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219 lines
8.4 KiB
C++
219 lines
8.4 KiB
C++
//
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// Copyright (C) 2005-2013 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef UNIFORMGRID3D_H_20050124_1703
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#define UNIFORMGRID3D_H_20050124_1703
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#include "point.h"
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#include <DataStructs/DiscreteValueVect.h>
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#include "Grid3D.h"
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namespace RDGeom {
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class RDKIT_RDGEOMETRYLIB_EXPORT UniformGrid3D
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: public Grid3D<RDKit::DiscreteValueVect, int, unsigned int> {
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public:
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//! \brief ctor
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/*
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\param dimX: the x dimension of the grid, in Angstroms
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\param dimY: the y dimension of the grid, in Angstroms
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\param dimZ: the z dimension of the grid, in Angstroms
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\param spacing: the grid spacing, in Angstroms
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\param valType: the data type of the grid (determines the number of bits
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per point)
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\param offset: OPTIONAL: the offset of the grid from (0,0,0), in
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Angstroms.
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\b Note: the values of arguments such as \c dimX and \c spacing
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don't actually need to be in Angstroms, but they should be internally
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consistent.
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*/
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UniformGrid3D(double dimX, double dimY, double dimZ, double spacing = 0.5,
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RDKit::DiscreteValueVect::DiscreteValueType valType =
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RDKit::DiscreteValueVect::TWOBITVALUE,
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const RDGeom::Point3D *offset = nullptr) {
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if (offset == nullptr) {
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initGrid(dimX, dimY, dimZ, spacing, valType,
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Point3D(-0.5 * dimX, -0.5 * dimY, -0.5 * dimZ));
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} else {
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initGrid(dimX, dimY, dimZ, spacing, valType, *offset);
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}
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}
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//! copy ctor
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UniformGrid3D(const UniformGrid3D &other);
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//! construct from a string pickle
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UniformGrid3D(const std::string &pkl);
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//! construct from a text pickle
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UniformGrid3D(const char *pkl, unsigned int);
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UniformGrid3D &operator=(const UniformGrid3D &other);
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~UniformGrid3D() override;
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//! \brief Get the index of the grid point closest to point
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//!
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//! \return the integer index, -1 if the specified point is outside the grid
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int getGridPointIndex(const Point3D &point) const override;
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//! \brief Get the value at the grid point closest to the specified point
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//!
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//! \return the integer value, -1 if the specified index is outside the grid
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int getVal(const Point3D &point) const override;
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//! \brief Get the value at a specified grid point
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//!
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//! \return the unsigned integer value
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unsigned int getVal(unsigned int pointId) const override;
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//! \brief Set the value at the grid point closest to the specified point
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//!
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//! doesn't do anything if the point is outside the grid
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void setVal(const Point3D &point, unsigned int val) override;
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//! \brief get the location of the specified grid point
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Point3D getGridPointLoc(unsigned int pointId) const override;
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//! \brief Set the value at the specified grid point
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void setVal(unsigned int pointId, unsigned int val) override;
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//! \brief get the size of the grid (number of grid points)
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unsigned int getSize() const override { return d_numX * d_numY * d_numZ; }
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//! \brief set the occupancy for a multi-layered sphere
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/*!
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This function encodes the occupancy for a sphere and multiple layers around
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it
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\param center location of the sphere center
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\param radius Radius of the base sphere
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\param stepSize thickness of each layer on top of the base sphere
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\param maxNumLayers maximum number of layers, if -1 this is
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determined by
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the number of bits used per grid points in the
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storage
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\param ignoreOutOfBound if true, ignore if center is outside the grid,
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otherwise throw
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an exception
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*/
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void setSphereOccupancy(const Point3D ¢er, double radius, double stepSize,
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int maxNumLayers = -1, bool ignoreOutOfBound = true);
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//! \brief get the index of the grid point given the x, y, z indices
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//!
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//! \return the integer value, -1 if the indices are outside the grid
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int getGridIndex(unsigned int xi, unsigned int yi, unsigned int zi) const;
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//! \brief get the x, y, and z indices of a grid-point index
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//!
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void getGridIndices(unsigned int idx, unsigned int &xi, unsigned int &yi,
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unsigned int &zi) const;
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//! \brief get the number of grid points along x-axis
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unsigned int getNumX() const { return d_numX; }
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//! \brief get the number of grid points along y-axis
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unsigned int getNumY() const { return d_numY; }
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//! \brief get the number of grid points along z-axis
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unsigned int getNumZ() const { return d_numZ; }
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//! \brief get the grid's offset
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const Point3D &getOffset() const { return d_offSet; }
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//! \brief get the grid's spacing
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double getSpacing() const { return d_spacing; }
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//! \brief return a \b const pointer to our occupancy vector
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const RDKit::DiscreteValueVect *getOccupancyVect() const override {
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return dp_storage;
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}
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//! \brief returns true if the grid \c other has parameters
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//! compatible with ours.
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virtual bool compareParams(const UniformGrid3D &other) const;
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//! \brief calculates the union between the data on this grid and
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//! that on \c other.
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//! This grid is modified.
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//! NOTE that the grids must have the same parameters.
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UniformGrid3D &operator|=(const UniformGrid3D &other);
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//! \brief calculates the intersection between the data on this grid and
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//! that on \c other.
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//! This grid is modified.
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//! NOTE that the grids must have the same parameters.
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UniformGrid3D &operator&=(const UniformGrid3D &other);
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//! \brief calculates the sum of the data on this grid and
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//! that on \c other.
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//! This grid is modified.
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//! NOTE that the grids must have the same parameters.
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UniformGrid3D &operator+=(const UniformGrid3D &other);
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//! \brief calculates the difference between the data on this grid and
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//! that on \c other.
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//! This grid is modified.
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//! NOTE that the grids must have the same parameters.
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UniformGrid3D &operator-=(const UniformGrid3D &other);
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//! \brief create and return a pickle
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std::string toString() const;
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UniformGrid3D operator&(const UniformGrid3D &other) const {
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PRECONDITION(dp_storage, "bad storage");
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PRECONDITION(compareParams(other), "mismatched params");
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UniformGrid3D res(d_numX * d_spacing, d_numY * d_spacing,
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d_numZ * d_spacing, d_spacing, dp_storage->getValueType(),
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&d_offSet);
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return res;
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}
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private:
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//! \brief internal initialization code
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/*
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\param dimX: the x dimension of the grid, in Angstroms
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\param dimY: the y dimension of the grid, in Angstroms
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\param dimZ: the z dimension of the grid, in Angstroms
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\param spacing: the grid spacing, in Angstroms
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\param valType: the data type of the grid (determines the number of bits
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per point)
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\param offset: the offset of the grid from (0,0,0), in Angstroms.
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\param data: (optional) a pointer to a DiscreteValueVect to use, we
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take
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ownership of the pointer.
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*/
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void initGrid(double dimX, double dimY, double dimZ, double spacing,
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RDKit::DiscreteValueVect::DiscreteValueType valType,
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const RDGeom::Point3D &offSet,
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RDKit::DiscreteValueVect *data = nullptr);
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unsigned int d_numX; //!< number of grid points along x axis
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unsigned int d_numY; //!< number of grid points along y axis
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unsigned int d_numZ; //!< number of grid points along z axis
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double d_spacing; //!< grid spacing
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Point3D d_offSet; //!< the grid offset (from the origin)
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RDKit::DiscreteValueVect
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*dp_storage; //!< storage for values at each grid point
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//! \brief construct from a pickle
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void initFromText(const char *pkl, const unsigned int length);
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};
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//! \brief writes the contents of the grid to a stream
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/*
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The grid is written in GRD format
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*/
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RDKIT_RDGEOMETRYLIB_EXPORT void writeGridToStream(const UniformGrid3D &grid,
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std::ostream &outStrm);
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//! \brief writes the contents of the grid to a named file
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/*
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The grid is written in GRD format
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*/
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RDKIT_RDGEOMETRYLIB_EXPORT void writeGridToFile(const UniformGrid3D &grid,
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const std::string &filename);
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} // namespace RDGeom
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#endif
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