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/* -------------------------------------------------------------------------- *
* MMB (MacroMoleculeBuilder) *
* -------------------------------------------------------------------------- *
* *
* Copyright (c) 2011-12 by the Author. *
* Author: Samuel Flores *
* *
* See RNABuilder.cpp for the copyright and usage agreement. *
* -------------------------------------------------------------------------- */
#ifndef DensityMap_H_
#define DensityMap_H_
#include "SimTKmolmodel.h"
#include "UnitCellParameters.h"
#define LINESIZE 1024
using namespace std;
using namespace SimTK;
class Quadrant {
public:
bool positiveX, positiveY, positiveZ;
};
struct AmplitudeFrequencyAndRandomPhases {
double amplitude;
double frequencyX;
double frequencyY;
double frequencyZ;
double phaseX;
double phaseY;
double phaseZ;
};
struct GridPoint {
double noiseFreeDensity;
double density;
double noise;/*
float ddxPositiveXGradient;
float ddyPositiveXGradient;
float ddzPositiveXGradient;
float ddxPositiveYGradient;
float ddyPositiveYGradient;
float ddzPositiveYGradient;
float ddxPositiveZGradient;
float ddyPositiveZGradient;
float ddzPositiveZGradient;*/
Vec3 position;
Vec3 firstQuadrantGradient;
};
class GridIndices {
public:
GridIndices(int x, int y, int z) :
z{z},
y{y},
x{x}
{}
const int z;
const int y;
const int x;
};
class MMB_EXPORT DensityMap {
protected:
//double minX, minY, minZ, maxX, maxY, maxZ, gridXSpacing, gridYSpacing, gridZSpacing;
int unitCellNumGridX;
int unitCellNumGridY;
int unitCellNumGridZ;
int totalNumGridX;
int totalNumGridY;
int totalNumGridZ;
UnitCellParameters unitCellParameters;
char * dxGets( char *s, int n, FILE *stream);
private:
double noiseTemperature;
double noiseScale;
double forceConstant;
String densityFileName;
std::vector<GridPoint> m_gridPoints;
const GridPoint & gridPoint(int z, int y, int x) const;
GridPoint & gridPoint(int z, int y, int x);
public:
DensityMap();
void initializeMap();
void validateGridParameters();
size_t getSizeOfArrayOfGridPoints() const ;//
// {return ArrayOfGridPoints.size()*ArrayOfGridPoints[0].size()*ArrayOfGridPoints[0][0].size();};
std::vector<std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> > > vectorOfAmplitudeFrequencyAndRandomPhases;
bool hasGridPoint(const GridIndices &indices) const;
const GridPoint & getGridPoint(const GridIndices &indices) const;
const GridPoint & getGridPoint(const Vec3 &pos) const;
GridPoint & updGridPoint(const GridIndices &indices);
GridPoint & updGridPoint(const Vec3 &pos);
void validateGridPoint(const GridIndices &indices) const;
//const bool hasNearbyGridIndices(Vec3 position);
GridIndices calcNearestGridIndices(const Vec3 &position) const;
GridIndices calcLowerLeftGridIndices(const Vec3 &position) const;
//const double getDensity(Vec3);
double getDensity(const SimTK::Vec3 &);
void initializeArrayOfGridPoints();
void setNoiseTemperature(double myTemperature){noiseTemperature=myTemperature;};
void setNoiseScale(double myNoiseScale){noiseScale = myNoiseScale;};
double getNoiseScale(){return noiseScale ;};
//void addNoiseToMap(double temperature, double amplitude);
void initializeVectorOfAmplitudeAndRandomPhases();
//void resizeNoiseMap();
void resizeVectorOfAmplitudeAndRandomPhases();
void normalizeNoiseMap(const double totalNoiseEverywhere);
void densityAutocorrelation(const bool computeNoiseAutocorrelation, const bool computeDensityAutocorrelation ) const;
void populateNoiseMap();
double getForceConstant () const {return forceConstant; };
void setForceConstant (double myForceConstant ) {forceConstant = myForceConstant ;};
String getDensityFileName() const {return densityFileName;};
void setDensityFileName(String myDensityFileName) {densityFileName = myDensityFileName;};
void loadParametersAndDensity() ;
void loadParametersAndDensity_XPLOR() ;
void loadParametersAndDensity_CCP4MAP() ;
void writeDensityMapXplor(const String outDensityFileName, const bool writeDensity = 1, const bool writeNoise =1);
//void loadParametersAndDensity_OpenDX(const String densityFileName) ;
//void loadParametersAndDensity_Situs(const String densityFileName) ;
void precomputeGradient();
//void precomputeGradientDerivatives();
Vec3 fetchGradient(const Vec3 &position);
const Vec3 & fetchFirstQuadrantGradient(const Vec3 &position);
//Vec3 calcInterpolatedFirstQuadrantGradient(Vec3 position);
const Vec3 & calcInterpolatedFirstQuadrantGradient(const Vec3 &position) const;
// Functions which were moved from GridPoint to DensityMap for memory savings
void initializeGradient(GridPoint & gridPoint );
void initialize(GridPoint & gridPoint );
void validatePosition(const GridPoint & gridPoint, const Vec3 &myPosition)const ;
void validateDensity (const GridPoint & gridPoint, double ) const;
void validate(const GridPoint & gridPoint) const;
void setDensity(GridPoint & gridPoint, Real myDensity);
void setPosition(GridPoint & gridPoint, const Vec3 &myPosition);
//Quadrant calcQuadrant(GridPoint & gridPoint, Vec3 queryPosition) const;
//Vec3 fetchGradient(GridPoint & gridPoint, Vec3 queryPosition) const;
const Vec3 & fetchFirstQuadrantGradient(const GridPoint & gridPoint) const ;
double getDensity(const GridPoint & gridPoint) const;
double getDensity(const GridPoint & gridPoint, const Vec3 &myPosition) const;
void setPositiveXGradient(GridPoint & gridPoint, Real);
//void setddxPositiveXGradient(GridPoint & gridPoint, Real);
//void setddyPositiveXGradient(GridPoint & gridPoint, Real);
//void setddzPositiveXGradient(GridPoint & gridPoint, Real);
void setPositiveYGradient(GridPoint & gridPoint,Real);
//void setddxPositiveYGradient(GridPoint & gridPoint, Real);
//void setddyPositiveYGradient(GridPoint & gridPoint, Real);
//void setddzPositiveYGradient(GridPoint & gridPoint, Real);
void setPositiveZGradient(GridPoint & gridPoint, Real);
//void setddxPositiveZGradient(GridPoint & gridPoint, Real);
//void setddyPositiveZGradient(GridPoint & gridPoint, Real);
//void setddzPositiveZGradient(GridPoint & gridPoint, Real);
void setNegativeXGradient(GridPoint & gridPoint, Real);
void setNegativeYGradient(GridPoint & gridPoint, Real);
void setNegativeZGradient(GridPoint & gridPoint, Real);
//void printSecondDerivatives(GridPoint & gridPoint) const;
const Vec3 & calcInterpolatedFirstQuadrantGradient(const GridPoint & gridPoint, const Vec3 &queryPosition) const;
};
// #define LINESIZE 1024
// class MMB_EXPORT DensityMap_OpenDX : DensityMap
// {
// protected:
// char * dxGets( char *s, int n, FILE *stream);
// public:
// DensityMap_OpenDX();
// ~DensityMap_OpenDX();
// void loadParametersAndDensity(const String densityFileName) ;
// };
#endif
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