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/********************************************************************** |
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rotor.h - Rotate torsional according to rotor rules. |
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|
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Copyright (C) 1998-2000 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_ROTOR_H |
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#define OB_ROTOR_H |
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|
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#include "parsmart.hpp" |
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#include "typer.hpp" |
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|
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namespace OpenBabel |
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{ |
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|
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class OBRotor; |
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class OBRotorList; |
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class OBRotorRule; |
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class OBRotorRules; |
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|
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//! \brief A rule for torsional conformer searching, defined by a SMARTS pattern |
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//! |
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//! Rules define a SMARTS pattern to match and a set of 4 reference atoms |
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//! defining the dihedral angle. The rule can either define a set of possible |
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//! dihedral angles in degrees or a "delta" (i.e., all multiples of delta will |
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//! be considered) |
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class OBAPI OBRotorRule |
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{ |
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int _ref[4]; |
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double _delta; |
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std::string _s; |
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OBSmartsPattern* _sp; |
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std::vector<double> _vals; |
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public: |
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|
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OBRotorRule(char *buffer,int ref[4],std::vector<double> &vals,double d): |
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_delta(d), _s(buffer), _vals(vals) |
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{ |
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_sp = new OBSmartsPattern; |
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_sp->Init(buffer); |
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memcpy(_ref,ref,sizeof(int)*4); |
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} |
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~OBRotorRule() |
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{ |
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if (_sp) |
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{ |
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delete _sp; |
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_sp = NULL; |
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} |
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} |
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|
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bool IsValid() { return(_sp->IsValid()); } |
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void GetReferenceAtoms(int ref[4]) { memcpy(ref,_ref,sizeof(int)*4); } |
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void SetDelta(double d) { _delta = d; } |
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double GetDelta() { return(_delta); } |
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std::string &GetSmartsString(){ return(_s); } |
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std::vector<double> &GetTorsionVals() { return(_vals); } |
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OBSmartsPattern *GetSmartsPattern() { return(_sp); } |
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}; |
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|
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//! Database of default hybridization torsional rules and SMARTS-defined OBRotorRule objects |
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class OBAPI OBRotorRules : public OBGlobalDataBase |
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{ |
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bool _quiet; |
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std::vector<OBRotorRule*> _vr; |
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std::vector<double> _sp3sp3; |
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std::vector<double> _sp3sp2; |
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std::vector<double> _sp2sp2; |
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public: |
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OBRotorRules(); |
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~OBRotorRules(); |
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|
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void ParseLine(const char*); |
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//! \return the number of rotor rules |
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unsigned int GetSize() { return _vr.size();} |
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|
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//! Set the filename to be used for the database. Default = torlib.txt |
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void SetFilename(std::string &s) { _filename = s; } |
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|
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void GetRotorIncrements(OBMol&,OBBond*,int [4],std::vector<double>&,double &delta); |
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void Quiet() { _quiet=true; } |
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}; |
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|
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//! A single rotatable OBBond as part of rotomer searching |
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class OBAPI OBRotor |
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{ |
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int _idx,_ref[4]; |
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int *_rotatoms,_size,_numcoords; |
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double _delta; |
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double _imag,_refang; |
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OBBond *_bond; |
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std::vector<int> _torsion; |
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OBBitVec _fixedatoms,_evalatoms; |
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std::vector<double> _res; //!< torsion resolution |
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std::vector<double> _invmag; |
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std::vector<std::vector<double> > _sn,_cs,_t; |
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public: |
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OBRotor(); |
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~OBRotor() |
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{ |
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if (_rotatoms) |
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delete [] _rotatoms; |
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} |
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int Size() |
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{ |
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return((_res.empty())?0:_res.size()); |
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} |
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int GetIdx() const |
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{ |
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return(_idx); |
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} |
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void SetNumCoords(int nc) |
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{ |
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_numcoords = nc; |
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} |
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void SetBond(OBBond *bond) |
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{ |
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_bond = bond; |
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} |
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void SetEvalAtoms(OBBitVec &bv) |
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{ |
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_evalatoms = bv; |
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} |
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void SetDihedralAtoms(std::vector<int> &vi) |
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{ |
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_torsion = vi; |
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} |
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void SetDelta(double d) |
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{ |
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_delta = d; |
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} |
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void SetDihedralAtoms(int ref[4]); |
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void SetRotAtoms(std::vector<int>&); |
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inline void SetToAngle(double *c,double setang) |
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{ |
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double dx,dy,dz,sn,cs,t,ang,mag; |
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ang = setang - CalcTorsion(c); |
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if (fabs(ang) < 1e-5) |
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return; |
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|
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sn = sin(ang); |
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cs = cos(ang); |
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t = 1 - cs; |
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dx = c[_torsion[1]] - c[_torsion[2]]; |
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dy = c[_torsion[1]+1] - c[_torsion[2]+1]; |
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dz = c[_torsion[1]+2] - c[_torsion[2]+2]; |
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mag = sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz)); |
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Set(c,sn,cs,t,1.0/mag); |
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} |
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void SetRotor(double *,int,int prev=-1); |
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void Set(double*,int); |
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void Precompute(double*); |
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void Set(double *c,int ridx,int cidx) |
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{ |
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Set(c,_sn[cidx][ridx],_cs[cidx][ridx],_t[cidx][ridx],_invmag[cidx]); |
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} |
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void Set(double*,double,double,double,double); |
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void Precalc(std::vector<double*>&); |
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void SetIdx(int idx) |
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{ |
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_idx = idx; |
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} |
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void SetFixedAtoms(OBBitVec &bv) |
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{ |
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_fixedatoms = bv; |
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} |
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void SetTorsionValues(std::vector<double> &tmp) |
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{ |
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_res = tmp; |
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} |
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void RemoveSymTorsionValues(int); |
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void GetDihedralAtoms(int ref[4]) |
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{ |
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for (int i=0;i<4;i++) |
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ref[i]=_ref[i]; |
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} |
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void *GetRotAtoms() |
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{ |
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return(_rotatoms); |
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} |
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double CalcTorsion(double *); |
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double CalcBondLength(double*); |
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double GetDelta() |
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{ |
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return(_delta); |
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} |
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OBBond *GetBond() |
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{ |
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return(_bond); |
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} |
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std::vector<int> &GetDihedralAtoms() |
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{ |
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return(_torsion); |
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} |
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std::vector<double> &GetResolution() |
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{ |
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return(_res); |
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} |
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std::vector<double>::iterator BeginTorIncrement() |
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{ |
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return(_res.begin()); |
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} |
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std::vector<double>::iterator EndTorIncrement() |
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{ |
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return(_res.end()); |
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} |
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OBBitVec &GetEvalAtoms() |
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{ |
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return(_evalatoms); |
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} |
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OBBitVec &GetFixedAtoms() |
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{ |
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return(_fixedatoms); |
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} |
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}; |
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|
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//! Given an OBMol, set up a list of possibly rotatable torsions, |
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class OBAPI OBRotorList |
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{ |
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bool _quiet,_removesym; |
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OBBitVec _fix; |
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OBRotorRules _rr; |
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std::vector<int> _dffv; //!< distance from fixed |
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std::vector<OBRotor*> _rotor; |
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std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym2; |
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std::vector<std::pair<OBSmartsPattern*,std::pair<int,int> > > _vsym3; |
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public: |
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OBRotorList(); |
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~OBRotorList(); |
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|
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int Size() |
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{ |
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return((_rotor.empty()) ? 0: _rotor.size()); |
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} |
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void Init(std::string &fname) |
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{ |
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_rr.SetFilename(fname); |
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_rr.Init(); |
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} |
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void SetFixAtoms(OBBitVec &fix) |
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{ |
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_fix = fix; |
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} |
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void SetQuiet() |
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{ |
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_quiet=true; |
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_rr.Quiet(); |
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} |
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void IgnoreSymmetryRemoval() |
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{ |
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_removesym=false; |
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} |
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void Clear(); |
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void RemoveSymVals(OBMol&); |
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void SetRotAtomsByFix(OBMol&); |
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bool SetRotAtoms(OBMol&); |
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bool Setup(OBMol &); |
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bool FindRotors(OBMol &); |
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bool IdentifyEvalAtoms(OBMol &); |
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bool SetEvalAtoms(OBMol&); |
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bool AssignTorVals(OBMol &); |
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bool IsFixedBond(OBBond*); |
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bool HasFixedAtoms() |
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{ |
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return(!_fix.Empty()); |
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} |
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OBRotor *BeginRotor(std::vector<OBRotor*>::iterator &i) |
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{ |
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i = _rotor.begin(); |
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return((i ==_rotor.end()) ? NULL:*i); |
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} |
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OBRotor *NextRotor(std::vector<OBRotor*>::iterator &i) |
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{ |
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i++; |
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return((i ==_rotor.end()) ? NULL:*i); |
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} |
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std::vector<OBRotor*>::iterator BeginRotors() |
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{ |
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return(_rotor.begin()); |
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} |
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std::vector<OBRotor*>::iterator EndRotors() |
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{ |
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return(_rotor.end()); |
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} |
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}; |
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|
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} // end namespace OpenBabel |
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|
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#ifndef SQUARE |
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#define SQUARE(x) ((x)*(x)) |
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#endif |
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|
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#endif // OB_ROTOR_H |
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|
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//! \file rotor.h |
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//! \brief Rotate torsional according to rotor rules. |
