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protocols::qsar::scoring_grid::ConstantScoreBase Class Referenceabstract

#include <ConstantScoreBase.hh>

Inheritance diagram for protocols::qsar::scoring_grid::ConstantScoreBase:
Inheritance graph
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Public Member Functions

 ConstantScoreBase ()
 
 ~ConstantScoreBase () override
 
GridBaseOP clone () const override=0
 Make a copy of the grid, respecting the subclassing. More...
 
void initialize (core::Vector const &, core::Real, core::Real) override
 initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...
 
void refresh (core::pose::Pose const &, core::Vector const &, core::Size const &) override
 populate the grid with values based on a passed pose More...
 
void refresh (core::pose::Pose const &, core::Vector const &, utility::vector1< core::Size >) override
 populate the grid with values based on a passed pose More...
 
void refresh (core::pose::Pose const &, core::Vector const &) override
 populate the grid with values based on a passed pose More...
 
void parse_my_tag (utility::tag::TagCOP tag) override=0
 a grid based on RosettaScripts input More...
 
core::Real score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override=0
 return the current score of an UltraLightResidue using the current grid More...
 
core::Real atom_score (core::conformation::UltraLightResidue const &, core::Size, qsarMapCOP) const override
 return the current score of an atom using the current grid More...
 
core::Real score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override=0
 return the current score of a residue using the current grid More...
 
core::Real atom_score (core::conformation::Residue const &, core::Size, qsarMapCOP) const override
 return the current score of an atom using the current grid More...
 
std::string get_type () const override=0
 get the type of the grid More...
 
void set_chain (char) override
 set the chain the grid applies to More...
 
void dump_BRIX (std::string const &) const override
 output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More...
 
utility::json_spirit::Value serialize () const override=0
 Serialize the GridBase object into a json_spirit Value. More...
 
void deserialize (utility::json_spirit::mObject data) override=0
 deserialize a json spirit Value into a GridBase object More...
 
bool is_in_grid (core::conformation::UltraLightResidue const &) const override
 determine if all residue atoms are in a grid More...
 
bool is_in_grid (core::conformation::Residue const &) const override
 determine if all residue atoms are in a grid More...
 
void show (std::ostream &out) const override=0
 Print a brief summary about this grid to the provided output stream. More...
 
- Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
 GridBase ()
 
 ~GridBase () override
 
virtual std::string hash_fingerprint () const =0
 Return a string representing the settings which don't change based on reinitialization. More...
 

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::ConstantScoreBase::ConstantScoreBase ( )
inline
protocols::qsar::scoring_grid::ConstantScoreBase::~ConstantScoreBase ( )
inlineoverride

Member Function Documentation

core::Real protocols::qsar::scoring_grid::ConstantScoreBase::atom_score ( core::conformation::UltraLightResidue const &  ,
core::Size  ,
qsarMapCOP   
) const
inlineoverridevirtual

return the current score of an atom using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

core::Real protocols::qsar::scoring_grid::ConstantScoreBase::atom_score ( core::conformation::Residue const &  ,
core::Size  ,
qsarMapCOP   
) const
inlineoverridevirtual

return the current score of an atom using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

GridBaseOP protocols::qsar::scoring_grid::ConstantScoreBase::clone ( ) const
overridepure virtual

Make a copy of the grid, respecting the subclassing.

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

void protocols::qsar::scoring_grid::ConstantScoreBase::deserialize ( utility::json_spirit::mObject  data)
overridepure virtual

deserialize a json spirit Value into a GridBase object

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

void protocols::qsar::scoring_grid::ConstantScoreBase::dump_BRIX ( std::string const &  ) const
inlineoverridevirtual

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

Implements protocols::qsar::scoring_grid::GridBase.

std::string protocols::qsar::scoring_grid::ConstantScoreBase::get_type ( ) const
overridepure virtual
void protocols::qsar::scoring_grid::ConstantScoreBase::initialize ( core::Vector const &  ,
core::Real  ,
core::Real   
)
inlineoverridevirtual

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

Implements protocols::qsar::scoring_grid::GridBase.

bool protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid ( core::conformation::UltraLightResidue const &  ) const
inlineoverridevirtual

determine if all residue atoms are in a grid

Implements protocols::qsar::scoring_grid::GridBase.

bool protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid ( core::conformation::Residue const &  ) const
inlineoverridevirtual

determine if all residue atoms are in a grid

Implements protocols::qsar::scoring_grid::GridBase.

void protocols::qsar::scoring_grid::ConstantScoreBase::parse_my_tag ( utility::tag::TagCOP  tag)
overridepure virtual

a grid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

void protocols::qsar::scoring_grid::ConstantScoreBase::refresh ( core::pose::Pose const &  ,
core::Vector const &  ,
core::Size const &   
)
inlineoverridevirtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

void protocols::qsar::scoring_grid::ConstantScoreBase::refresh ( core::pose::Pose const &  ,
core::Vector const &  ,
utility::vector1< core::Size  
)
inlineoverridevirtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

void protocols::qsar::scoring_grid::ConstantScoreBase::refresh ( core::pose::Pose const &  ,
core::Vector const &   
)
inlineoverridevirtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

core::Real protocols::qsar::scoring_grid::ConstantScoreBase::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridepure virtual

return the current score of an UltraLightResidue using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

core::Real protocols::qsar::scoring_grid::ConstantScoreBase::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridepure virtual

return the current score of a residue using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

utility::json_spirit::Value protocols::qsar::scoring_grid::ConstantScoreBase::serialize ( ) const
overridepure virtual

Serialize the GridBase object into a json_spirit Value.

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.

void protocols::qsar::scoring_grid::ConstantScoreBase::set_chain ( char  )
inlineoverridevirtual

set the chain the grid applies to

Implements protocols::qsar::scoring_grid::GridBase.

void protocols::qsar::scoring_grid::ConstantScoreBase::show ( std::ostream &  out) const
overridepure virtual

Print a brief summary about this grid to the provided output stream.

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::LigandPropertyScore.


The documentation for this class was generated from the following file: