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protocols::qsar::scoring_grid::PCSMultiGrid Class Reference

#include <PCSMultiGrid.hh>

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

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

 PCSMultiGrid ()
 default constructor More...
 
 PCSMultiGrid (std::string const &filename, Real const weight=1.0)
 construct from PCS input file More...
 
 PCSMultiGrid (PCSMultiGrid const &other)
 copy constructor More...
 
PCSMultiGridoperator= (PCSMultiGrid const &rhs)
 copy assignment More...
 
 ~PCSMultiGrid () override
 destructor More...
 
GridBaseOP clone () const override
 Make a copy of the grid, respecting the subclassing. More...
 
void initialize (Vector const &center, Real width, Real resolution) override
 setup a vector of PCSSingleGrid objects initialize each PCSSingleGrid with a given center point, width and resolution (in angstroms) and set grid values to zero. More...
 
void refresh (Pose const &pose, Vector const &center) override
 populate grids in the vector 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 grids in the vector 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 grids in the vector 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 PCSMultiGrid 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 PCSMultiGrid 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 PCSMultiGrid 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 PCSMultiGrid More...
 
std::string get_type () const override
 get the type of the grid More...
 
void set_chain (char chain) override
 set the chain the grid applies to More...
 
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...
 
utility::json_spirit::Value serialize () const override
 serialize the PCSMultiGrid to a json_spirit object More...
 
void deserialize (utility::json_spirit::mObject data) override
 deserialize a json_spirit object to a PCSMultiGrid More...
 
void parse_my_tag (utility::tag::TagCOP tag) override
 setup a PCSMultiGrid based on RosettaScripts input More...
 
bool is_in_grid (UltraLightResidue const &residue) const override
 determine if all residue atoms are in a grid More...
 
bool is_in_grid (Residue const &residue) const override
 determine if all residue atoms are in a grid More...
 
std::string hash_fingerprint () const override
 Return a string representing the settings which don't change based on reinitialization. More...
 
void show (std::ostream &out) const override
 Print a brief summary about this grid to the provided output stream. More...
 
core::Size get_number_pcs_grids () const
 
utility::vector1< SingleGridOP >
const & 
get_pcs_grids () const
 
utility::vector1< SingleGridOP > & get_pcs_grids ()
 
Real get_weight () const
 
void set_weight (Real w)
 
- 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 initialize_pcs_data_from_input_file (std::string const &filename)
 

Private Attributes

std::string type_
 
std::string pcs_input_file_
 
utility::vector1< SingleGridOPpcs_grid_vector_
 
Real weight_
 
bool pcs_data_initialized_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::PCSMultiGrid::PCSMultiGrid ( )

default constructor

Referenced by clone().

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

construct from PCS input file

References initialize_pcs_data_from_input_file(), and pcs_data_initialized_.

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

copy constructor

References pcs_grid_vector_.

protocols::qsar::scoring_grid::PCSMultiGrid::~PCSMultiGrid ( )
override

destructor

Member Function Documentation

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

return the current score of an atom using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

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

return the current score of an atom using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

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

Make a copy of the grid, respecting the subclassing.

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

References PCSMultiGrid().

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

deserialize a json_spirit object to a PCSMultiGrid

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

References pcs_grid_vector_, pcs_input_file_, type_, and weight_.

void protocols::qsar::scoring_grid::PCSMultiGrid::dump_BRIX ( std::string const &  prefix) const
overridevirtual

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

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

core::Size protocols::qsar::scoring_grid::PCSMultiGrid::get_number_pcs_grids ( ) const
inline

References pcs_grid_vector_.

utility::vector1< SingleGridOP > const& protocols::qsar::scoring_grid::PCSMultiGrid::get_pcs_grids ( ) const
inline

References pcs_grid_vector_.

utility::vector1< SingleGridOP >& protocols::qsar::scoring_grid::PCSMultiGrid::get_pcs_grids ( )
inline

References pcs_grid_vector_.

std::string protocols::qsar::scoring_grid::PCSMultiGrid::get_type ( ) const
overridevirtual

get the type of the grid

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

References grid_name().

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

References weight_.

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

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

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

References grid_name(), pcs_data_initialized_, pcs_grid_vector_, pcs_input_file_, type_, and weight_.

void protocols::qsar::scoring_grid::PCSMultiGrid::initialize ( Vector const &  center,
Real  width,
Real  resolution 
)
overridevirtual

setup a vector of PCSSingleGrid objects initialize each PCSSingleGrid with a given center point, width and resolution (in angstroms) and set grid values to zero.

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

References initialize_pcs_data_from_input_file(), pcs_data_initialized_, pcs_grid_vector_, and pcs_input_file_.

void protocols::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file ( std::string const &  filename)
private
bool protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid ( UltraLightResidue const &  residue) const
overridevirtual

determine if all residue atoms are in a grid

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

References pcs_grid_vector_.

Referenced by is_in_grid().

bool protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid ( Residue const &  residue) const
overridevirtual

determine if all residue atoms are in a grid

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

References is_in_grid(), and pcs_grid_vector_.

PCSMultiGrid & protocols::qsar::scoring_grid::PCSMultiGrid::operator= ( PCSMultiGrid const &  rhs)
void protocols::qsar::scoring_grid::PCSMultiGrid::parse_my_tag ( utility::tag::TagCOP  tag)
overridevirtual
void protocols::qsar::scoring_grid::PCSMultiGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::qsar::scoring_grid::PCSMultiGrid::refresh ( Pose const &  pose,
Vector const &  center 
)
overridevirtual

populate grids in the vector with PCS values based on a passed pose

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

References pcs_grid_vector_.

Referenced by refresh().

void protocols::qsar::scoring_grid::PCSMultiGrid::refresh ( Pose const &  pose,
Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
)
overridevirtual

populate grids in the vector with PCS values based on a passed pose

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

References refresh().

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

populate grids in the vector with PCS values based on a passed pose

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

References refresh().

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

return the current score of an UltraLightResidue using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

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

return the current score of a residue using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

utility::json_spirit::Value protocols::qsar::scoring_grid::PCSMultiGrid::serialize ( ) const
overridevirtual

serialize the PCSMultiGrid to a json_spirit object

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

References pcs_grid_vector_, pcs_input_file_, type_, and weight_.

void protocols::qsar::scoring_grid::PCSMultiGrid::set_chain ( char  chain)
overridevirtual

set the chain the grid applies to

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

References pcs_grid_vector_.

void protocols::qsar::scoring_grid::PCSMultiGrid::set_weight ( Real  w)
inline

References weight_.

void protocols::qsar::scoring_grid::PCSMultiGrid::show ( std::ostream &  out) const
overridevirtual

Print a brief summary about this grid to the provided output stream.

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

References pcs_grid_vector_.

Member Data Documentation

bool protocols::qsar::scoring_grid::PCSMultiGrid::pcs_data_initialized_
private
utility::vector1< SingleGridOP > protocols::qsar::scoring_grid::PCSMultiGrid::pcs_grid_vector_
private
std::string protocols::qsar::scoring_grid::PCSMultiGrid::pcs_input_file_
private
std::string protocols::qsar::scoring_grid::PCSMultiGrid::type_
private
Real protocols::qsar::scoring_grid::PCSMultiGrid::weight_
private

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