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protocols::qsar::scoring_grid::SolvationMetaGrid Class Reference

#include <SolvationMetaGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::SolvationMetaGrid:
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Public Member Functions

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

Static Public Member Functions

static std::string grid_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

std::string type_
 
std::map< core::ShortSize,
SingleGridOP
grid_set_
 

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::SolvationMetaGrid::SolvationMetaGrid ( )
protocols::qsar::scoring_grid::SolvationMetaGrid::SolvationMetaGrid ( SolvationMetaGrid const &  other)

References grid_set_.

protocols::qsar::scoring_grid::SolvationMetaGrid::~SolvationMetaGrid ( )
overridedefault

Member Function Documentation

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score ( core::conformation::UltraLightResidue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
overridevirtual

return the current score of an atom using the current grid

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

References grid_set_, and core::conformation::UltraLightResidue::residue().

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score ( core::conformation::Residue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
overridevirtual

return the current score of an atom using the current grid

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

References core::conformation::Residue::atom(), and grid_set_.

GridBaseOP protocols::qsar::scoring_grid::SolvationMetaGrid::clone ( ) const
overridevirtual

Make a copy of the grid, respecting the subclassing.

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

void protocols::qsar::scoring_grid::SolvationMetaGrid::deserialize ( utility::json_spirit::mObject  data)
overridevirtual

deserialize a json spirit Value into a GridBase object

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

References grid_set_, and type_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::dump_BRIX ( std::string const &  prefix) const
overridevirtual

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::SolvationMetaGrid::get_type ( ) const
overridevirtual

get the type of the grid

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

References grid_name().

std::string protocols::qsar::scoring_grid::SolvationMetaGrid::grid_name ( )
static
std::string protocols::qsar::scoring_grid::SolvationMetaGrid::hash_fingerprint ( ) const
overridevirtual

Return a string representing the settings which don't change based on reinitialization.

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

References grid_name(), grid_set_, and type_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::initialize ( core::Vector const &  center,
core::Real  width,
core::Real  resolution 
)
overridevirtual

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

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

References grid_set_.

bool protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid ( core::conformation::UltraLightResidue const &  residue) const
overridevirtual

determine if all residue atoms are in a grid

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

References grid_set_.

bool protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid ( core::conformation::Residue const &  residue) const
overridevirtual

determine if all residue atoms are in a grid

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

References grid_set_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::parse_my_tag ( utility::tag::TagCOP  tag)
overridevirtual

a grid based on RosettaScripts input

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

void protocols::qsar::scoring_grid::SolvationMetaGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::qsar::scoring_grid::SolvationMetaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
)
overridevirtual

populate the grid with values based on a passed pose

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

Referenced by refresh().

void protocols::qsar::scoring_grid::SolvationMetaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
utility::vector1< core::Size ligand_chain_ids_to_exclude 
)
overridevirtual

populate the grid with values based on a passed pose

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

References refresh().

void protocols::qsar::scoring_grid::SolvationMetaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center 
)
overridevirtual

populate the grid with values based on a passed pose

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

References grid_set_.

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual
core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual

return the current score of a residue using the current grid

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

References core::conformation::Residue::atom(), grid_set_, core::conformation::Residue::natoms(), and core::scoring::total_score.

utility::json_spirit::Value protocols::qsar::scoring_grid::SolvationMetaGrid::serialize ( ) const
overridevirtual

Serialize the GridBase object into a json_spirit Value.

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

References grid_set_, and type_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::set_chain ( char  chain)
overridevirtual

set the chain the grid applies to

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

References grid_set_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::show ( std::ostream &  out) const
overridevirtual

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

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

References grid_set_, and type_.

Member Data Documentation

std::map<core::ShortSize,SingleGridOP> protocols::qsar::scoring_grid::SolvationMetaGrid::grid_set_
private
std::string protocols::qsar::scoring_grid::SolvationMetaGrid::type_
private

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