Rosetta 3.4
Public Member Functions | Static Public Member Functions
protocols::qsar::scoring_grid::GridManager Class Reference

#include <GridManager.hh>

Collaboration diagram for protocols::qsar::scoring_grid::GridManager:
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List of all members.

Public Member Functions

void reset ()
 reset GridManager to the default settings
void set_width (core::Real width)
 set width (must be done before initialization)
void set_resolution (core::Real resolution)
 set resolution (must be done before initialization)
void make_new_grid (utility::tag::TagPtr const tag)
 make a new grid from grid tag, and insert it into the grid manager
void insert_grid (std::string const name, GridBaseOP const grid)
 insert a grid pointer into the grid manager
void set_qsar_map (qsarMapOP qsar_map)
 set the qsar_map
bool is_qsar_map_attached ()
 is a qsar map attached to the grid manager?
GridBaseOP get_grid (std::string const &grid_name)
 given a grid type, return a pointer to the grid
utility::vector1< std::string > get_grid_names ()
 get a list of grid names
core::Real total_score (core::conformation::Residue const &residue)
 return the total score of a residue on the grid
core::Real total_score (core::pose::Pose const &pose, core::Size const chain_id)
 return the total score of a chain on the grid
void update_grids (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
 recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!
void update_grids (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
 recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!
void update_grids (core::pose::Pose const &pose, core::Vector const &center)
 recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!
void update_grids (core::pose::Pose const &pose, core::Vector const &center, std::string const &tag)
 recalculate all grids for a pose, but only if the tag has changed
void initialize_all_grids (core::Vector const &center)
 initialize all grids and fill with 0s given a center point
core::Size size ()
 return the number of grids in the manager
ScoreMap get_cached_scores ()
 get a map of cached scores
void append_cached_scores (jd2::JobOP job)
 append all cached scores to a current job
void write_grids (std::string prefix)
 write all grids out using the BRIX format

Static Public Member Functions

static GridManagerget_instance ()

Member Function Documentation

void protocols::qsar::scoring_grid::GridManager::append_cached_scores ( jd2::JobOP  job)

append all cached scores to a current job

References total_score().

Referenced by protocols::qsar::qsarMover::apply().

ScoreMap protocols::qsar::scoring_grid::GridManager::get_cached_scores ( )
GridBaseOP protocols::qsar::scoring_grid::GridManager::get_grid ( std::string const &  grid_name)

given a grid type, return a pointer to the grid

Referenced by protocols::qsar::qsarMover::apply().

utility::vector1< std::string > protocols::qsar::scoring_grid::GridManager::get_grid_names ( )

get a list of grid names

GridManager * protocols::qsar::scoring_grid::GridManager::get_instance ( ) [static]
void protocols::qsar::scoring_grid::GridManager::initialize_all_grids ( core::Vector const &  center)

initialize all grids and fill with 0s given a center point

Referenced by protocols::qsar::qsarMover::apply(), protocols::ligand_docking::Translate::apply(), and protocols::ligand_docking::Transform::apply().

void protocols::qsar::scoring_grid::GridManager::insert_grid ( std::string const  name,
GridBaseOP const  grid 
)

insert a grid pointer into the grid manager

References make_table_of_pilot_apps::name.

Referenced by make_new_grid().

bool protocols::qsar::scoring_grid::GridManager::is_qsar_map_attached ( )

is a qsar map attached to the grid manager?

void protocols::qsar::scoring_grid::GridManager::make_new_grid ( utility::tag::TagPtr const  tag)
void protocols::qsar::scoring_grid::GridManager::reset ( void  )

reset GridManager to the default settings

void protocols::qsar::scoring_grid::GridManager::set_qsar_map ( qsarMapOP  qsar_map)

set the qsar_map

Referenced by protocols::qsar::qsarMover::apply().

void protocols::qsar::scoring_grid::GridManager::set_resolution ( core::Real  resolution)

set resolution (must be done before initialization)

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

void protocols::qsar::scoring_grid::GridManager::set_width ( core::Real  width)

set width (must be done before initialization)

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

core::Size protocols::qsar::scoring_grid::GridManager::size ( )
core::Real protocols::qsar::scoring_grid::GridManager::total_score ( core::conformation::Residue const &  residue)
core::Real protocols::qsar::scoring_grid::GridManager::total_score ( core::pose::Pose const &  pose,
core::Size const  chain_id 
)

return the total score of a chain on the grid

References core::pose::get_chain_residues(), and total_score().

void protocols::qsar::scoring_grid::GridManager::update_grids ( core::pose::Pose const &  pose,
core::Vector const &  center 
)

recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!

References protocols::qsar::scoring_grid::GridManagerTracer().

void protocols::qsar::scoring_grid::GridManager::update_grids ( core::pose::Pose const &  pose,
core::Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
)

recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!

Referenced by protocols::qsar::qsarMover::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Transform::apply(), and update_grids().

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

recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!

void protocols::qsar::scoring_grid::GridManager::update_grids ( core::pose::Pose const &  pose,
core::Vector const &  center,
std::string const &  tag 
)

recalculate all grids for a pose, but only if the tag has changed

References update_grids().

void protocols::qsar::scoring_grid::GridManager::write_grids ( std::string  prefix)

write all grids out using the BRIX format


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