1 |
/********************************************************************** |
2 |
grid.h - Handle grids of values. |
3 |
|
4 |
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
5 |
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
6 |
|
7 |
This file is part of the Open Babel project. |
8 |
For more information, see <http://openbabel.sourceforge.net/> |
9 |
|
10 |
This program is free software; you can redistribute it and/or modify |
11 |
it under the terms of the GNU General Public License as published by |
12 |
the Free Software Foundation version 2 of the License. |
13 |
|
14 |
This program is distributed in the hope that it will be useful, |
15 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
16 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
17 |
GNU General Public License for more details. |
18 |
***********************************************************************/ |
19 |
|
20 |
#ifndef OB_GRID_H |
21 |
#define OB_GRID_H |
22 |
|
23 |
#include "config.h" |
24 |
|
25 |
#if HAVE_IOSTREAM |
26 |
#include <iostream> |
27 |
#elif HAVE_IOSTREAM_H |
28 |
#include <iostream.h> |
29 |
#endif |
30 |
|
31 |
#include <algorithm> |
32 |
#include <vector> |
33 |
#include <string> |
34 |
|
35 |
#ifndef OBPolarGrid |
36 |
#define OBPolarGrid 0x01 /* polar interactions? */ |
37 |
#endif //OBPolarGrid |
38 |
|
39 |
#ifndef OBLipoGrid |
40 |
#define OBLipoGrid 0x02 /* lipophilicity? */ |
41 |
#endif //OBLipoGrid |
42 |
|
43 |
namespace OpenBabel |
44 |
{ |
45 |
|
46 |
//! A grid for determining the proximity of a given point to atoms in an OBMol |
47 |
class OBAPI OBProxGrid |
48 |
{ |
49 |
int _gridtype; |
50 |
int _nxinc,_nyinc,_nzinc,_maxinc; |
51 |
double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax,_inc; |
52 |
std::vector<std::vector<int> > cell; |
53 |
|
54 |
public: |
55 |
|
56 |
OBProxGrid(int gridtype=0) |
57 |
{ |
58 |
_gridtype=gridtype; |
59 |
} |
60 |
~OBProxGrid() |
61 |
{} |
62 |
void Setup(OBMol &mol,OBMol &box, double cutoff,double resolution = 0.5); |
63 |
void Setup(OBMol &mol,OBMol &box, double cutoff, |
64 |
std::vector<bool> &use,double resolution = 0.5); |
65 |
std::vector<int> *GetProxVector(double,double,double); |
66 |
std::vector<int> *GetProxVector(double*); |
67 |
|
68 |
bool LipoGrid() |
69 |
{ |
70 |
return((_gridtype&OBLipoGrid) ? true : false); |
71 |
} |
72 |
bool PolarGrid() |
73 |
{ |
74 |
return(_gridtype&OBPolarGrid); |
75 |
} |
76 |
void SetGridType(int gridtype) |
77 |
{ |
78 |
_gridtype = gridtype; |
79 |
} |
80 |
bool PointIsInBox(double x,double y,double z) |
81 |
{ |
82 |
return (x>=_xmin) && (x<=_xmax) && |
83 |
(y>=_ymin) && (y<=_ymax) && |
84 |
(z>=_zmin) && (z<=_zmax); |
85 |
} |
86 |
}; |
87 |
|
88 |
//! Handle floating-point 3D grids (i.e., charge density around an OBMol) |
89 |
class OBAPI OBFloatGrid |
90 |
{ |
91 |
protected: |
92 |
double *_val; //!< doubleing point values |
93 |
int *_ival; //!< for integer values (deprecated) |
94 |
double _midz,_midx,_midy; //!< center of grid in world coordinates |
95 |
int _ydim,_xdim,_zdim; //!< grid dimensions |
96 |
double _spacing,_inv_spa; //!< spacing between grid points and its invers |
97 |
double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax; //!< the min/max values in XYZ axes (i.e., the box) |
98 |
double _halfSpace; //!< half of the grid spacing */ |
99 |
|
100 |
public: |
101 |
|
102 |
OBFloatGrid() : _halfSpace(0.0) |
103 |
{ |
104 |
_val=NULL; |
105 |
_ival=NULL; |
106 |
} |
107 |
~OBFloatGrid() |
108 |
{ |
109 |
if (_ival) |
110 |
{ |
111 |
delete [] _ival; |
112 |
_ival = NULL; |
113 |
} |
114 |
if (_val) |
115 |
{ |
116 |
delete [] _val; |
117 |
_val = NULL; |
118 |
} |
119 |
} |
120 |
//! Initialize the grid using this molecule as a box (plus a padding) |
121 |
//! with the supplied spacing between points |
122 |
void Init(OBMol &box,double spacing, double pad= 0.0); |
123 |
//! \return whether the supplied XYZ coordinates fall within the box |
124 |
bool PointIsInBox(double x,double y,double z) |
125 |
{ |
126 |
return (x>=_xmin) && (x<=_xmax) && |
127 |
(y>=_ymin) && (y<=_ymax) && |
128 |
(z>=_zmin) && (z<=_zmax); |
129 |
} |
130 |
//! \return true if the point falls within the box |
131 |
bool PointIsInBox(double *c) |
132 |
{ |
133 |
return (c[0]>=_xmin) && (c[0]<=_xmax) && |
134 |
(c[1]>=_ymin) && (c[1]<=_ymax) && |
135 |
(c[2]>=_zmin) && (c[2]<=_zmax); |
136 |
} |
137 |
double GetXmin() const { return(_xmin); } |
138 |
double GetYmin() const { return(_ymin); } |
139 |
double GetZmin() const { return(_zmin); } |
140 |
double GetXmax() const { return(_xmax); } |
141 |
double GetYmax() const { return(_ymax); } |
142 |
double GetZmax() const { return(_zmax); } |
143 |
void GetMin(double *a) |
144 |
{ |
145 |
a[0]=_xmin; |
146 |
a[1]=_ymin; |
147 |
a[2]=_zmin; |
148 |
} |
149 |
void GetMax(double *a) |
150 |
{ |
151 |
a[0]=_xmax; |
152 |
a[1]=_ymax; |
153 |
a[2]=_zmax; |
154 |
} |
155 |
|
156 |
double GetSpacing() const { return(_spacing); } |
157 |
void GetSpacing(double &s) |
158 |
{ |
159 |
s=_spacing; |
160 |
} |
161 |
double GetScale() const { return(_inv_spa); } |
162 |
double GetHalfSpace() const {return(_halfSpace);} |
163 |
int GetXdim() const { return(_xdim); } |
164 |
int GetYdim() const { return(_ydim); } |
165 |
int GetZdim() const { return(_zdim); } |
166 |
void GetDim(int *a) |
167 |
{ |
168 |
a[0]=_xdim; |
169 |
a[1]=_ydim; |
170 |
a[2]=_zdim; |
171 |
} |
172 |
vector3 GetMidpointVector() |
173 |
{ |
174 |
vector3 v; |
175 |
v.Set(_midx,_midy,_midz); |
176 |
return(v); |
177 |
} |
178 |
double *GetVals() { return(_val); } |
179 |
void SetVals(double *ptr) { _val = ptr; } |
180 |
vector3 Center() |
181 |
{ |
182 |
return vector3(_midx,_midy,_midz); |
183 |
} |
184 |
|
185 |
friend std::ostream& operator<< ( std::ostream&, const OBFloatGrid& ) ; |
186 |
friend std::istream& operator>> ( std::istream&,OBFloatGrid& ) ; |
187 |
|
188 |
//! \return the value at the given point (rounding as needed) |
189 |
double Inject(double x,double y,double z); |
190 |
|
191 |
void IndexToCoords(int idx, double &x, double &y, double &z); |
192 |
void CoordsToIndex(int*,double*); |
193 |
int CoordsToIndex(double &x, double &y, double &z); |
194 |
//! \return the interpolated value for the given point |
195 |
double Interpolate(double,double,double); |
196 |
//! \return the interpolated value for the given point and set the dx, dy, dz derivatives |
197 |
double InterpolateDerivatives(double,double,double,double *derivatives); |
198 |
}; |
199 |
|
200 |
// scoring function used: PLP = Piecewise Linear Potential or ChemScore algorithm |
201 |
typedef enum { Undefined = -1, PLP, ChemScore } score_t; |
202 |
|
203 |
//! A base class for scoring docking interactions between multiple molecules |
204 |
class OBAPI OBScoreGrid |
205 |
{ |
206 |
protected: |
207 |
|
208 |
score_t gridtype; |
209 |
bool verbose; |
210 |
|
211 |
public: |
212 |
|
213 |
double score; |
214 |
|
215 |
OBScoreGrid(void) |
216 |
{ |
217 |
verbose = false; |
218 |
} |
219 |
virtual ~OBScoreGrid(void) |
220 |
{} |
221 |
|
222 |
void SetVerbose(bool v) |
223 |
{ |
224 |
verbose = v; |
225 |
} |
226 |
void SetType(score_t type) |
227 |
{ |
228 |
gridtype = type; |
229 |
} |
230 |
score_t GetType(void) |
231 |
{ |
232 |
return gridtype; |
233 |
} |
234 |
|
235 |
virtual void Clear(void) |
236 |
{ } |
237 |
virtual double Eval(double *) |
238 |
{ |
239 |
return -1; |
240 |
} |
241 |
virtual double Eval(OBMol &mol) |
242 |
{ |
243 |
return Eval(mol.GetCoordinates()); |
244 |
} |
245 |
virtual void Init(OBMol &, OBMol &, std::string &, double) |
246 |
{} |
247 |
virtual void Setup(OBMol &) |
248 |
{} |
249 |
virtual void Setup(OBMol &, std::vector<int> &) |
250 |
{} |
251 |
virtual void Setup(std::vector<int> &) |
252 |
{} |
253 |
virtual void Config(std::string) |
254 |
{} |
255 |
virtual bool Read(std::string) |
256 |
{ |
257 |
return false; |
258 |
} |
259 |
virtual bool Write(std::string) |
260 |
{ |
261 |
return false; |
262 |
} |
263 |
virtual vector3 Center() |
264 |
{ |
265 |
return VZero; |
266 |
} |
267 |
virtual vector3 CenterMol(OBMol &) |
268 |
{ |
269 |
return VZero; |
270 |
} |
271 |
}; |
272 |
|
273 |
} // end namespace OpenBabel |
274 |
|
275 |
#endif // OB_GRID_H |
276 |
|
277 |
//! \file grid.h |
278 |
//! \brief Handle grids of values. |