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protocols::qsar::scoring_grid::ShapeGrid Class Reference

#include <ShapeGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::ShapeGrid:
Inheritance graph
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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::Sizeget_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)
 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

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

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

Member Function Documentation

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().

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().

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

Make a copy of the grid, respecting the subclassing.

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

void protocols::qsar::scoring_grid::ShapeGrid::deserialize ( utility::json_spirit::mObject  data)
overridevirtual
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::aa_gly, core::kinematics::distance(), get_score_from_angles(), score(), and core::scoring::total_score.

Referenced by refresh().

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 distance_bin_width_, kbp_data_, phi_bin_width_, and theta_bin_width_.

Referenced by get_point_score().

std::string protocols::qsar::scoring_grid::ShapeGrid::grid_name ( )
static
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_.

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().

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.

void protocols::qsar::scoring_grid::ShapeGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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.

Referenced by refresh().

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

core::Real protocols::qsar::scoring_grid::ShapeGrid::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual
core::Real protocols::qsar::scoring_grid::ShapeGrid::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual
utility::json_spirit::Value protocols::qsar::scoring_grid::ShapeGrid::serialize ( ) const
overridevirtual

Member Data Documentation

core::Real protocols::qsar::scoring_grid::ShapeGrid::distance_bin_width_
private
boost::unordered_map<std::string, KBPGridCOP > protocols::qsar::scoring_grid::ShapeGrid::kbp_data_
private
core::Real protocols::qsar::scoring_grid::ShapeGrid::phi_bin_width_
private
core::Real protocols::qsar::scoring_grid::ShapeGrid::theta_bin_width_
private

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