Open Babel: rotor.h Source File

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# rotor.h

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    00001 /**********************************************************************
    00002 rotor.h - Rotate torsional according to rotor rules.
    00003
    00004 Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc.
    00005 Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
    00006
    00007 This file is part of the Open Babel project.
    00008 For more information, see <http://openbabel.org/>
    00009
    00010 This program is free software; you can redistribute it and/or modify
    00011 it under the terms of the GNU General Public License as published by
    00012 the Free Software Foundation version 2 of the License.
    00013
    00014 This program is distributed in the hope that it will be useful,
    00015 but WITHOUT ANY WARRANTY; without even the implied warranty of
    00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    00017 GNU General Public License for more details.
    00018 ***********************************************************************/
    00019
    00020 #ifndef OB_ROTOR_H
    00021 #define OB_ROTOR_H
    00022
    00023 #include <openbabel/parsmart.h>
    00024 #include <openbabel/typer.h>
    00025
    00026 namespace OpenBabel
    00027 {
    00028
    00029 #ifndef SQUARE
    00030 #define SQUARE(x) ((x)*(x))
    00031 #endif
    00032
    00040   class OBAPI OBRotorRule
    00041   {
    00042     int                 _ref[4];
    00043     double              _delta;
    00044     std::string         _s;
    00045     OBSmartsPattern*    _sp;
    00046     std::vector<double> _vals;
    00047   public:
    00048
    00049   OBRotorRule(char *buffer,int ref[4],std::vector<double> &vals,double d):
    00050     _delta(d), _s(buffer), _vals(vals)
    00051     {
    00052       _sp = new OBSmartsPattern;
    00053       _sp->Init(buffer);
    00054       memcpy(_ref,ref,sizeof(int)*4);
    00055     }
    00056
    00057     ~OBRotorRule()
    00058       {
    00059         if (_sp)
    00060           {
    00061             delete _sp;
    00062             _sp = NULL;
    00063           }
    00064       }
    00065
    00067     bool    IsValid()    {        return(_sp->IsValid());       }
    00071     void    GetReferenceAtoms(int ref[4]) { memcpy(ref,_ref,sizeof(int)*4); }
    00073     void    SetDelta(double d)    {       _delta = d;           }
    00075     double  GetDelta()            {       return(_delta);       }
    00077     std::vector<double>   &GetTorsionVals()    { return(_vals); }
    00079     std::string  &GetSmartsString(){      return(_s);           }
    00081     OBSmartsPattern *GetSmartsPattern() {  return(_sp);         }
    00082   };
    00083
    00090  class OBAPI OBRotorRules : public OBGlobalDataBase
    00091   {
    00092     bool                       _quiet;
    00093     std::vector<OBRotorRule*>  _vr;
    00094     std::vector<double>        _sp3sp3;
    00095     std::vector<double>        _sp3sp2;
    00096     std::vector<double>        _sp2sp2;
    00097   public:
    00098     OBRotorRules();
    00099     ~OBRotorRules();
    00100
    00101     void ParseLine(const char*);
    00103     size_t GetSize()                 { return _vr.size();}
    00104
    00106     void SetFilename(std::string &s)       { _filename = s;    }
    00107
    00114     void GetRotorIncrements(OBMol& mol,OBBond* bond,int refs[4],
    00115                             std::vector<double> &vals,double &delta);
    00117     void Quiet()                           { _quiet=true;      }
    00118   };
    00119
    00124   class OBAPI OBRotor
    00125   {
    00126     int _idx;
    00127     std::vector<int> _rotatoms;
    00128     double _imag, _refang;
    00129     OBBond *_bond;
    00130     std::vector<int> _ref, _torsion;
    00131     OBBitVec _fixedatoms,_fixedbonds, _evalatoms;
    00132     std::vector<double> _torsionAngles;
    00133     std::vector<double> _invmag;
    00134     std::vector<std::vector<double> > _sn,_cs,_t;
    00135   public:
    00139     OBRotor();
    00143     ~OBRotor()
    00144     {
    00145     }
    00146
    00149
    00152     void SetBond(OBBond *bond)
    00153     {
    00154       _bond = bond;
    00155     }
    00159     void SetIdx(int idx)
    00160     {
    00161       _idx = idx;
    00162     }
    00167     void SetDihedralAtoms(std::vector<int> &ref);
    00172     void SetDihedralAtoms(int ref[4]);
    00178     void SetRotAtoms(std::vector<int> &atoms);
    00182     void SetTorsionValues(std::vector<double> &angles)
    00183     {
    00184       _torsionAngles = angles;
    00185     }
    00189     void SetFixedBonds(OBBitVec &bv)
    00190     {
    00191       _fixedbonds = bv;
    00192     }
    00194
    00197
    00202     inline void SetToAngle(double *coordinates, double setang)
    00203     {
    00204       double /*dx,dy,dz,*/ sn,cs,t,ang,mag;
    00205       // compute the angle to rotate (radians)
    00206       ang = setang - CalcTorsion(coordinates);
    00207       // if the angle to rotate is too small, we're done
    00208       if (fabs(ang) < 1e-5)
    00209         return;
    00210
    00211       // compute the bond length
    00212       mag = CalcBondLength(coordinates);
    00213       // compute some rotation matrix elements
    00214       sn = sin(ang);
    00215       cs = cos(ang);
    00216       t = 1 - cs;
    00217
    00218       // perform rotation
    00219       Set(coordinates, sn, cs, t, 1.0 / mag);
    00220     }
    00231     void SetRotor(double *coordinates, int next, int prev = -1);
    00236     void Set(double *coordinates, double sine, double cosine, double translation, double invmag);
    00285     void Precompute(double *coordinates);
    00293     void Set(double *coordinates, int idx);
    00300     void Precalc(std::vector<double*> &conformers);
    00310     void Set(double *coordinates, int conformer, int idx)
    00311     {
    00312       Set(coordinates, _sn[conformer][idx], _cs[conformer][idx], _t[conformer][idx], _invmag[conformer]);
    00313     }
    00315
    00316
    00319
    00322     OBBond *GetBond()
    00323     {
    00324       return(_bond);
    00325     }
    00330     size_t Size()
    00331     {
    00332       return _torsionAngles.size();
    00333     }
    00337     int GetIdx() const
    00338     {
    00339       return _idx;
    00340     }
    00344     void GetDihedralAtoms(int ref[4])
    00345     {
    00346       for (int i = 0; i < 4; ++i)
    00347         ref[i] = _ref[i];
    00348     }
    00352     std::vector<int> &GetDihedralAtoms()
    00353     {
    00354       return _ref;
    00355     }
    00360     const std::vector<int>& GetRotAtoms() const
    00361     {
    00362       return _rotatoms;
    00363     }
    00367     const std::vector<double> &GetTorsionValues() const
    00368     {
    00369       return _torsionAngles;
    00370     }
    00375     OBBitVec &GetFixedBonds()
    00376     {
    00377       return _fixedbonds;
    00378     }
    00384     double CalcTorsion(double *coordinates);
    00389     double CalcBondLength(double *coordinates);
    00391
    00392
    00395     std::vector<double>::iterator BeginTorIncrement()
    00396     {
    00397       return _torsionAngles.begin();
    00398     }
    00399     std::vector<double>::iterator EndTorIncrement()
    00400     {
    00401       return _torsionAngles.end();
    00402     }
    00404
    00405     void RemoveSymTorsionValues(int);
    00406
    00409
    00410     void SetDelta(double UNUSED(d)) {}
    00412     double GetDelta() { return 10.0; }
    00414     OBBitVec &GetFixedAtoms() { return _fixedatoms; }
    00416     void SetFixedAtoms(OBBitVec &bv) { _fixedatoms = bv; }
    00418     OBBitVec &GetEvalAtoms() { return _evalatoms; }
    00420     void SetEvalAtoms(OBBitVec &bv) { _evalatoms = bv; }
    00422     void* GetRotAtoms() { return &_rotatoms; }
    00424     std::vector<double> &GetResolution() { return _torsionAngles; }
    00426     void SetNumCoords(int UNUSED(nc)) {}
    00428
    00429   };
    00430
    00431
    00433   typedef std::vector<OBRotor*>::iterator OBRotorIterator;
    00434
    00439   class OBAPI OBRotorList
    00440   {
    00441     bool _quiet;
    00442     bool _removesym;
    00443     OBBitVec _fixedatoms, _fixedbonds;
    00444     OBRotorRules _rr;
    00445     std::vector<int> _dffv;
    00446     std::vector<OBRotor*> _rotor;
    00447
    00448     std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym2;
    00450     std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym3;
    00451   public:
    00455     OBRotorList();
    00459     ~OBRotorList();
    00460
    00464     void Clear();
    00468     size_t Size()
    00469     {
    00470       return((_rotor.empty()) ? (size_t)0: _rotor.size());
    00471     }
    00478     bool IsFixedBond(OBBond*);
    00482     bool HasFixedBonds()
    00483     {
    00484       return !_fixedbonds.Empty();
    00485     }
    00489     void RemoveSymVals(OBMol&);
    00490
    00491
    00493
    00499     bool Setup(OBMol &mol);
    00503     void SetFixedBonds(OBBitVec &fix)
    00504     {
    00505       _fixedbonds = fix;
    00506       _fixedatoms.Clear();
    00507     }
    00511     void Init(std::string &fname)
    00512     {
    00513       _rr.SetFilename(fname);
    00514       _rr.Init();
    00515     }
    00519     void SetQuiet() {
    00520       _quiet=true;
    00521       _rr.Quiet();
    00522     }
    00527     bool SetRotAtoms(OBMol&);
    00539     bool FindRotors(OBMol &mol);
    00543     bool SetEvalAtoms(OBMol&);
    00552     bool AssignTorVals(OBMol &);
    00554
    00556
    00557
    00561     OBRotor *BeginRotor(OBRotorIterator &i)
    00562     {
    00563       i = _rotor.begin();
    00564       return((i ==_rotor.end()) ? NULL:*i);
    00565     }
    00570     OBRotor *NextRotor(OBRotorIterator &i)
    00571     {
    00572       ++i;
    00573       return((i ==_rotor.end()) ? NULL:*i);
    00574     }
    00578     OBRotorIterator BeginRotors()   { return(_rotor.begin()); }
    00582     OBRotorIterator EndRotors()     { return(_rotor.end());   }
    00584
    00587     // Not declared
    00589     bool   IdentifyEvalAtoms(OBMol &mol) { return SetEvalAtoms(mol); }
    00594     void SetFixAtoms(OBBitVec &fix)
    00595     {
    00596       _fixedatoms = fix;
    00597       _fixedbonds.Clear();
    00598     }
    00603     bool HasFixedAtoms()
    00604     {
    00605       return(!_fixedatoms.Empty());
    00606     }
    00609     void IgnoreSymmetryRemoval()    { _removesym = false;}
    00613     void SetRotAtomsByFix(OBMol&);
    00615
    00616   };
    00617
    00619   class rotor_digit {
    00620     public:
    00621       rotor_digit(unsigned int rs)
    00622       {
    00623         resolution_size = rs;
    00624         state = 0;
    00625       }
    00626
    00627       rotor_digit()
    00628       {
    00629         resolution_size = 0;
    00630         state = 0;
    00631       }
    00632
    00633       void set_size(unsigned int rs)
    00634       {
    00635         resolution_size = rs;
    00636         state = 0;
    00637       }
    00638
    00639       void set_state(int st)
    00640       {
    00641         state = st;
    00642       }
    00643
    00644       int get_state()
    00645       {
    00646         return state;
    00647       }
    00648
    00649       unsigned int size()
    00650       {
    00651         return resolution_size;
    00652       }
    00653
    00654       bool next()
    00655       {
    00656         if (state < static_cast<int>(resolution_size - 1)) {
    00657           ++state;
    00658           return false;
    00659         } else
    00660           state = 0;
    00661
    00662         return true;
    00663       }
    00664     private:
    00665       unsigned int resolution_size;
    00666       int state;
    00667 #ifndef SWIG
    00668   } typedef rotor_digit;
    00669 #else
    00670   };
    00671 #endif
    00672
    00673
    00676   class OBAPI OBRotorKeys
    00677   {
    00723     public:
    00725       OBRotorKeys()
    00726       {
    00727         _vr.clear();
    00728       }
    00729
    00731       void Clear(){
    00732         _vr.clear();
    00733       }
    00734
    00736       unsigned int NumKeys()
    00737       {
    00738         unsigned int numKeys = 0;
    00739
    00740         while (Next())
    00741           numKeys++;
    00742
    00743         return numKeys;
    00744       }
    00745
    00748       void AddRotor(unsigned int size)
    00749       {
    00750         rotor_digit rd(size);
    00751         _vr.push_back(rd);
    00752       }
    00753
    00756       bool Next()
    00757       {
    00758         if(_vr.size() == 0)
    00759           return false;
    00760
    00761         bool carry = _vr[0].next();
    00762         unsigned int i = 1;
    00763         while (carry) {
    00764           if(i == _vr.size())
    00765             return false;
    00766
    00767           carry = _vr[i].next();
    00768           i++;
    00769         }
    00770         return true;
    00771       }
    00772
    00775       std::vector<int> GetKey()
    00776       {
    00777         std::vector<int> rt;
    00778         rt.clear();
    00779         rt.push_back(0);
    00780         for(unsigned int i = 0; i < _vr.size(); i++){
    00781           rt.push_back(_vr[i].get_state());
    00782         }
    00783
    00784         return rt;
    00785       }
    00786
    00787     private:
    00788       std::vector<rotor_digit> _vr;
    00789   };
    00790
    00791
    00792 } // end namespace OpenBabel
    00793
    00794 #endif // OB_ROTOR_H
    00795

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