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protocols::qsar::scoring_grid::PCSSingleGrid Class Reference

#include <PCSSingleGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::PCSSingleGrid:
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Public Types

typedef
core::scoring::nmr::pcs::PCSSingle 
PCSSingle
 
typedef
core::scoring::nmr::pcs::PCSSingleOP 
PCSSingleOP
 
typedef
core::scoring::nmr::pcs::PCSTensor 
PCSTensor
 
typedef
core::scoring::nmr::pcs::PCSTensorOP 
PCSTensorOP
 
typedef
core::scoring::nmr::pcs::PCSTensorCOP 
PCSTensorCOP
 
typedef core::pose::Pose Pose
 
typedef core::conformation::Residue Residue
 
typedef
core::conformation::UltraLightResidue 
UltraLightResidue
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::Vector Vector
 

Public Member Functions

 PCSSingleGrid ()
 Default constructor. More...
 
 PCSSingleGrid (std::string const &filename, PCSTensorOP tensor, Real const weight=1.0)
 construct from PCS datafile and fixed PCS tensor More...
 
 PCSSingleGrid (std::string const &filename, utility::vector1< Real > const &tensor_vals, Real const weight=1.0)
 construct from PCS datafile and vector of PCS tensor values More...
 
 PCSSingleGrid (std::string const &filename, PCSTensorOP tensor, Pose const &pose, Real const weight=1.0)
 construct from PCS datafile and fixed PCS tensor More...
 
 PCSSingleGrid (std::string const &filename, utility::vector1< Real > const &tensor_vals, Pose const &pose, Real const weight=1.0)
 construct from PCS datafile and vector of PCS tensor values More...
 
 PCSSingleGrid (PCSSingleGrid const &other)
 copy constructor More...
 
PCSSingleGridoperator= (PCSSingleGrid const &rhs)
 copy assignment More...
 
GridBaseOP clone () const override
 Make a copy of the grid, respecting the subclassing. More...
 
void refresh (Pose const &pose, Vector const &center) override
 populate the grid with PCS values based on a passed pose More...
 
void refresh (Pose const &pose, Vector const &center, core::Size const &ligand_chain_id_to_exclude) override
 populate the grid with PCS values based on a passed pose More...
 
void refresh (Pose const &pose, Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude) override
 populate the grid with PCS values based on a passed pose More...
 
Real score (UltraLightResidue const &residue, Real const max_score, qsarMapCOP qsar_map) const override
 return the current score of an UltraLightResidue using the current PCSSingleGrid More...
 
Real atom_score (UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
 return the current score of an atom using the current PCSSingleGrid More...
 
Real score (Residue const &residue, Real const max_score, qsarMapCOP qsar_map) const override
 return the current score of a residue using the current PCSSingleGrid More...
 
Real atom_score (Residue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
 return the current score of an atom using the current PCSSingleGrid More...
 
utility::json_spirit::Value serialize () const override
 serialize the PCSSingleGrid to a json_spirit object More...
 
void deserialize (utility::json_spirit::mObject data) override
 deserialize a json_spirit object to a PCSSingleGrid More...
 
void parse_my_tag (utility::tag::TagCOP tag) override
 setup a PCSSingleGrid based on RosettaScripts input More...
 
std::string hash_fingerprint () const override
 Return a string representing the settings which don't change based on reinitialization. More...
 
utility::vector1< PCSSingleOP >
const & 
get_pcs_values () const
 
PCSTensorCOP get_tensor () const
 
Real get_weight () const
 
void set_weight (Real w)
 
- 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 Member Functions

void init_pcs_values_from_file (std::string const &filename, Pose const &pose)
 

Private Attributes

std::string pcs_file_
 
utility::vector1< PCSSingleOPpcs_values_
 
PCSTensorOP tensor_
 
Real weight_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( )

Default constructor.

default constructor

Referenced by clone().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( std::string const &  filename,
PCSTensorOP  tensor,
Real const  weight = 1.0 
)

construct from PCS datafile and fixed PCS tensor

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( std::string const &  filename,
utility::vector1< Real > const &  tensor_vals,
Real const  weight = 1.0 
)

construct from PCS datafile and vector of PCS tensor values

References tensor_.

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( std::string const &  filename,
PCSTensorOP  tensor,
Pose const &  pose,
Real const  weight = 1.0 
)

construct from PCS datafile and fixed PCS tensor

References init_pcs_values_from_file().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( std::string const &  filename,
utility::vector1< Real > const &  tensor_vals,
Pose const &  pose,
Real const  weight = 1.0 
)

construct from PCS datafile and vector of PCS tensor values

References init_pcs_values_from_file().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( PCSSingleGrid const &  other)

copy constructor

References pcs_values_.

Member Function Documentation

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::atom_score ( UltraLightResidue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
overridevirtual

return the current score of an atom using the current PCSSingleGrid

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

References core::conformation::UltraLightResidue::residue().

Referenced by atom_score().

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::atom_score ( Residue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
overridevirtual
GridBaseOP protocols::qsar::scoring_grid::PCSSingleGrid::clone ( ) const
overridevirtual

Make a copy of the grid, respecting the subclassing.

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

References PCSSingleGrid().

void protocols::qsar::scoring_grid::PCSSingleGrid::deserialize ( utility::json_spirit::mObject  data)
overridevirtual
utility::vector1<PCSSingleOP> const& protocols::qsar::scoring_grid::PCSSingleGrid::get_pcs_values ( ) const
inline

References pcs_values_.

PCSTensorCOP protocols::qsar::scoring_grid::PCSSingleGrid::get_tensor ( ) const
inline

References tensor_.

Real protocols::qsar::scoring_grid::PCSSingleGrid::get_weight ( ) const
inline

References weight_.

std::string protocols::qsar::scoring_grid::PCSSingleGrid::grid_name ( )
static
std::string protocols::qsar::scoring_grid::PCSSingleGrid::hash_fingerprint ( ) const
overridevirtual

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

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

References protocols::qsar::scoring_grid::SingleGrid::get_type(), grid_name(), pcs_file_, pcs_values_, tensor_, and weight_.

void protocols::qsar::scoring_grid::PCSSingleGrid::init_pcs_values_from_file ( std::string const &  filename,
Pose const &  pose 
)
private
PCSSingleGrid & protocols::qsar::scoring_grid::PCSSingleGrid::operator= ( PCSSingleGrid const &  rhs)

copy assignment

References pcs_file_, pcs_values_, tensor_, and weight_.

void protocols::qsar::scoring_grid::PCSSingleGrid::parse_my_tag ( utility::tag::TagCOP  tag)
overridevirtual

setup a PCSSingleGrid based on RosettaScripts input

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

References pcs_file_, tensor_, and weight_.

void protocols::qsar::scoring_grid::PCSSingleGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::qsar::scoring_grid::PCSSingleGrid::refresh ( Pose const &  pose,
Vector const &  center 
)
overridevirtual
void protocols::qsar::scoring_grid::PCSSingleGrid::refresh ( Pose const &  pose,
Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
)
overridevirtual

populate the grid with PCS values based on a passed pose

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

References refresh().

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

populate the grid with PCS values based on a passed pose

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

References refresh().

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::score ( UltraLightResidue const &  residue,
Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual

return the current score of an UltraLightResidue using the current PCSSingleGrid

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

References core::conformation::UltraLightResidue::residue().

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::score ( Residue const &  residue,
Real const  max_score,
qsarMapCOP  qsar_map 
) const
overridevirtual
utility::json_spirit::Value protocols::qsar::scoring_grid::PCSSingleGrid::serialize ( ) const
overridevirtual
void protocols::qsar::scoring_grid::PCSSingleGrid::set_weight ( Real  w)
inline

References weight_.

Member Data Documentation

std::string protocols::qsar::scoring_grid::PCSSingleGrid::pcs_file_
private
utility::vector1<PCSSingleOP> protocols::qsar::scoring_grid::PCSSingleGrid::pcs_values_
private
PCSTensorOP protocols::qsar::scoring_grid::PCSSingleGrid::tensor_
private
Real protocols::qsar::scoring_grid::PCSSingleGrid::weight_
private

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