Chemical Data Processing Library C++ API - Version 1.1.1
Public Types | Public Member Functions | Static Public Attributes | List of all members
CDPL::GRAIL::GRAILDataSetGenerator Class Reference

GRAILDataSetGenerator. More...

#include <GRAILDataSetGenerator.hpp>

Public Types

typedef std::shared_ptr< GRAILDataSetGenerator > SharedPointer
 
typedef FeatureInteractionScoreGridCalculator::ScoringFunction ScoringFunction
 
typedef FeatureInteractionScoreGridCalculator::ScoreCombinationFunction ScoreCombinationFunction
 
typedef std::function< void(CDPL::Pharm::Pharmacophore &)> PharmacophoreProcessingFunction
 

Public Member Functions

 GRAILDataSetGenerator ()
 
virtual ~GRAILDataSetGenerator ()
 
void enableInteraction (unsigned int ftr_type, unsigned int tgt_ftr_type, bool enable)
 
bool isInteractionEnabled (unsigned int ftr_type, unsigned int tgt_ftr_type) const
 
void clearEnabledInteractions ()
 
void setScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type, const ScoringFunction &func)
 
const ScoringFunction & getScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type) const
 
void removeScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type)
 
void setGridName (unsigned int ftr_type, unsigned int tgt_ftr_type, const std::string &name)
 
const std::string & getGridName (unsigned int ftr_type, unsigned int tgt_ftr_type) const
 
void removeGridName (unsigned int ftr_type, unsigned int tgt_ftr_type)
 
void setScoreCombinationFunction (const ScoreCombinationFunction &func)
 
const ScoreCombinationFunction & getScoreCombinationFunction () const
 
void normalizeScores (bool normalize)
 
bool scoresNormalized () const
 
void diminishScoresByAtomDensity (bool diminish)
 
bool scoresDiminishedByAtomDensity () const
 
void storeEnvironmentAtomDensityGrid (bool store)
 
bool environmentAtomDensityGridStored () const
 
void setEnvironmentAtomDensityGridName (const std::string &name)
 
const std::string & getEnvironmentAtomDensityGridName () const
 
const Math::Matrix4D & getGridTransform () const
 
template<typename T >
void setGridTransform (const T &xform)
 
double getGridStepSize () const
 
void setGridStepSize (double size)
 
std::size_t getGridXSize () const
 
void setGridXSize (std::size_t size)
 
std::size_t getGridYSize () const
 
void setGridYSize (std::size_t size)
 
std::size_t getGridZSize () const
 
void setGridZSize (std::size_t size)
 
void setGridParamsForBoundingBox (const Math::Vector3D &bbox_min, const Math::Vector3D &bbox_max, double step_size=DEF_GRID_STEP_SIZE)
 
const Pharm::DefaultPharmacophoreGenerator & getPharmacophoreGenerator () const
 
Pharm::DefaultPharmacophoreGenerator & getPharmacophoreGenerator ()
 
void setPharmacophoreProcessingFunction (const PharmacophoreProcessingFunction &func)
 
const PharmacophoreProcessingFunction & getPharmacophoreProcessingFunction () const
 
void calcInteractionGrids (const Chem::MolecularGraph &tgt_env, const Chem::Atom3DCoordinatesFunction &coords_func, Grid::DRegularGridSet &grid_set, bool append=false)
 
Grid::DRegularGrid::SharedPointer calcAtomDensityGrid (const Chem::AtomContainer &atoms, const Chem::Atom3DCoordinatesFunction &coords_func, const std::string &grid_name)
 

Static Public Attributes

static constexpr double DEF_GRID_STEP_SIZE = 0.5
 

Detailed Description

GRAILDataSetGenerator.

See also
[GRAIL]

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<GRAILDataSetGenerator> CDPL::GRAIL::GRAILDataSetGenerator::SharedPointer

◆ ScoringFunction

typedef FeatureInteractionScoreGridCalculator::ScoringFunction CDPL::GRAIL::GRAILDataSetGenerator::ScoringFunction

◆ ScoreCombinationFunction

typedef FeatureInteractionScoreGridCalculator::ScoreCombinationFunction CDPL::GRAIL::GRAILDataSetGenerator::ScoreCombinationFunction

◆ PharmacophoreProcessingFunction

typedef std::function<void(CDPL::Pharm::Pharmacophore&)> CDPL::GRAIL::GRAILDataSetGenerator::PharmacophoreProcessingFunction

Constructor & Destructor Documentation

◆ GRAILDataSetGenerator()

CDPL::GRAIL::GRAILDataSetGenerator::GRAILDataSetGenerator ( )

◆ ~GRAILDataSetGenerator()

virtual CDPL::GRAIL::GRAILDataSetGenerator::~GRAILDataSetGenerator ( )
inlinevirtual

Member Function Documentation

◆ enableInteraction()

void CDPL::GRAIL::GRAILDataSetGenerator::enableInteraction ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type,
bool  enable 
)

◆ isInteractionEnabled()

bool CDPL::GRAIL::GRAILDataSetGenerator::isInteractionEnabled ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type 
) const

◆ clearEnabledInteractions()

void CDPL::GRAIL::GRAILDataSetGenerator::clearEnabledInteractions ( )

◆ setScoringFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setScoringFunction ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type,
const ScoringFunction &  func 
)

◆ getScoringFunction()

const ScoringFunction& CDPL::GRAIL::GRAILDataSetGenerator::getScoringFunction ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type 
) const

◆ removeScoringFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::removeScoringFunction ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type 
)

◆ setGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridName ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type,
const std::string &  name 
)

◆ getGridName()

const std::string& CDPL::GRAIL::GRAILDataSetGenerator::getGridName ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type 
) const

◆ removeGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::removeGridName ( unsigned int  ftr_type,
unsigned int  tgt_ftr_type 
)

◆ setScoreCombinationFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setScoreCombinationFunction ( const ScoreCombinationFunction &  func)

◆ getScoreCombinationFunction()

const ScoreCombinationFunction& CDPL::GRAIL::GRAILDataSetGenerator::getScoreCombinationFunction ( ) const

◆ normalizeScores()

void CDPL::GRAIL::GRAILDataSetGenerator::normalizeScores ( bool  normalize)

◆ scoresNormalized()

bool CDPL::GRAIL::GRAILDataSetGenerator::scoresNormalized ( ) const

◆ diminishScoresByAtomDensity()

void CDPL::GRAIL::GRAILDataSetGenerator::diminishScoresByAtomDensity ( bool  diminish)

◆ scoresDiminishedByAtomDensity()

bool CDPL::GRAIL::GRAILDataSetGenerator::scoresDiminishedByAtomDensity ( ) const

◆ storeEnvironmentAtomDensityGrid()

void CDPL::GRAIL::GRAILDataSetGenerator::storeEnvironmentAtomDensityGrid ( bool  store)

◆ environmentAtomDensityGridStored()

bool CDPL::GRAIL::GRAILDataSetGenerator::environmentAtomDensityGridStored ( ) const

◆ setEnvironmentAtomDensityGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::setEnvironmentAtomDensityGridName ( const std::string &  name)

◆ getEnvironmentAtomDensityGridName()

const std::string& CDPL::GRAIL::GRAILDataSetGenerator::getEnvironmentAtomDensityGridName ( ) const

◆ getGridTransform()

const Math::Matrix4D& CDPL::GRAIL::GRAILDataSetGenerator::getGridTransform ( ) const

◆ setGridTransform()

template<typename T >
void CDPL::GRAIL::GRAILDataSetGenerator::setGridTransform ( const T &  xform)
inline

◆ getGridStepSize()

double CDPL::GRAIL::GRAILDataSetGenerator::getGridStepSize ( ) const

◆ setGridStepSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridStepSize ( double  size)

◆ getGridXSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridXSize ( ) const

◆ setGridXSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridXSize ( std::size_t  size)

◆ getGridYSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridYSize ( ) const

◆ setGridYSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridYSize ( std::size_t  size)

◆ getGridZSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridZSize ( ) const

◆ setGridZSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridZSize ( std::size_t  size)

◆ setGridParamsForBoundingBox()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridParamsForBoundingBox ( const Math::Vector3D &  bbox_min,
const Math::Vector3D &  bbox_max,
double  step_size = DEF_GRID_STEP_SIZE 
)

◆ getPharmacophoreGenerator() [1/2]

const Pharm::DefaultPharmacophoreGenerator& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreGenerator ( ) const

◆ getPharmacophoreGenerator() [2/2]

Pharm::DefaultPharmacophoreGenerator& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreGenerator ( )

◆ setPharmacophoreProcessingFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setPharmacophoreProcessingFunction ( const PharmacophoreProcessingFunction &  func)

◆ getPharmacophoreProcessingFunction()

const PharmacophoreProcessingFunction& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreProcessingFunction ( ) const

◆ calcInteractionGrids()

void CDPL::GRAIL::GRAILDataSetGenerator::calcInteractionGrids ( const Chem::MolecularGraph &  tgt_env,
const Chem::Atom3DCoordinatesFunction &  coords_func,
Grid::DRegularGridSet &  grid_set,
bool  append = false 
)

◆ calcAtomDensityGrid()

Grid::DRegularGrid::SharedPointer CDPL::GRAIL::GRAILDataSetGenerator::calcAtomDensityGrid ( const Chem::AtomContainer &  atoms,
const Chem::Atom3DCoordinatesFunction &  coords_func,
const std::string &  grid_name 
)

Member Data Documentation

◆ DEF_GRID_STEP_SIZE

constexpr double CDPL::GRAIL::GRAILDataSetGenerator::DEF_GRID_STEP_SIZE = 0.5
staticconstexpr
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