#include <VdwGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::VdwGrid:

[legend]

Public Member Functions
	VdwGrid ()

	~VdwGrid () override

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

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

void	parse_my_tag (utility::tag::TagCOP tag) override
	setup 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...

utility::json_spirit::Value	serialize () const override
	serialize the Interpolator to a json_spirit object More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to a Interpolator 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::SingleGrid
	SingleGrid (std::string const &type)

	~SingleGrid () override

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	set_chain (char chain) override
	set the chain around which to calculate the grid More...

char	get_chain ()
	get the chain around which the grid is calculated More...

core::grid::CartGrid< core::Real > const &	get_grid () const
	return a constant reference to the grid More...

void	set_type (std::string type)
	set the grid type More...

std::string	get_type () const override
	return the grids type More...

void	set_center (core::Vector center)
	set the center of the grid More...

core::Vector	get_center () const
	get the center of the grid More...

core::Real	get_min_value () const
	get the max score value in the grid More...

core::Real	get_max_value () const
	get the minimum score value in the grid More...

core::Real	get_point (core::Real x, core::Real y, core::Real z) const
	get the value of a single point in the grid based on pdb coordinates More...

core::Real	get_point (core::Vector coords) const
	get the value of a single point in the grid based on pdb coordinates More...

numeric::xyzVector< core::Size >	get_dimensions ()
	get dimensions of the grid More...

core::Vector	get_pdb_coords (int x, int y, int z)
	get the pdb coordinates based on grid point coordinates More...

core::Vector	get_pdb_coords (core::grid::CartGrid< core::Real >::GridPt gridpt)
	get the pdb coordinates based on grid point coordinates More...

void	grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride)

bool	is_in_grid (core::conformation::UltraLightResidue const &residue) const override
	check to see if residue is in grid More...

bool	is_in_grid (core::conformation::Residue const &residue) const override
	check to see if residue is in grid More...

std::list< std::pair< core::Vector, core::Real > >	get_point_value_list_within_range (core::Real lower_bound, core::Real upper_bound, core::Size stride) const

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...

void	set_sphere (core::Vector const &coords, core::Real radius, core::Real value)

void	set_ring (core::Vector const &coords, core::Real inner_radius, core::Real outer_radius, core::Real value)

void	diffuse_ring (core::Vector const &coords, core::Real radius, core::Real width, core::Real magnitude)

void	set_point (core::Vector const &coords, core::Real value)

void	set_distance_sphere_for_atom (core::Real const &atom_shell, core::Vector const &coords, core::Real cutoff)

void	set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorCOP lj_spline, core::Vector const &coords, core::Real cutoff)

void	fill_with_value (core::Real)
	@fill the entire grid with some value More...

void	show (std::ostream &out) const override
	Print a brief summary about this grid to the provided output stream. 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
numeric::interpolation::spline::InterpolatorCOP	lj_spline_

core::Real	cutoff_

Constructor & Destructor Documentation

◆ VdwGrid()

protocols::qsar::scoring_grid::VdwGrid::VdwGrid ( )

References lj_spline_.

◆ ~VdwGrid()

protocols::qsar::scoring_grid::VdwGrid::~VdwGrid ( )

overridedefault

Member Function Documentation

◆ atom_score() [1/2]

core::Real protocols::qsar::scoring_grid::VdwGrid::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

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References core::conformation::Residue::atom_type(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), core::chemical::AtomType::lj_radius(), lj_spline_, and core::conformation::Residue::xyz().

◆ atom_score() [2/2]

core::Real protocols::qsar::scoring_grid::VdwGrid::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

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), lj_spline_, and core::conformation::UltraLightResidue::residue().

◆ clone()

GridBaseOP protocols::qsar::scoring_grid::VdwGrid::clone ( ) const

overridevirtual

Make a copy of the grid, respecting the subclassing.

Implements protocols::qsar::scoring_grid::SingleGrid.

◆ deserialize()

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

overridevirtual

deserialize a json_spirit object to a Interpolator

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References cutoff_, protocols::qsar::scoring_grid::SingleGrid::deserialize(), and lj_spline_.

◆ grid_name()

std::string protocols::qsar::scoring_grid::VdwGrid::grid_name ( )

static

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

◆ hash_fingerprint()

std::string protocols::qsar::scoring_grid::VdwGrid::hash_fingerprint ( ) const

overridevirtual

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

Implements protocols::qsar::scoring_grid::SingleGrid.

References cutoff_, protocols::qsar::scoring_grid::SingleGrid::get_type(), and grid_name().

◆ parse_my_tag()

void protocols::qsar::scoring_grid::VdwGrid::parse_my_tag ( utility::tag::TagCOP tag )

overridevirtual

setup a grid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::SingleGrid.

◆ provide_xml_schema()

void protocols::qsar::scoring_grid::VdwGrid::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::VdwGridCreator::provide_xml_schema().

◆ refresh() [1/3]

void protocols::qsar::scoring_grid::VdwGrid::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::SingleGrid.

References core::conformation::Residue::atom_type(), core::conformation::Residue::chain(), cutoff_, protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_chain(), core::pose::get_chain_id_from_chain(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), core::pose::Pose::size(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

◆ refresh() [2/3]

void protocols::qsar::scoring_grid::VdwGrid::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::SingleGrid.

References core::conformation::membrane::center.

Referenced by refresh().

◆ refresh() [3/3]

void protocols::qsar::scoring_grid::VdwGrid::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::SingleGrid.

References core::conformation::membrane::center, and refresh().

◆ score() [1/2]

core::Real protocols::qsar::scoring_grid::VdwGrid::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

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References core::conformation::Residue::atom_type(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), core::chemical::AtomType::lj_radius(), lj_spline_, core::conformation::Residue::natoms(), score(), and core::conformation::Residue::xyz().

◆ score() [2/2]

core::Real protocols::qsar::scoring_grid::VdwGrid::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

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), lj_spline_, core::conformation::UltraLightResidue::natoms(), and core::conformation::UltraLightResidue::residue().

Referenced by score().

◆ serialize()

utility::json_spirit::Value protocols::qsar::scoring_grid::VdwGrid::serialize ( ) const

overridevirtual

serialize the Interpolator to a json_spirit object

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References cutoff_, lj_spline_, and protocols::qsar::scoring_grid::SingleGrid::serialize().

Member Data Documentation

◆ cutoff_

core::Real protocols::qsar::scoring_grid::VdwGrid::cutoff_

private

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

◆ lj_spline_

numeric::interpolation::spline::InterpolatorCOP protocols::qsar::scoring_grid::VdwGrid::lj_spline_

private

Referenced by atom_score(), deserialize(), score(), serialize(), and VdwGrid().

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

src/protocols/qsar/scoring_grid/VdwGrid.hh
src/protocols/qsar/scoring_grid/VdwGrid.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ VdwGrid()

◆ ~VdwGrid()

Member Function Documentation

◆ atom_score() [1/2]

◆ atom_score() [2/2]

◆ clone()

◆ deserialize()

◆ grid_name()

◆ hash_fingerprint()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ refresh() [1/3]

◆ refresh() [2/3]

◆ refresh() [3/3]

◆ score() [1/2]

◆ score() [2/2]

◆ serialize()

Member Data Documentation

◆ cutoff_

◆ lj_spline_