00001 /********************************************************************** 00002 grid.h - Handle grids of values. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison 00006 Some Portions Copyright (C) 2008 by Marcus D. Hanwell 00007 00008 This file is part of the Open Babel project. 00009 For more information, see <http://openbabel.sourceforge.net/> 00010 00011 This program is free software; you can redistribute it and/or modify 00012 it under the terms of the GNU General Public License as published by 00013 the Free Software Foundation version 2 of the License. 00014 00015 This program is distributed in the hope that it will be useful, 00016 but WITHOUT ANY WARRANTY; without even the implied warranty of 00017 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00018 GNU General Public License for more details. 00019 ***********************************************************************/ 00020 00021 #ifndef OB_GRID_H 00022 #define OB_GRID_H 00023 00024 #include <openbabel/babelconfig.h> 00025 #include <openbabel/math/vector3.h> 00026 00027 #include <iosfwd> 00028 #include <algorithm> 00029 #include <vector> 00030 #include <string> 00031 00032 namespace OpenBabel 00033 { 00034 00035 // Forward declaration 00036 class OBMol; 00037 00040 class OBAPI OBGrid: public OBBase 00041 { 00042 protected: 00043 double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax; 00044 00045 public: 00046 OBGrid() {} 00047 00051 virtual void Init(OBMol &box); 00052 00054 double GetXmin() const { return(_xmin); } 00056 double GetYmin() const { return(_ymin); } 00058 double GetZmin() const { return(_zmin); } 00060 double GetXmax() const { return(_xmax); } 00062 double GetYmax() const { return(_ymax); } 00064 double GetZmax() const { return(_zmax); } 00065 00067 bool PointIsInBox(double x,double y,double z) 00068 { 00069 return (x>=_xmin) && (x<=_xmax) && 00070 (y>=_ymin) && (y<=_ymax) && 00071 (z>=_zmin) && (z<=_zmax); 00072 } 00074 bool PointIsInBox(double *c) 00075 { 00076 return (c[0]>=_xmin) && (c[0]<=_xmax) && 00077 (c[1]>=_ymin) && (c[1]<=_ymax) && 00078 (c[2]>=_zmin) && (c[2]<=_zmax); 00079 } 00080 00082 bool PointIsInBox(vector3 v) 00083 { 00084 return (v.x() >= _xmin) && (v.x() <=_xmax) && 00085 (v.y()>=_ymin) && (v.y()<=_ymax) && 00086 (v.z()>=_zmin) && (v.z()<=_zmax); 00087 } 00088 }; 00089 00097 class OBAPI OBFloatGrid: public OBGrid 00098 { 00099 protected: 00100 std::vector<double> _values; 00101 int *_ival; 00102 double _midz,_midx,_midy; 00103 int _ydim,_xdim,_zdim; 00104 double _spacing,_inv_spa; 00105 double _halfSpace; 00106 00107 vector3 _xAxis, _yAxis, _zAxis; 00108 00109 public: 00110 00111 OBFloatGrid() : _ival(NULL), _halfSpace(0.0) {} 00112 ~OBFloatGrid() 00113 { 00114 if (_ival) delete [] _ival; 00115 } 00116 00119 void Init(OBMol &box,double spacing, double pad=0.0); 00120 00122 vector3 GetMin() { return vector3(_xmin, _ymin, _zmin); } 00123 00127 void GetMin(double *a) 00128 { 00129 a[0]=_xmin; 00130 a[1]=_ymin; 00131 a[2]=_zmin; 00132 } 00133 00135 vector3 GetMax() { return vector3(_xmax, _ymax, _zmax); } 00136 00140 void GetMax(double *a) 00141 { 00142 a[0]=_xmax; 00143 a[1]=_ymax; 00144 a[2]=_zmax; 00145 } 00146 00148 double GetSpacing() const { return(_spacing); } 00152 void GetSpacing(double &s) 00153 { 00154 s=_spacing; 00155 } 00157 double GetScale() const { return(_inv_spa); } 00159 double GetHalfSpace() const {return(_halfSpace);} 00161 int GetXdim() const { return(_xdim); } 00163 int GetYdim() const { return(_ydim); } 00165 int GetZdim() const { return(_zdim); } 00169 void GetDim(int *a) 00170 { 00171 a[0]=_xdim; 00172 a[1]=_ydim; 00173 a[2]=_zdim; 00174 } 00175 00177 vector3 GetMidpointVector() 00178 { 00179 vector3 v; 00180 v.Set(_midx,_midy,_midz); 00181 return(v); 00182 } 00183 00185 vector3 GetXAxis() const 00186 { 00187 return _xAxis; 00188 } 00189 00191 vector3 GetYAxis() const 00192 { 00193 return _yAxis; 00194 } 00195 00197 vector3 GetZAxis() const 00198 { 00199 return _zAxis; 00200 } 00201 00203 void SetNumberOfPoints(int nx, int ny, int nz); 00204 00206 void SetXAxis(vector3); 00208 void SetYAxis(vector3); 00210 void SetZAxis(vector3); 00211 00216 void SetLimits(const vector3& origin, const vector3& x, const vector3& y, 00217 const vector3& z); 00220 void SetLimits(const double origin[3], const double x[3], const double y[3], 00221 const double z[3]); 00222 00224 std::vector<double> GetDataVector(); 00228 void SetVals(const std::vector<double> & vals); 00229 00234 double *GetVals() { return(&_values[0]); } 00235 00237 double GetValue(int i, int j, int k) 00238 { 00239 if (i*_ydim*_zdim + j*_zdim + k > _xdim*_ydim*_zdim) 00240 return 0.0; 00241 else 00242 return _values[i*_ydim*_zdim + j*_zdim + k]; 00243 } 00244 00247 void SetVals(double *ptr) 00248 { 00249 for (int i = 0; i < _xdim*_ydim*_zdim; ++i) 00250 _values[i] = ptr[i]; 00251 } 00252 00254 bool SetValue(int i, int j, int k, double val) 00255 { 00256 if (i*_ydim*_zdim + j*_zdim + k > _xdim*_ydim*_zdim) 00257 return false; 00258 00259 _values[i*_ydim*_zdim + j*_zdim + k] = val; 00260 return true; 00261 } 00262 00264 vector3 Center() 00265 { 00266 return vector3(_midx,_midy,_midz); 00267 } 00268 00269 friend std::ostream& operator<< ( std::ostream&, const OBFloatGrid& ) ; 00270 friend std::istream& operator>> ( std::istream&,OBFloatGrid& ) ; 00271 00273 double Inject(double x,double y,double z); 00274 void IndexToCoords(int idx, double &x, double &y, double &z); 00275 void CoordsToIndex(int*,double*); 00276 int CoordsToIndex(double x, double y, double z); 00278 double Interpolate(double,double,double); 00280 double InterpolateDerivatives(double,double,double,double *derivatives); 00281 }; 00282 00283 #ifndef OBPolarGrid 00284 #define OBPolarGrid 0x01 /* polar interactions? */ 00285 #endif //OBPolarGrid 00286 00287 #ifndef OBLipoGrid 00288 #define OBLipoGrid 0x02 /* lipophilicity? */ 00289 #endif //OBLipoGrid 00290 00294 class OBAPI OBProxGrid: public OBGrid 00295 { 00296 protected: 00297 int _gridtype; 00298 int _nxinc,_nyinc,_nzinc,_maxinc; 00299 double _inc; 00300 std::vector<std::vector<int> > cell; 00301 00302 public: 00303 00304 OBProxGrid(int gridtype=0) 00305 { 00306 _gridtype=gridtype; 00307 } 00308 ~OBProxGrid() 00309 {} 00310 void Setup(OBMol &mol,OBMol &box, double cutoff,double resolution = 0.5); 00311 void Setup(OBMol &mol,OBMol &box, double cutoff, 00312 std::vector<bool> &use,double resolution = 0.5); 00313 std::vector<int> *GetProxVector(double,double,double); 00314 std::vector<int> *GetProxVector(double*); 00315 00316 bool LipoGrid() 00317 { 00318 return((_gridtype&OBLipoGrid) ? true : false); 00319 } 00320 bool PolarGrid() 00321 { 00322 return(_gridtype&OBPolarGrid); 00323 } 00324 void SetGridType(int gridtype) 00325 { 00326 _gridtype = gridtype; 00327 } 00328 }; 00329 00330 // scoring function used: PLP = Piecewise Linear Potential or ChemScore algorithm 00331 typedef enum { Undefined = -1, PLP, ChemScore } score_t; 00332 00336 class OBAPI OBScoreGrid 00337 { 00338 protected: 00339 score_t gridtype; 00340 bool verbose; 00341 00342 public: 00343 00344 double score; 00345 00346 OBScoreGrid(void) { verbose = false; } 00347 virtual ~OBScoreGrid(void) {} 00348 00349 void SetVerbose(bool v) { verbose = v; } 00350 void SetType(score_t type) { gridtype = type; } 00351 score_t GetType(void) { return gridtype; } 00352 00353 virtual void Clear(void) { } 00354 virtual double Eval(double *) { return -1; } 00355 virtual double Eval(OBMol &mol){return Eval(mol.GetCoordinates());} 00356 virtual void Init(OBMol &, OBMol &, std::string &, double){} 00357 virtual void Setup(OBMol &) {} 00358 virtual void Setup(OBMol &, std::vector<int> &){} 00359 virtual void Setup(std::vector<int> &) {} 00360 virtual void Config(std::string) {} 00361 virtual bool Read(std::string) { return false; } 00362 virtual bool Write(std::string) { return false; } 00363 virtual vector3 Center() { return VZero; } 00364 virtual vector3 CenterMol(OBMol &) { return VZero; } 00365 }; 00366 00367 } // end namespace OpenBabel 00368 00369 #endif // OB_GRID_H 00370
This file is part of the documentation for Open Babel, version 2.2.0.
1.5.6.