1 //
2 //   Copyright (C) 2005-2013 Greg Landrum and Rational Discovery LLC
3 //
4 //   @@ All Rights Reserved @@
5 //  This file is part of the RDKit.
6 //  The contents are covered by the terms of the BSD license
7 //  which is included in the file license.txt, found at the root
8 //  of the RDKit source tree.
9 //
10 #include <RDGeneral/export.h>
11 #ifndef _UNIFORMGRID3D_H_20050124_1703
12 #define _UNIFORMGRID3D_H_20050124_1703
13 
14 #include "point.h"
15 #include <DataStructs/DiscreteValueVect.h>
16 #include "Grid3D.h"
17 #include <iostream>
18 
19 namespace RDGeom {
20 class RDKIT_RDGEOMETRYLIB_EXPORT UniformGrid3D : public Grid3D {
21  public:
22   //! \brief ctor
23   /*
24       \param dimX:    the x dimension of the grid, in Angstroms
25       \param dimY:    the y dimension of the grid, in Angstroms
26       \param dimZ:    the z dimension of the grid, in Angstroms
27       \param spacing: the grid spacing, in Angstroms
28       \param valType: the data type of the grid (determines the number of bits
29                       per point)
30       \param offset:  OPTIONAL: the offset of the grid from (0,0,0), in
31      Angstroms.
32 
33       \b Note: the values of arguments such as \c dimX and \c spacing
34       don't actually need to be in Angstroms, but they should be internally
35       consistent.
36 
37   */
38   UniformGrid3D(double dimX, double dimY, double dimZ, double spacing = 0.5,
39                 RDKit::DiscreteValueVect::DiscreteValueType valType =
40                     RDKit::DiscreteValueVect::TWOBITVALUE,
41                 const RDGeom::Point3D *offset = nullptr) {
42     if (offset == nullptr) {
43       initGrid(dimX, dimY, dimZ, spacing, valType,
44                Point3D(-0.5 * dimX, -0.5 * dimY, -0.5 * dimZ));
45     } else {
46       initGrid(dimX, dimY, dimZ, spacing, valType, *offset);
47     }
48   }
49   //! copy ctor
50   UniformGrid3D(const UniformGrid3D &other);
51   //! construct from a string pickle
52   UniformGrid3D(const std::string &pkl);
53   //! construct from a text pickle
54   UniformGrid3D(const char *pkl, unsigned int);
55   UniformGrid3D &operator=(const UniformGrid3D &other);
56 
57   ~UniformGrid3D();
58 
59   //! \brief Get the index of the grid point closest to point
60   //!
61   //! \return the integer index, -1 if the specified point is outside the grid
62   int getGridPointIndex(const Point3D &point) const;
63 
64   //! \brief Get the value at the grid point closest to the specified point
65   //!
66   //! \return the integer value, -1 if the specified index is outside the grid
67   int getVal(const Point3D &point) const;
68 
69   //! \brief Get the value at a specified grid point
70   //!
71   //! \return the unsigned integer value
72   unsigned int getVal(unsigned int pointId) const;
73 
74   //! \brief Set the value at the grid point closest to the specified point
75   //!
76   //! doesn't do anything if the point is outside the grid
77   void setVal(const Point3D &point, unsigned int val);
78 
79   //! \brief get the location of the specified grid point
80   Point3D getGridPointLoc(unsigned int pointId) const;
81 
82   //! \brief Set the value at the specified grid point
83   void setVal(unsigned int pointId, unsigned int val);
84 
85   //! \brief get the size of the grid (number of grid points)
getSize()86   unsigned int getSize() const { return d_numX * d_numY * d_numZ; };
87 
88   //! \brief set the occupancy for a multi-layered sphere
89   /*!
90     This function encodes the occupancy for a sphere and multiple layers around
91     it
92     \param center              location of the sphere center
93     \param radius              Radius of the base sphere
94     \param stepSize            thickness of each layer on top of the base sphere
95     \param maxNumLayers        maximum number of layers, if -1 this is
96     determined by
97                                the number of bits used per grid points in the
98     storage
99     \param ignoreOutOfBound    if true, ignore if center is outside the grid,
100     otherwise throw
101                                an exception
102 
103   */
104   void setSphereOccupancy(const Point3D &center, double radius, double stepSize,
105                           int maxNumLayers = -1, bool ignoreOutOfBound = true);
106 
107   //! \brief get the index of the grid point given the x, y, z indices
108   //!
109   //! \return the integer value, -1 if the indices are outside the grid
110   int getGridIndex(unsigned int xi, unsigned int yi, unsigned int zi) const;
111 
112   //! \brief get the x, y, and z indices of a grid-point index
113   //!
114   void getGridIndices(unsigned int idx, unsigned int &xi, unsigned int &yi,
115                       unsigned int &zi) const;
116 
117   //! \brief get the number of grid points along x-axis
getNumX()118   unsigned int getNumX() const { return d_numX; };
119 
120   //! \brief get the number of grid points along y-axis
getNumY()121   unsigned int getNumY() const { return d_numY; };
122 
123   //! \brief get the number of grid points along z-axis
getNumZ()124   unsigned int getNumZ() const { return d_numZ; };
125 
126   //! \brief get the grid's offset
getOffset()127   const Point3D &getOffset() const { return d_offSet; };
128 
129   //! \brief get the grid's spacing
getSpacing()130   double getSpacing() const { return d_spacing; };
131 
132   //! \brief return a \b const pointer to our occupancy vector
getOccupancyVect()133   const RDKit::DiscreteValueVect *getOccupancyVect() const {
134     return dp_storage;
135   };
136 
137   //! \brief returns true if the grid \c other has parameters
138   //!        compatible with ours.
139   virtual bool compareParams(const UniformGrid3D &other) const;
140   //! \brief calculates the union between the data on this grid and
141   //!  that on \c other.
142   //!  This grid is modified.
143   //!  NOTE that the grids must have the same parameters.
144   UniformGrid3D &operator|=(const UniformGrid3D &other);
145   //! \brief calculates the intersection between the data on this grid and
146   //!  that on \c other.
147   //!  This grid is modified.
148   //!  NOTE that the grids must have the same parameters.
149   UniformGrid3D &operator&=(const UniformGrid3D &other);
150   //! \brief calculates the sum of the data on this grid and
151   //!  that on \c other.
152   //!  This grid is modified.
153   //!  NOTE that the grids must have the same parameters.
154   UniformGrid3D &operator+=(const UniformGrid3D &other);
155   //! \brief calculates the difference between the data on this grid and
156   //!  that on \c other.
157   //!  This grid is modified.
158   //!  NOTE that the grids must have the same parameters.
159   UniformGrid3D &operator-=(const UniformGrid3D &other);
160 
161   //! \brief create and return a pickle
162   std::string toString() const;
163 
164   UniformGrid3D operator&(const UniformGrid3D &other) const {
165     PRECONDITION(dp_storage, "bad storage");
166     PRECONDITION(compareParams(other), "mismatched params");
167     UniformGrid3D res(d_numX * d_spacing, d_numY * d_spacing,
168                       d_numZ * d_spacing, d_spacing, dp_storage->getValueType(),
169                       &d_offSet);
170     return res;
171   };
172 
173  private:
174   //! \brief internal initialization code
175   /*
176       \param dimX:    the x dimension of the grid, in Angstroms
177       \param dimY:    the y dimension of the grid, in Angstroms
178       \param dimZ:    the z dimension of the grid, in Angstroms
179       \param spacing: the grid spacing, in Angstroms
180       \param valType: the data type of the grid (determines the number of bits
181                       per point)
182       \param offset:  the offset of the grid from (0,0,0), in Angstroms.
183       \param data:    (optional) a pointer to a DiscreteValueVect to use, we
184      take
185                       ownership of the pointer.
186   */
187   void initGrid(double dimX, double dimY, double dimZ, double spacing,
188                 RDKit::DiscreteValueVect::DiscreteValueType valType,
189                 const RDGeom::Point3D &offSet,
190                 RDKit::DiscreteValueVect *data = nullptr);
191   unsigned int d_numX, d_numY,
192       d_numZ;        //! number of grid points along x, y, z axes
193   double d_spacing;  //! grid spacing
194   Point3D d_offSet;  //! the grid offset (from the origin)
195   RDKit::DiscreteValueVect
196       *dp_storage;  //! storage for values at each grid point
197 
198   //! \brief construct from a pickle
199   void initFromText(const char *pkl, const unsigned int length);
200 };
201 
202 //! \brief writes the contents of the grid to a stream
203 /*
204   The grid is written in GRD format
205 */
206 RDKIT_RDGEOMETRYLIB_EXPORT void writeGridToStream(const UniformGrid3D &grid,
207                                                   std::ostream &outStrm);
208 
209 //! \brief writes the contents of the grid to a named file
210 /*
211   The grid is written in GRD format
212 */
213 RDKIT_RDGEOMETRYLIB_EXPORT void writeGridToFile(const UniformGrid3D &grid,
214                                                 const std::string &filename);
215 }  // namespace RDGeom
216 
217 #endif
218