#include <GridBase.hh>

Inheritance diagram for protocols::qsar::scoring_grid::GridBase:

Public Member Functions
	GridBase ()

	~GridBase () override

virtual GridBaseOP	clone () const =0
	Make a copy of the grid, respecting the subclassing. More...

virtual void	initialize (core::Vector const &center, core::Real width, core::Real resolution)=0
	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)=0
	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)=0
	populate the grid with values based on a passed pose More...

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center)=0
	populate the grid with values based on a passed pose More...

virtual void	parse_my_tag (utility::tag::TagCOP tag)=0
	a grid based on RosettaScripts input More...

virtual core::Real	score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const =0
	return the current scoer of an UltraLightResidue using the current grid More...

virtual core::Real	atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const =0
	return the current score of an atom using the current grid More...

virtual core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const =0
	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, qsarMapCOP qsar_map) const =0
	return the current score of an atom using the current grid More...

virtual std::string	get_type () const =0
	get the type of the grid More...

virtual void	set_chain (char chain)=0
	set the chain the grid applies to More...

virtual void	dump_BRIX (std::string const &prefix) const =0
	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 () const =0
	Serialize the GridBase object into a json_spirit Value. More...

virtual void	deserialize (utility::json_spirit::mObject data)=0
	deserialize a json spirit Value into a GridBase object More...

virtual bool	is_in_grid (core::conformation::UltraLightResidue const &residue) const =0
	determine if all residue atoms are in a grid More...

virtual bool	is_in_grid (core::conformation::Residue const &residue) const =0
	determine if all residue atoms are in a grid More...

virtual void	show (std::ostream &out) const =0
	Print a brief summary about this grid to the provided output stream. More...

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::GridBase::GridBase ( )

inline

protocols::qsar::scoring_grid::GridBase::~GridBase ( )

inlineoverride

Member Function Documentation

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

pure virtual

return the current score of an atom using the current grid

Implemented in protocols::qsar::scoring_grid::PCSSingleGrid, protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, and protocols::qsar::scoring_grid::HbaGrid.

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

pure virtual

return the current score of an atom using the current grid

Implemented in protocols::qsar::scoring_grid::PCSSingleGrid, protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, and protocols::qsar::scoring_grid::HbaGrid.

virtual GridBaseOP protocols::qsar::scoring_grid::GridBase::clone ( ) const

pure virtual

Make a copy of the grid, respecting the subclassing.

Note that due to the heavy use of modification to reset positions you need to be sure to do deep copying on anything that can be changed with refresh/initialize.

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

pure virtual

deserialize a json spirit Value into a GridBase object

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

pure virtual

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

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, and protocols::qsar::scoring_grid::SolvationMetaGrid.

virtual std::string protocols::qsar::scoring_grid::GridBase::get_type ( ) const

pure virtual

get the type of the grid

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, and protocols::qsar::scoring_grid::LigandPropertyScore.

virtual std::string protocols::qsar::scoring_grid::GridBase::hash_fingerprint ( ) const

pure virtual

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

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

pure virtual

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

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, and protocols::qsar::scoring_grid::ConstantScoreBase.

virtual bool protocols::qsar::scoring_grid::GridBase::is_in_grid ( core::conformation::UltraLightResidue const & residue ) const

pure virtual

determine if all residue atoms are in a grid

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, and protocols::qsar::scoring_grid::SolvationMetaGrid.

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

pure virtual

determine if all residue atoms are in a grid

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SingleGrid, and protocols::qsar::scoring_grid::SolvationMetaGrid.

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

pure virtual

a grid based on RosettaScripts input

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

pure virtual

populate the grid with values based on a passed pose

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

pure virtual

populate the grid with values based on a passed pose

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

pure virtual

populate the grid with values based on a passed pose

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

pure virtual

return the current scoer of an UltraLightResidue using the current grid

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

pure virtual

return the current score of a residue using the current grid

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

pure virtual

Serialize the GridBase object into a json_spirit Value.

virtual void protocols::qsar::scoring_grid::GridBase::set_chain ( char chain )

pure virtual

set the chain the grid applies to

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SolvationMetaGrid, and protocols::qsar::scoring_grid::SingleGrid.

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

pure virtual

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

Implemented in protocols::qsar::scoring_grid::PCSMultiGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SolvationMetaGrid, and protocols::qsar::scoring_grid::LigandPropertyScore.

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

src/protocols/qsar/scoring_grid/GridBase.hh

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation