src/openbabel/rotor.hpp

/**********************************************************************
rotor.h - Rotate torsional according to rotor rules.
 
Copyright (C) 1998-2000 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_ROTOR_H
#define OB_ROTOR_H

#include "parsmart.hpp"
#include "typer.hpp"

namespace OpenBabel
{

class OBRotor;
class OBRotorList;
class OBRotorRule;
class OBRotorRules;

//! \brief A rule for torsional conformer searching, defined by a SMARTS pattern
//!
//! Rules define a SMARTS pattern to match and a set of 4 reference atoms
//! defining the dihedral angle. The rule can either define a set of possible
//! dihedral angles in degrees or a "delta" (i.e., all multiples of delta will
//! be considered)
class OBAPI OBRotorRule
{
    int              _ref[4];
    double            _delta;
    std::string           _s;
    OBSmartsPattern* _sp;
    std::vector<double>    _vals;
public:

    OBRotorRule(char *buffer,int ref[4],std::vector<double> &vals,double d):
       _delta(d), _s(buffer), _vals(vals)
    {
        _sp = new OBSmartsPattern;
        _sp->Init(buffer);
        memcpy(_ref,ref,sizeof(int)*4);
    }
    ~OBRotorRule()
    {
        if (_sp)
        {
            delete _sp;
            _sp = NULL;
        }
    }

    bool    IsValid()    {        return(_sp->IsValid());       }
    void    GetReferenceAtoms(int ref[4]) { memcpy(ref,_ref,sizeof(int)*4); }
    void    SetDelta(double d)    {       _delta = d;           }
    double  GetDelta()            {       return(_delta);       }
    std::string  &GetSmartsString(){      return(_s);           }
    std::vector<double>   &GetTorsionVals()    { return(_vals); }
    OBSmartsPattern *GetSmartsPattern() {  return(_sp);         }
};

//! Database of default hybridization torsional rules and SMARTS-defined OBRotorRule objects
class OBAPI OBRotorRules : public OBGlobalDataBase
{
    bool                 _quiet;
    std::vector<OBRotorRule*> _vr;
    std::vector<double>        _sp3sp3;
    std::vector<double>        _sp3sp2;
    std::vector<double>        _sp2sp2;
public:
    OBRotorRules();
    ~OBRotorRules();

    void ParseLine(const char*);
    //! \return the number of rotor rules
    unsigned int GetSize()                 { return _vr.size();}

    //! Set the filename to be used for the database. Default = torlib.txt
    void SetFilename(std::string &s)       { _filename = s;    }

    void GetRotorIncrements(OBMol&,OBBond*,int [4],std::vector<double>&,double &delta);
    void Quiet()                           { _quiet=true;      }
};

//! A single rotatable OBBond as part of rotomer searching
class OBAPI OBRotor
{
    int _idx,_ref[4];
    int *_rotatoms,_size,_numcoords;
    double _delta;
    double _imag,_refang;
    OBBond *_bond;
    std::vector<int> _torsion;
    OBBitVec _fixedatoms,_evalatoms;
    std::vector<double> _res;  //!< torsion resolution
    std::vector<double> _invmag;
    std::vector<std::vector<double> > _sn,_cs,_t;
public:
    OBRotor();
    ~OBRotor()
    {
        if (_rotatoms)
            delete [] _rotatoms;
    }
    int     Size()
    {
        return((_res.empty())?0:_res.size());
    }
    int     GetIdx() const
    {
        return(_idx);
    }
    void    SetNumCoords(int nc)
    {
        _numcoords = nc;
    }
    void    SetBond(OBBond *bond)
    {
        _bond = bond;
    }
    void    SetEvalAtoms(OBBitVec &bv)
    {
        _evalatoms = bv;
    }
    void    SetDihedralAtoms(std::vector<int> &vi)
    {
        _torsion = vi;
    }
    void    SetDelta(double d)
    {
        _delta = d;
    }
    void    SetDihedralAtoms(int ref[4]);
    void    SetRotAtoms(std::vector<int>&);
    inline void SetToAngle(double *c,double setang)
    {
        double dx,dy,dz,sn,cs,t,ang,mag;
        ang = setang - CalcTorsion(c);
        if (fabs(ang) < 1e-5)
            return;

        sn = sin(ang);
        cs = cos(ang);
        t = 1 - cs;
        dx = c[_torsion[1]]   - c[_torsion[2]];
        dy = c[_torsion[1]+1] - c[_torsion[2]+1];
        dz = c[_torsion[1]+2] - c[_torsion[2]+2];
        mag = sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz));
        Set(c,sn,cs,t,1.0/mag);
    }
    void    SetRotor(double *,int,int prev=-1);
    void    Set(double*,int);
    void    Precompute(double*);
    void    Set(double *c,int ridx,int cidx)
    {
        Set(c,_sn[cidx][ridx],_cs[cidx][ridx],_t[cidx][ridx],_invmag[cidx]);
    }
    void    Set(double*,double,double,double,double);
    void    Precalc(std::vector<double*>&);
    void    SetIdx(int idx)
    {
        _idx = idx;
    }
    void    SetFixedAtoms(OBBitVec &bv)
    {
        _fixedatoms = bv;
    }
    void    SetTorsionValues(std::vector<double> &tmp)
    {
        _res = tmp;
    }
    void    RemoveSymTorsionValues(int);
    void    GetDihedralAtoms(int ref[4])
    {
        for (int i=0;i<4;i++)
            ref[i]=_ref[i];
    }
    void    *GetRotAtoms()
    {
        return(_rotatoms);
    }
    double   CalcTorsion(double *);
    double   CalcBondLength(double*);
    double   GetDelta()
    {
        return(_delta);
    }
    OBBond *GetBond()
    {
        return(_bond);
    }
    std::vector<int> &GetDihedralAtoms()
    {
        return(_torsion);
    }
    std::vector<double> &GetResolution()
    {
        return(_res);
    }
    std::vector<double>::iterator BeginTorIncrement()
    {
        return(_res.begin());
    }
    std::vector<double>::iterator EndTorIncrement()
    {
        return(_res.end());
    }
    OBBitVec &GetEvalAtoms()
    {
        return(_evalatoms);
    }
    OBBitVec &GetFixedAtoms()
    {
        return(_fixedatoms);
    }
};

//! Given an OBMol, set up a list of possibly rotatable torsions, 
class OBAPI OBRotorList
{
    bool _quiet,_removesym;
    OBBitVec _fix;
    OBRotorRules _rr;
    std::vector<int> _dffv;         //!< distance from fixed
    std::vector<OBRotor*> _rotor;
    std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym2;
    std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym3;
public:
    OBRotorList();
    ~OBRotorList();

    int    Size()
    {
        return((_rotor.empty()) ? 0: _rotor.size());
    }
    void   Init(std::string &fname)
    {
        _rr.SetFilename(fname);
        _rr.Init();
    }
    void   SetFixAtoms(OBBitVec &fix)
    {
        _fix = fix;
    }
    void   SetQuiet()
    {
        _quiet=true;
        _rr.Quiet();
    }
    void   IgnoreSymmetryRemoval()
    {
        _removesym=false;
    }
    void   Clear();
    void   RemoveSymVals(OBMol&);
    void   SetRotAtomsByFix(OBMol&);
    bool   SetRotAtoms(OBMol&);
    bool   Setup(OBMol &);
    bool   FindRotors(OBMol &);
    bool   IdentifyEvalAtoms(OBMol &);
    bool   SetEvalAtoms(OBMol&);
    bool   AssignTorVals(OBMol &);
    bool   IsFixedBond(OBBond*);
    bool   HasFixedAtoms()
    {
        return(!_fix.Empty());
    }
    OBRotor *BeginRotor(std::vector<OBRotor*>::iterator &i)
    {
        i = _rotor.begin();
        return((i ==_rotor.end()) ? NULL:*i);
    }
    OBRotor *NextRotor(std::vector<OBRotor*>::iterator &i)
    {
        i++;
        return((i ==_rotor.end()) ? NULL:*i);
    }
    std::vector<OBRotor*>::iterator BeginRotors()
    {
        return(_rotor.begin());
    }
    std::vector<OBRotor*>::iterator EndRotors()
    {
        return(_rotor.end());
    }
};

} // end namespace OpenBabel

#ifndef SQUARE
#define SQUARE(x) ((x)*(x))
#endif

#endif // OB_ROTOR_H

//! \file rotor.h
//! \brief Rotate torsional according to rotor rules.
Revision:	741
Committed:	Wed Nov 16 19:42:11 2005 UTC (19 years, 5 months ago) by tim
File size:	8169 byte(s)
Log Message:	adding openbabel
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			rotor.h - Rotate torsional according to rotor rules.
3
4			Copyright (C) 1998-2000 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_ROTOR_H
21			#define OB_ROTOR_H
22
23			#include "parsmart.hpp"
24			#include "typer.hpp"
25
26			namespace OpenBabel
27			{
28
29			class OBRotor;
30			class OBRotorList;
31			class OBRotorRule;
32			class OBRotorRules;
33
34			//! \brief A rule for torsional conformer searching, defined by a SMARTS pattern
35			//!
36			//! Rules define a SMARTS pattern to match and a set of 4 reference atoms
37			//! defining the dihedral angle. The rule can either define a set of possible
38			//! dihedral angles in degrees or a "delta" (i.e., all multiples of delta will
39			//! be considered)
40			class OBAPI OBRotorRule
41			{
42			int _ref[4];
43			double _delta;
44			std::string _s;
45			OBSmartsPattern* _sp;
46			std::vector<double> _vals;
47			public:
48
49			OBRotorRule(char *buffer,int ref[4],std::vector<double> &vals,double d):
50			_delta(d), _s(buffer), _vals(vals)
51			{
52			_sp = new OBSmartsPattern;
53			_sp->Init(buffer);
54			memcpy(_ref,ref,sizeof(int)*4);
55			}
56			~OBRotorRule()
57			{
58			if (_sp)
59			{
60			delete _sp;
61			_sp = NULL;
62			}
63			}
64
65			bool IsValid() { return(_sp->IsValid()); }
66			void GetReferenceAtoms(int ref[4]) { memcpy(ref,_ref,sizeof(int)*4); }
67			void SetDelta(double d) { _delta = d; }
68			double GetDelta() { return(_delta); }
69			std::string &GetSmartsString(){ return(_s); }
70			std::vector<double> &GetTorsionVals() { return(_vals); }
71			OBSmartsPattern *GetSmartsPattern() { return(_sp); }
72			};
73
74			//! Database of default hybridization torsional rules and SMARTS-defined OBRotorRule objects
75			class OBAPI OBRotorRules : public OBGlobalDataBase
76			{
77			bool _quiet;
78			std::vector<OBRotorRule*> _vr;
79			std::vector<double> _sp3sp3;
80			std::vector<double> _sp3sp2;
81			std::vector<double> _sp2sp2;
82			public:
83			OBRotorRules();
84			~OBRotorRules();
85
86			void ParseLine(const char*);
87			//! \return the number of rotor rules
88			unsigned int GetSize() { return _vr.size();}
89
90			//! Set the filename to be used for the database. Default = torlib.txt
91			void SetFilename(std::string &s) { _filename = s; }
92
93			void GetRotorIncrements(OBMol&,OBBond*,int [4],std::vector<double>&,double &delta);
94			void Quiet() { _quiet=true; }
95			};
96
97			//! A single rotatable OBBond as part of rotomer searching
98			class OBAPI OBRotor
99			{
100			int _idx,_ref[4];
101			int *_rotatoms,_size,_numcoords;
102			double _delta;
103			double _imag,_refang;
104			OBBond *_bond;
105			std::vector<int> _torsion;
106			OBBitVec _fixedatoms,_evalatoms;
107			std::vector<double> _res; //!< torsion resolution
108			std::vector<double> _invmag;
109			std::vector<std::vector<double> > _sn,_cs,_t;
110			public:
111			OBRotor();
112			~OBRotor()
113			{
114			if (_rotatoms)
115			delete [] _rotatoms;
116			}
117			int Size()
118			{
119			return((_res.empty())?0:_res.size());
120			}
121			int GetIdx() const
122			{
123			return(_idx);
124			}
125			void SetNumCoords(int nc)
126			{
127			_numcoords = nc;
128			}
129			void SetBond(OBBond *bond)
130			{
131			_bond = bond;
132			}
133			void SetEvalAtoms(OBBitVec &bv)
134			{
135			_evalatoms = bv;
136			}
137			void SetDihedralAtoms(std::vector<int> &vi)
138			{
139			_torsion = vi;
140			}
141			void SetDelta(double d)
142			{
143			_delta = d;
144			}
145			void SetDihedralAtoms(int ref[4]);
146			void SetRotAtoms(std::vector<int>&);
147			inline void SetToAngle(double *c,double setang)
148			{
149			double dx,dy,dz,sn,cs,t,ang,mag;
150			ang = setang - CalcTorsion(c);
151			if (fabs(ang) < 1e-5)
152			return;
153
154			sn = sin(ang);
155			cs = cos(ang);
156			t = 1 - cs;
157			dx = c[_torsion[1]] - c[_torsion[2]];
158			dy = c[_torsion[1]+1] - c[_torsion[2]+1];
159			dz = c[_torsion[1]+2] - c[_torsion[2]+2];
160			mag = sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz));
161			Set(c,sn,cs,t,1.0/mag);
162			}
163			void SetRotor(double *,int,int prev=-1);
164			void Set(double*,int);
165			void Precompute(double*);
166			void Set(double *c,int ridx,int cidx)
167			{
168			Set(c,_sn[cidx][ridx],_cs[cidx][ridx],_t[cidx][ridx],_invmag[cidx]);
169			}
170			void Set(double*,double,double,double,double);
171			void Precalc(std::vector<double*>&);
172			void SetIdx(int idx)
173			{
174			_idx = idx;
175			}
176			void SetFixedAtoms(OBBitVec &bv)
177			{
178			_fixedatoms = bv;
179			}
180			void SetTorsionValues(std::vector<double> &tmp)
181			{
182			_res = tmp;
183			}
184			void RemoveSymTorsionValues(int);
185			void GetDihedralAtoms(int ref[4])
186			{
187			for (int i=0;i<4;i++)
188			ref[i]=_ref[i];
189			}
190			void *GetRotAtoms()
191			{
192			return(_rotatoms);
193			}
194			double CalcTorsion(double *);
195			double CalcBondLength(double*);
196			double GetDelta()
197			{
198			return(_delta);
199			}
200			OBBond *GetBond()
201			{
202			return(_bond);
203			}
204			std::vector<int> &GetDihedralAtoms()
205			{
206			return(_torsion);
207			}
208			std::vector<double> &GetResolution()
209			{
210			return(_res);
211			}
212			std::vector<double>::iterator BeginTorIncrement()
213			{
214			return(_res.begin());
215			}
216			std::vector<double>::iterator EndTorIncrement()
217			{
218			return(_res.end());
219			}
220			OBBitVec &GetEvalAtoms()
221			{
222			return(_evalatoms);
223			}
224			OBBitVec &GetFixedAtoms()
225			{
226			return(_fixedatoms);
227			}
228			};
229
230			//! Given an OBMol, set up a list of possibly rotatable torsions,
231			class OBAPI OBRotorList
232			{
233			bool _quiet,_removesym;
234			OBBitVec _fix;
235			OBRotorRules _rr;
236			std::vector<int> _dffv; //!< distance from fixed
237			std::vector<OBRotor*> _rotor;
238			std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym2;
239			std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym3;
240			public:
241			OBRotorList();
242			~OBRotorList();
243
244			int Size()
245			{
246			return((_rotor.empty()) ? 0: _rotor.size());
247			}
248			void Init(std::string &fname)
249			{
250			_rr.SetFilename(fname);
251			_rr.Init();
252			}
253			void SetFixAtoms(OBBitVec &fix)
254			{
255			_fix = fix;
256			}
257			void SetQuiet()
258			{
259			_quiet=true;
260			_rr.Quiet();
261			}
262			void IgnoreSymmetryRemoval()
263			{
264			_removesym=false;
265			}
266			void Clear();
267			void RemoveSymVals(OBMol&);
268			void SetRotAtomsByFix(OBMol&);
269			bool SetRotAtoms(OBMol&);
270			bool Setup(OBMol &);
271			bool FindRotors(OBMol &);
272			bool IdentifyEvalAtoms(OBMol &);
273			bool SetEvalAtoms(OBMol&);
274			bool AssignTorVals(OBMol &);
275			bool IsFixedBond(OBBond*);
276			bool HasFixedAtoms()
277			{
278			return(!_fix.Empty());
279			}
280			OBRotor BeginRotor(std::vector<OBRotor>::iterator &i)
281			{
282			i = _rotor.begin();
283			return((i ==_rotor.end()) ? NULL:*i);
284			}
285			OBRotor NextRotor(std::vector<OBRotor>::iterator &i)
286			{
287			i++;
288			return((i ==_rotor.end()) ? NULL:*i);
289			}
290			std::vector<OBRotor*>::iterator BeginRotors()
291			{
292			return(_rotor.begin());
293			}
294			std::vector<OBRotor*>::iterator EndRotors()
295			{
296			return(_rotor.end());
297			}
298			};
299
300			} // end namespace OpenBabel
301
302			#ifndef SQUARE
303			#define SQUARE(x) ((x)*(x))
304			#endif
305
306			#endif // OB_ROTOR_H
307
308			//! \file rotor.h
309			//! \brief Rotate torsional according to rotor rules.