#include <ShapeGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::ShapeGrid:

[legend]

Public Member Functions
	ShapeGrid ()

	~ShapeGrid () 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 grid information More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize the grid information 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...

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

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to a SingleGrid 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...

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...

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 Types
typedef utility::pointer::shared_ptr< core::grid::CartGrid< core::Real > >	KBPGridOP
	data store for the KBP data. key is the name3 of the amino acid This is being done with an unordered map to allow for constant lookup but still allow for KBP data about NCAAs to be introduced eventually if needed More...

typedef utility::pointer::shared_ptr< core::grid::CartGrid< core::Real > const >	KBPGridCOP

Private Member Functions
core::Real	get_score_from_angles (std::string const &name3, core::Real distance, core::Real theta, core::Real phi)
	get the appropriate score from the KBP tables More...

core::Real	get_point_score (numeric::kdtree::KDPointList const &nearest_residues, core::Vector const &query_coords)
	given a KDPointList and a set of query coordinates get the score to place in the grid More...

void	load_kbp_data ()
	the KBP data is stored as a compressed json file in the database. It is read during construction More...

Private Attributes
boost::unordered_map< std::string, KBPGridCOP >	kbp_data_

core::Real	distance_bin_width_

core::Real	theta_bin_width_

core::Real	phi_bin_width_

Member Typedef Documentation

◆ KBPGridCOP

typedef utility::pointer::shared_ptr< core::grid::CartGrid<core::Real> const > protocols::qsar::scoring_grid::ShapeGrid::KBPGridCOP

private

◆ KBPGridOP

typedef utility::pointer::shared_ptr< core::grid::CartGrid<core::Real> > protocols::qsar::scoring_grid::ShapeGrid::KBPGridOP

private

data store for the KBP data. key is the name3 of the amino acid This is being done with an unordered map to allow for constant lookup but still allow for KBP data about NCAAs to be introduced eventually if needed

Constructor & Destructor Documentation

◆ ShapeGrid()

protocols::qsar::scoring_grid::ShapeGrid::ShapeGrid ( )

References distance_bin_width_, load_kbp_data(), phi_bin_width_, and theta_bin_width_.

◆ ~ShapeGrid()

protocols::qsar::scoring_grid::ShapeGrid::~ShapeGrid ( )

overridedefault

Member Function Documentation

◆ atom_score() [1/2]

core::Real protocols::qsar::scoring_grid::ShapeGrid::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 protocols::qsar::scoring_grid::SingleGrid::get_point(), and core::conformation::Residue::xyz().

◆ atom_score() [2/2]

core::Real protocols::qsar::scoring_grid::ShapeGrid::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 protocols::qsar::scoring_grid::SingleGrid::get_point().

◆ clone()

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

overridevirtual

Make a copy of the grid, respecting the subclassing.

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

◆ deserialize()

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

overridevirtual

deserialize the grid information

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

References protocols::qsar::scoring_grid::SingleGrid::deserialize().

◆ get_point_score()

core::Real protocols::qsar::scoring_grid::ShapeGrid::get_point_score	(	numeric::kdtree::KDPointList const &	nearest_residues,
		core::Vector const &	query_coords
	)

private

given a KDPointList and a set of query coordinates get the score to place in the grid

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, core::chemical::ResidueType::atom_index(), core::chemical::ICoorAtomID::atomno(), core::kinematics::distance(), core::chemical::ResidueType::first_sidechain_atom(), get_score_from_angles(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), core::chemical::ResidueTypeBase::is_polymer(), score(), core::chemical::AtomICoor::stub_atom1(), and core::scoring::total_score.

Referenced by refresh().

◆ get_score_from_angles()

core::Real protocols::qsar::scoring_grid::ShapeGrid::get_score_from_angles	(	std::string const &	name3,
		core::Real	distance,
		core::Real	theta,
		core::Real	phi
	)

private

get the appropriate score from the KBP tables

References core::kinematics::distance(), distance_bin_width_, kbp_data_, phi_bin_width_, and theta_bin_width_.

Referenced by get_point_score().

◆ grid_name()

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

static

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

◆ hash_fingerprint()

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

overridevirtual

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

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

References distance_bin_width_, protocols::qsar::scoring_grid::SingleGrid::get_type(), grid_name(), phi_bin_width_, and theta_bin_width_.

◆ load_kbp_data()

void protocols::qsar::scoring_grid::ShapeGrid::load_kbp_data ( )

private

the KBP data is stored as a compressed json file in the database. It is read during construction

References protocols::abinitio::filename(), core::conformation::membrane::in, kbp_data_, and protocols::qsar::scoring_grid::TR().

Referenced by ShapeGrid().

◆ parse_my_tag()

void protocols::qsar::scoring_grid::ShapeGrid::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::ShapeGrid::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::ShapeGridCreator::provide_xml_schema().

◆ refresh() [1/3]

void protocols::qsar::scoring_grid::ShapeGrid::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 protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_chain(), core::pose::get_chain_id_from_chain(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(), get_point_score(), core::pose::Pose::residue(), protocols::qsar::scoring_grid::SingleGrid::set_point(), and core::pose::Pose::size().

◆ refresh() [2/3]

void protocols::qsar::scoring_grid::ShapeGrid::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::ShapeGrid::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::ShapeGrid::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 protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::conformation::Residue::natoms(), core::scoring::total_score, and core::conformation::Residue::xyz().

◆ score() [2/2]

core::Real protocols::qsar::scoring_grid::ShapeGrid::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 protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::conformation::UltraLightResidue::natoms(), and core::scoring::total_score.

Referenced by get_point_score().

◆ serialize()

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

overridevirtual

serialize the grid information

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

References protocols::qsar::scoring_grid::SingleGrid::serialize().

Member Data Documentation

◆ distance_bin_width_

core::Real protocols::qsar::scoring_grid::ShapeGrid::distance_bin_width_

private

Referenced by get_score_from_angles(), hash_fingerprint(), and ShapeGrid().

◆ kbp_data_

boost::unordered_map<std::string, KBPGridCOP > protocols::qsar::scoring_grid::ShapeGrid::kbp_data_

private

Referenced by get_score_from_angles(), and load_kbp_data().

◆ phi_bin_width_

core::Real protocols::qsar::scoring_grid::ShapeGrid::phi_bin_width_

private

Referenced by get_score_from_angles(), hash_fingerprint(), and ShapeGrid().

◆ theta_bin_width_

core::Real protocols::qsar::scoring_grid::ShapeGrid::theta_bin_width_

private

Referenced by get_score_from_angles(), hash_fingerprint(), and ShapeGrid().

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

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

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ KBPGridCOP

◆ KBPGridOP

Constructor & Destructor Documentation

◆ ShapeGrid()

◆ ~ShapeGrid()

Member Function Documentation

◆ atom_score() [1/2]

◆ atom_score() [2/2]

◆ clone()

◆ deserialize()

◆ get_point_score()

◆ get_score_from_angles()

◆ grid_name()

◆ hash_fingerprint()

◆ load_kbp_data()

◆ 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

◆ distance_bin_width_

◆ kbp_data_

◆ phi_bin_width_

◆ theta_bin_width_