rotor.h

Go to the documentation of this file.

/**********************************************************************
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.h"
#include "typer.h"

namespace OpenBabel
{

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

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);         }
};

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*);
    unsigned int GetSize()                 { return _vr.size();}

    void SetFilename(std::string &s)       { _filename = s;    }

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

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;  
    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);
    }
};

class OBAPI OBRotorList
{
    bool _quiet,_removesym;
    OBBitVec _fix;
    OBRotorRules _rr;
    std::vector<int> _dffv;         
    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

---

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

Documentation copyright © 1998-2005, the Open Babel Developers.
Open Babel is hosted by:
Generated on Thu Nov 30 20:18:01 2006 by  1.5.1.