protocols::qsar::scoring_grid::GridBase Class Reference

#include <GridBase.hh>

Public Member Functions
	GridBase ()
virtual	~GridBase ()
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, qsarMapOP qsar_map)=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, qsarMapOP qsar_map)=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, qsarMapOP qsar_map)=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, qsarMapOP qsar_map)=0
	return the current score of an atom using the current grid More...
virtual std::string	get_type ()=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)=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 ()=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)=0
	determine if all residue atoms are in a grid More...
virtual bool	is_in_grid (core::conformation::Residue const &residue)=0
	determine if all residue atoms are in a grid More...

Constructor & Destructor Documentation

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

inline

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

inlinevirtual

Member Function Documentation

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

pure virtual

return the current score of an atom using the current grid

Implemented in 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, qsarMapOP  qsar_map  )

pure virtual

return the current score of an atom using the current grid

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

pure virtual

deserialize a json spirit Value into a GridBase object

Implemented in protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::LigandPropertyScore, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

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

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::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, and protocols::qsar::scoring_grid::SolvationMetaGrid.

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

pure virtual

get the type of the grid

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

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::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, and protocols::qsar::scoring_grid::SolvationMetaGrid.

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

pure virtual

determine if all residue atoms are in a grid

Implemented in 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 )

pure virtual

determine if all residue atoms are in a grid

Implemented in 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

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, protocols::qsar::scoring_grid::ClassicGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::SolvationGrid, and protocols::qsar::scoring_grid::LigandPropertyScore.

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

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

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

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

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

Implemented in protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

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

pure virtual

return the current scoer of an UltraLightResidue using the current grid

Implemented in 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, protocols::qsar::scoring_grid::HbaGrid, and protocols::qsar::scoring_grid::LigandPropertyScore.

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

pure virtual

return the current score of a residue using the current grid

Implemented in 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, protocols::qsar::scoring_grid::HbaGrid, and protocols::qsar::scoring_grid::LigandPropertyScore.

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

pure virtual

Serialize the GridBase object into a json_spirit Value.

Implemented in protocols::qsar::scoring_grid::ConstantScoreBase, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::ShapeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::LigandPropertyScore, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

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::ConstantScoreBase, protocols::qsar::scoring_grid::SolvationMetaGrid, and protocols::qsar::scoring_grid::SingleGrid.

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

• symlinks/rosetta/src/protocols/qsar/scoring_grid/GridBase.hh