UniformGrid3D.h

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//
//   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.
//
#include <RDGeneral/export.h>
#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 RDKIT_RDGEOMETRYLIB_EXPORT 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 = nullptr) {
    if (offset == nullptr) {
      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 &operator=(const UniformGrid3D &other);
 
  ~UniformGrid3D() override;
 
  //! \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 override;
 
  //! \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 override;
 
  //! \brief Get the value at a specified grid point
  //!
  //! \return the unsigned integer value
  unsigned int getVal(unsigned int pointId) const override;
 
  //! \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) override;
 
  //! \brief get the location of the specified grid point
  Point3D getGridPointLoc(unsigned int pointId) const override;
 
  //! \brief Set the value at the specified grid point
  void setVal(unsigned int pointId, unsigned int val) override;
 
  //! \brief get the size of the grid (number of grid points)
  unsigned int getSize() const override { 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 override {
    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 = nullptr);
  unsigned int d_numX;  //!< number of grid points along x axis
  unsigned int d_numY;  //!< number of grid points along y axis
  unsigned int d_numZ;  //!< number of grid points along z axis
  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
*/
RDKIT_RDGEOMETRYLIB_EXPORT 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
*/
RDKIT_RDGEOMETRYLIB_EXPORT void writeGridToFile(const UniformGrid3D &grid,
                                                const std::string &filename);
}  // namespace RDGeom
 
#endif