#include <SolvationMetaGrid.hh>

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

Collaboration diagram for protocols::qsar::scoring_grid::SolvationMetaGrid:

Public Member Functions
	SolvationMetaGrid ()

virtual	~SolvationMetaGrid ()

virtual void	initialize (core::Vector const &center, core::Real width, core::Real resolution)
	initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
	populate the grid with values based on a passed pose More...

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
	populate the grid with values based on a passed pose More...

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center)
	populate the grid with values based on a passed pose More...

virtual void	parse_my_tag (utility::tag::TagPtr const tag)
	a grid based on RosettaScripts input More...

virtual core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapOP qsar_map)
	return the current score of a residue using the current grid More...

virtual core::Real	atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapOP qsar_map)
	return the current score of an atom using the current grid More...

virtual std::string	get_type ()
	get the type of the grid More...

virtual void	set_chain (char chain)
	set the chain the grid applies to More...

virtual void	dump_BRIX (std::string const &prefix)
	output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More...

virtual utility::json_spirit::Value	serialize ()
	Serialize the GridBase object into a json_spirit Value. More...

virtual void	deserialize (utility::json_spirit::mObject data)
	deserialize a json spirit Value into a GridBase object More...

virtual bool	is_in_grid (core::conformation::Residue const &residue)
	determine if all residue atoms are in a grid More...

Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
	GridBase ()

virtual	~GridBase ()

Private Attributes
std::string	type_

std::map< core::ShortSize, SingleGridOP >	grid_map_

Detailed Description

Definition at line 28 of file SolvationMetaGrid.hh.

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::SolvationMetaGrid::SolvationMetaGrid ( )

Definition at line 53 of file SolvationMetaGrid.cc.

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

virtual

Definition at line 58 of file SolvationMetaGrid.cc.

Member Function Documentation

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

virtual

return the current score of an atom using the current grid

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

Definition at line 123 of file SolvationMetaGrid.cc.

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

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

virtual

deserialize a json spirit Value into a GridBase object

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

Definition at line 179 of file SolvationMetaGrid.cc.

References grid_map_, and type_.

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

virtual

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

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

Definition at line 150 of file SolvationMetaGrid.cc.

std::string protocols::qsar::scoring_grid::SolvationMetaGrid::get_type ( )

virtual

get the type of the grid

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

Definition at line 136 of file SolvationMetaGrid.cc.

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

virtual

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

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

Definition at line 63 of file SolvationMetaGrid.cc.

References core::chemical::ChemicalManager::get_instance(), and grid_map_.

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

virtual

determine if all residue atoms are in a grid

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

Definition at line 193 of file SolvationMetaGrid.cc.

References grid_map_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::parse_my_tag ( utility::tag::TagPtr const tag)

virtual

a grid based on RosettaScripts input

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

Definition at line 99 of file SolvationMetaGrid.cc.

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

virtual

populate the grid with values based on a passed pose

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

Definition at line 79 of file SolvationMetaGrid.cc.

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
	)

virtual

populate the grid with values based on a passed pose

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

Definition at line 84 of file SolvationMetaGrid.cc.

References refresh().

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

virtual

populate the grid with values based on a passed pose

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

Definition at line 89 of file SolvationMetaGrid.cc.

References grid_map_.

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