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/********************************************************************** |
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parsmart.h - Daylight SMARTS parser. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#ifndef OB_PARSMART_H |
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#define OB_PARSMART_H |
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|
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#include <string> |
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#include <vector> |
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|
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#include "mol.hpp" |
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|
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/*==========================*/ |
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/* SMARTS Data Structures */ |
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/*==========================*/ |
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|
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#define AE_LEAF 0x01 |
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#define AE_RECUR 0x02 |
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#define AE_NOT 0x03 |
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#define AE_ANDHI 0x04 |
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#define AE_OR 0x05 |
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#define AE_ANDLO 0x06 |
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|
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#define AL_CONST 0x01 |
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#define AL_MASS 0x02 |
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#define AL_AROM 0x03 |
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#define AL_ELEM 0x04 |
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#define AL_HCOUNT 0x05 |
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#define AL_NEGATIVE 0x06 |
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#define AL_POSITIVE 0x07 |
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#define AL_CONNECT 0x08 |
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#define AL_DEGREE 0x09 |
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#define AL_IMPLICIT 0x0a |
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#define AL_RINGS 0x0b |
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#define AL_SIZE 0x0c |
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#define AL_VALENCE 0x0d |
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#define AL_CHIRAL 0x0e |
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#define AL_HYB 0x0f |
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#define AL_CLOCKWISE 1 |
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#define AL_ANTICLOCKWISE 2 |
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|
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namespace OpenBabel |
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{ |
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|
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//! \brief A SMARTS parser internal atomic expression |
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typedef union _AtomExpr { |
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int type; |
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struct |
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{ |
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int type; |
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int prop; |
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int value; |
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} |
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leaf; |
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struct |
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{ |
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int type; |
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void *recur; |
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} |
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recur; |
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struct |
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{ |
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int type; |
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union _AtomExpr *arg; |
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} |
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mon; |
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struct |
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{ |
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int type; |
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union _AtomExpr *lft; |
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union _AtomExpr *rgt; |
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} |
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bin; |
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} AtomExpr; |
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|
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#define BE_LEAF 0x01 |
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#define BE_ANDHI 0x02 |
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#define BE_ANDLO 0x03 |
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#define BE_NOT 0x04 |
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#define BE_OR 0x05 |
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|
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#define BL_CONST 0x01 |
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#define BL_TYPE 0x02 |
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|
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#define BT_SINGLE 0x01 |
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#define BT_DOUBLE 0x02 |
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#define BT_TRIPLE 0x03 |
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#define BT_AROM 0x04 |
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#define BT_UP 0x05 |
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#define BT_DOWN 0x06 |
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#define BT_UPUNSPEC 0x07 |
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#define BT_DOWNUNSPEC 0x08 |
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#define BT_RING 0x09 |
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|
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//! \brief A SMARTS parser internal bond expression |
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typedef union _BondExpr { |
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int type; |
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struct |
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{ |
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int type; |
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int prop; |
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int value; |
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} |
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leaf; |
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struct |
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{ |
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int type; |
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union _BondExpr *arg; |
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} |
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mon; |
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struct |
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{ |
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int type; |
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union _BondExpr *lft; |
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union _BondExpr *rgt; |
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} |
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bin; |
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} BondExpr; |
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|
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//! \brief A SMARTS parser internal bond specification |
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typedef struct |
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{ |
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BondExpr *expr; |
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int src,dst; |
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int visit; |
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bool grow; |
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} |
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BondSpec; |
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|
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//! \brief A SMARTS parser internal bond specification |
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typedef struct |
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{ |
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AtomExpr *expr; |
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int visit; |
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int part; |
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int chiral_flag; |
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int vb; |
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} |
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AtomSpec; |
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|
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//! \brief A SMARTS parser internal pattern |
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typedef struct |
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{ |
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int aalloc,acount; |
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int balloc,bcount; |
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bool ischiral; |
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AtomSpec *atom; |
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BondSpec *bond; |
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int parts; |
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} |
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Pattern; |
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|
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// class introduction in parsmart.cpp |
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//! \brief SMARTS (SMiles ARbitrary Target Specification) substructure searching |
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class OBAPI OBSmartsPattern |
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{ |
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protected: |
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std::vector<bool> _growbond; |
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std::vector<std::vector<int> > _mlist; |
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Pattern *_pat; |
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std::string _str; |
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|
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public: |
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OBSmartsPattern() |
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{ |
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_pat=NULL; |
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} |
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virtual ~OBSmartsPattern(); |
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|
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OBSmartsPattern(const OBSmartsPattern& cp) |
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{ |
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_pat = NULL; |
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*this = cp; |
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} |
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OBSmartsPattern& operator=(const OBSmartsPattern& cp) |
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{ |
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if (_pat) |
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delete [] _pat; |
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_pat = NULL; |
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std::string s = cp._str; |
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Init(s); |
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return (*this); |
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} |
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|
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unsigned int NumMatches() const |
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{ |
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return (unsigned int)_mlist.size(); |
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} |
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unsigned int NumAtoms() const |
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{ |
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return _pat ? _pat->acount : 0; |
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} |
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unsigned int NumBonds() const |
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{ |
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return _pat ? _pat->bcount : 0; |
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} |
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|
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int GetAtomicNum(int); |
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void GetBond(int&,int&,int&,int); |
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int GetCharge(int); |
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const std::string &GetSMARTS() const |
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{ |
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return _str; |
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} |
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std::string &GetSMARTS() |
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{ |
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return _str; |
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} |
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int GetVectorBinding(int idx) const |
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{ |
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return(_pat->atom[idx].vb); |
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} |
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bool Empty() const |
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{ |
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return(_pat == NULL); |
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} |
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bool IsValid() const |
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{ |
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return(_pat != NULL); |
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} |
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bool Init(const char*); |
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bool Init(const std::string&); |
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void WriteMapList(std::ostream&); |
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|
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bool Match(OBMol &mol, bool single=false); |
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bool RestrictedMatch(OBMol &mol, std::vector<std::pair<int,int> > &pairs, bool single=false); |
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bool RestrictedMatch(OBMol &mol, OBBitVec &bv, bool single=false); |
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|
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std::vector<std::vector<int> > &GetMapList() |
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{ |
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return(_mlist); |
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} |
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std::vector<std::vector<int> > &GetUMapList(); |
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std::vector<std::vector<int> >::iterator BeginMList() |
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{ |
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return(_mlist.begin()); |
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} |
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std::vector<std::vector<int> >::iterator EndMList() |
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{ |
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return(_mlist.end()); |
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} |
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}; |
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|
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//! Performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling. |
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class OBAPI OBSSMatch //used for fast exhaustive matching |
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{ |
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protected: |
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bool *_uatoms; |
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OBMol *_mol; |
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Pattern *_pat; |
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std::vector<int> _map; |
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|
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public: |
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OBSSMatch(OBMol&,Pattern*); |
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~OBSSMatch(); |
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void Match(std::vector<std::vector<int> > &v, int bidx=-1); |
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}; |
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|
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void SmartsLexReplace(std::string &, |
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std::vector<std::pair<std::string,std::string> > &); |
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|
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} // end namespace OpenBabel |
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|
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#endif // OB_PARSMART_H |
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|
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//! \file parsmart.h |
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//! \brief Daylight SMARTS parser. |
