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 00007 This file is part of the Open Babel project. 00008 For more information, see <http://openbabel.sourceforge.net/> 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_GRID_H 00021 #define OB_GRID_H 00022 00023 #include <openbabel/babelconfig.h> 00024 00025 #include <iosfwd> 00026 #include <algorithm> 00027 #include <vector> 00028 #include <string> 00029 00030 namespace OpenBabel 00031 { 00032 00033 // Forward declaration 00034 class OBMol; 00035 00038 class OBAPI OBGrid: public OBBase 00039 { 00040 protected: 00041 double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax; 00042 00043 public: 00044 OBGrid() {} 00045 00049 virtual void Init(OBMol &box); 00050 00052 double GetXmin() const { return(_xmin); } 00054 double GetYmin() const { return(_ymin); } 00056 double GetZmin() const { return(_zmin); } 00058 double GetXmax() const { return(_xmax); } 00060 double GetYmax() const { return(_ymax); } 00062 double GetZmax() const { return(_zmax); } 00063 00065 bool PointIsInBox(double x,double y,double z) 00066 { 00067 return (x>=_xmin) && (x<=_xmax) && 00068 (y>=_ymin) && (y<=_ymax) && 00069 (z>=_zmin) && (z<=_zmax); 00070 } 00072 bool PointIsInBox(double *c) 00073 { 00074 return (c[0]>=_xmin) && (c[0]<=_xmax) && 00075 (c[1]>=_ymin) && (c[1]<=_ymax) && 00076 (c[2]>=_zmin) && (c[2]<=_zmax); 00077 } 00078 }; 00079 00085 class OBAPI OBFloatGrid: public OBGrid 00086 { 00087 protected: 00088 double *_val; 00089 int *_ival; 00090 double _midz,_midx,_midy; 00091 int _ydim,_xdim,_zdim; 00092 double _spacing,_inv_spa; 00093 double _halfSpace; 00094 00095 public: 00096 00097 OBFloatGrid() : _val(NULL), _ival(NULL), _halfSpace(0.0) {} 00098 ~OBFloatGrid() 00099 { 00100 if (_ival) delete [] _ival; 00101 if (_val) delete [] _val; 00102 } 00105 void Init(OBMol &box,double spacing, double pad= 0.0); 00106 00107 void GetMin(double *a) 00108 { 00109 a[0]=_xmin; 00110 a[1]=_ymin; 00111 a[2]=_zmin; 00112 } 00113 void GetMax(double *a) 00114 { 00115 a[0]=_xmax; 00116 a[1]=_ymax; 00117 a[2]=_zmax; 00118 } 00119 00120 double GetSpacing() const { return(_spacing); } 00121 void GetSpacing(double &s) 00122 { 00123 s=_spacing; 00124 } 00125 double GetScale() const { return(_inv_spa); } 00126 double GetHalfSpace() const {return(_halfSpace);} 00127 int GetXdim() const { return(_xdim); } 00128 int GetYdim() const { return(_ydim); } 00129 int GetZdim() const { return(_zdim); } 00130 void GetDim(int *a) 00131 { 00132 a[0]=_xdim; 00133 a[1]=_ydim; 00134 a[2]=_zdim; 00135 } 00136 vector3 GetMidpointVector() 00137 { 00138 vector3 v; 00139 v.Set(_midx,_midy,_midz); 00140 return(v); 00141 } 00142 double *GetVals() { return(_val); } 00143 void SetVals(double *ptr) { _val = ptr; } 00144 vector3 Center() 00145 { 00146 return vector3(_midx,_midy,_midz); 00147 } 00148 00149 friend std::ostream& ".">operator<< ( std::ostream&, const OBFloatGrid& ) ; 00150 friend std::istream& operator>> ( std::istream&,OBFloatGrid& ) ; 00151 00153 double Inject(double x,double y,double z); 00154 00155 void IndexToCoords(int idx, double &x, double &y, double &z); 00156 void CoordsToIndex(int*,double*); 00157 int CoordsToIndex(double &x, double &y, double &z); 00159 double Interpolate(double,double,double); 00161 double InterpolateDerivatives(double,double,double,double *derivatives); 00162 }; 00163 00164 #ifndef OBPolarGrid 00165 #define OBPolarGrid 0x01 /* polar interactions? */ 00166 #endif //OBPolarGrid 00167 00168 #ifndef OBLipoGrid 00169 #define OBLipoGrid 0x02 /* lipophilicity? */ 00170 #endif //OBLipoGrid 00171 00175 class OBAPI OBProxGrid: public OBGrid 00176 { 00177 protected: 00178 int _gridtype; 00179 int _nxinc,_nyinc,_nzinc,_maxinc; 00180 double _inc; 00181 std::vector<std::vector<int> > cell; 00182 00183 public: 00184 00185 OBProxGrid(int gridtype=0) 00186 { 00187 _gridtype=gridtype; 00188 } 00189 ~OBProxGrid() 00190 {} 00191 void Setup(OBMol &mol,OBMol &box, double cutoff,double resolution = 0.5); 00192 void Setup(OBMol &mol,OBMol &box, double cutoff, 00193 std::vector<bool> &use,double resolution = 0.5); 00194 std::vector<int> *GetProxVector(double,double,double); 00195 std::vector<int> *GetProxVector(double*); 00196 00197 bool LipoGrid() 00198 { 00199 return((_gridtype&OBLipoGrid) ? true : false); 00200 } 00201 bool PolarGrid() 00202 { 00203 return(_gridtype&OBPolarGrid); 00204 } 00205 void SetGridType(int gridtype) 00206 { 00207 _gridtype = gridtype; 00208 } 00209 }; 00210 00211 // scoring function used: PLP = Piecewise Linear Potential or ChemScore algorithm 00212 typedef enum { Undefined = -1, PLP, ChemScore } score_t; 00213 00217 class OBAPI OBScoreGrid 00218 { 00219 protected: 00220 score_t gridtype; 00221 bool verbose; 00222 00223 public: 00224 00225 double score; 00226 00227 OBScoreGrid(void) { verbose = false; } 00228 virtual ~OBScoreGrid(void) {} 00229 00230 void SetVerbose(bool v) { verbose = v; } 00231 void SetType(score_t type) { gridtype = type; } 00232 score_t GetType(void) { return gridtype; } 00233 00234 virtual void Clear(void) { } 00235 virtual double Eval(double *) { return -1; } 00236 virtual double Eval(OBMol &mol){return Eval(mol.GetCoordinates());} 00237 virtual void Init(OBMol &, OBMol &, std::string &, double){} 00238 virtual void Setup(OBMol &) {} 00239 virtual void Setup(OBMol &, std::vector<int> &){} 00240 virtual void Setup(std::vector<int> &) {} 00241 virtual void Config(std::string) {} 00242 virtual bool Read(std::string) { return false; } 00243 virtual bool Write(std::string) { return false; } 00244 virtual vector3 Center() { return VZero; } 00245 virtual vector3 CenterMol(OBMol &) { return VZero; } 00246 }; 00247 00248 } // end namespace OpenBabel 00249 00250 #endif // OB_GRID_H 00251
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.