/usr/include/rdkit/Geometry/UniformGrid3D.h is in librdkit-dev 201503-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 | //
// Copyright (C) 2005-2013 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef _UNIFORMGRID3D_H_20050124_1703
#define _UNIFORMGRID3D_H_20050124_1703
#include "point.h"
#include <DataStructs/DiscreteValueVect.h>
#include "Grid3D.h"
#include <iostream>
namespace RDGeom {
class UniformGrid3D : public Grid3D {
public:
//! \brief ctor
/*
\param dimX: the x dimension of the grid, in Angstroms
\param dimY: the y dimension of the grid, in Angstroms
\param dimZ: the z dimension of the grid, in Angstroms
\param spacing: the grid spacing, in Angstroms
\param valType: the data type of the grid (determines the number of bits
per point)
\param offset: OPTIONAL: the offset of the grid from (0,0,0), in Angstroms.
\b Note: the values of arguments such as \c dimX and \c spacing
don't actually need to be in Angstroms, but they should be internally
consistent.
*/
UniformGrid3D(double dimX, double dimY, double dimZ, double spacing=0.5,
RDKit::DiscreteValueVect::DiscreteValueType valType=RDKit::DiscreteValueVect::TWOBITVALUE,
const RDGeom::Point3D *offset=0){
if (offset == 0) {
initGrid(dimX, dimY, dimZ, spacing, valType,
Point3D(-0.5*dimX, -0.5*dimY, -0.5*dimZ));
} else {
initGrid(dimX, dimY, dimZ, spacing, valType, *offset);
}
}
//! copy ctor
UniformGrid3D(const UniformGrid3D &other);
//! construct from a string pickle
UniformGrid3D(const std::string pkl);
//! construct from a text pickle
UniformGrid3D(const char *pkl,unsigned int);
~UniformGrid3D();
//! \brief Get the index of the grid point closest to point
//!
//! \return the integer index, -1 if the specified point is outside the grid
int getGridPointIndex(const Point3D &point) const;
//! \brief Get the value at the grid point closest to the specified point
//!
//! \return the integer value, -1 if the specified index is outside the grid
int getVal(const Point3D &point) const;
//! \brief Get the value at a specified grid point
//!
//! \return the unsigned integer value
unsigned int getVal(unsigned int pointId) const;
//! \brief Set the value at the grid point closest to the specified point
//!
//! doesn't do anything if the point is outside the grid
void setVal(const Point3D &point, unsigned int val);
//! \brief get the location of the specified grid point
Point3D getGridPointLoc(unsigned int pointId) const;
//! \brief Set the value at the specified grid point
void setVal(unsigned int pointId, unsigned int val);
//! \brief get the size of the grid (number of grid points)
unsigned int getSize() const { return d_numX*d_numY*d_numZ; };
//! \brief set the occupancy for a multi-layered sphere
/*!
This function encodes the occupancy for a sphere and multiple layers around it
\param center location of the sphere center
\param radius Radius of the base sphere
\param stepSize thickness of each layer on top of the base sphere
\param maxNumLayers maximum number of layers, if -1 this is determined by
the number of bits used per grid points in the storage
\param ignoreOutOfBound if true, ignore if center is outside the grid, otherwise throw
an exception
*/
void setSphereOccupancy(const Point3D & center, double radius,
double stepSize, int maxNumLayers=-1,
bool ignoreOutOfBound=true);
//! \brief get the index of the grid point given the x, y, z indices
//!
//! \return the integer value, -1 if the indices are outside the grid
int getGridIndex(unsigned int xi, unsigned int yi, unsigned int zi) const;
//! \brief get the x, y, and z indices of a grid-point index
//!
void getGridIndices(unsigned int idx,unsigned int &xi, unsigned int &yi, unsigned int &zi) const;
//! \brief get the number of grid points along x-axis
unsigned int getNumX() const { return d_numX; };
//! \brief get the number of grid points along y-axis
unsigned int getNumY() const { return d_numY; };
//! \brief get the number of grid points along z-axis
unsigned int getNumZ() const { return d_numZ; };
//! \brief get the grid's offset
const Point3D &getOffset() const { return d_offSet; };
//! \brief get the grid's spacing
double getSpacing() const { return d_spacing; };
//! \brief return a \b const pointer to our occupancy vector
const RDKit::DiscreteValueVect *getOccupancyVect() const { return dp_storage;} ;
//! \brief returns true if the grid \c other has parameters
//! compatible with ours.
virtual bool compareParams(const UniformGrid3D &other) const;
//! \brief calculates the union between the data on this grid and
//! that on \c other.
//! This grid is modified.
//! NOTE that the grids must have the same parameters.
UniformGrid3D &operator|=(const UniformGrid3D &other);
//! \brief calculates the intersection between the data on this grid and
//! that on \c other.
//! This grid is modified.
//! NOTE that the grids must have the same parameters.
UniformGrid3D &operator&=(const UniformGrid3D &other);
//! \brief calculates the sum of the data on this grid and
//! that on \c other.
//! This grid is modified.
//! NOTE that the grids must have the same parameters.
UniformGrid3D &operator+=(const UniformGrid3D &other);
//! \brief calculates the difference between the data on this grid and
//! that on \c other.
//! This grid is modified.
//! NOTE that the grids must have the same parameters.
UniformGrid3D &operator-=(const UniformGrid3D &other);
//! \brief create and return a pickle
std::string toString() const;
UniformGrid3D operator& (const UniformGrid3D &other) const{
PRECONDITION(dp_storage,"bad storage");
PRECONDITION(compareParams(other),"mismatched params");
UniformGrid3D res(d_numX*d_spacing,d_numY*d_spacing,d_numZ*d_spacing,
d_spacing,dp_storage->getValueType(),&d_offSet);
return res;
};
private:
//! \brief internal initialization code
/*
\param dimX: the x dimension of the grid, in Angstroms
\param dimY: the y dimension of the grid, in Angstroms
\param dimZ: the z dimension of the grid, in Angstroms
\param spacing: the grid spacing, in Angstroms
\param valType: the data type of the grid (determines the number of bits
per point)
\param offset: the offset of the grid from (0,0,0), in Angstroms.
\param data: (optional) a pointer to a DiscreteValueVect to use, we take
ownership of the pointer.
*/
void initGrid(double dimX, double dimY, double dimZ, double spacing,
RDKit::DiscreteValueVect::DiscreteValueType valType,
const RDGeom::Point3D &offSet,RDKit::DiscreteValueVect *data=0);
unsigned int d_numX, d_numY, d_numZ; //! number of grid points along x, y, z axes
double d_spacing; //! grid spacing
Point3D d_offSet; //! the grid offset (from the origin)
RDKit::DiscreteValueVect *dp_storage; //! storage for values at each grid point
//! \brief construct from a pickle
void initFromText(const char *pkl,const unsigned int length);
};
//! \brief writes the contents of the grid to a stream
/*
The grid is written in GRD format
*/
void writeGridToStream(const UniformGrid3D &grid, std::ostream &outStrm);
//! \brief writes the contents of the grid to a named file
/*
The grid is written in GRD format
*/
void writeGridToFile(const UniformGrid3D &grid, std::string filename);
}
#endif
|