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

#include <SolvationMetaGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::SolvationMetaGrid:

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

Referenced by get_type(), hash_fingerprint(), protocols::qsar::scoring_grid::SolvationMetaGridCreator::keyname(), and provide_xml_schema().

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

References grid_name(), and protocols::qsar::scoring_grid::xsd_type_definition_w_attributes().

Referenced by protocols::qsar::scoring_grid::SolvationMetaGridCreator::provide_xml_schema().

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

return the current score of an UltraLightResidue using the current grid

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

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

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

Referenced by atom_score(), deserialize(), hash_fingerprint(), initialize(), is_in_grid(), refresh(), score(), serialize(), set_chain(), show(), and SolvationMetaGrid().

std::string protocols::qsar::scoring_grid::SolvationMetaGrid::type_

private

Referenced by deserialize(), hash_fingerprint(), serialize(), and show().

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

• src/protocols/qsar/scoring_grid/SolvationMetaGrid.hh
• src/protocols/qsar/scoring_grid/SolvationMetaGrid.cc