());
265			}
266			};
267
268			//! Performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling.
269			class OBAPI OBSSMatch //used for fast exhaustive matching
270			{
271			protected:
272			bool *_uatoms;
273			OBMol *_mol;
274			Pattern *_pat;
275			std::vector<int> _map;
276
277			public:
278			OBSSMatch(OBMol&,Pattern*);
279			~OBSSMatch();
280			void Match(std::vector<std::vector<int> > &v, int bidx=-1);
281			};
282
283			void SmartsLexReplace(std::string &,
284			std::vector<std::pair<std::string,std::string> > &);
285
286			} // end namespace OpenBabel
287
288			#endif // OB_PARSMART_H
289
290			//! \file parsmart.h
291			//! \brief Daylight SMARTS parser.