Rosetta 3.4
Public Member Functions
protocols::qsar::scoring_grid::GridBase Class Reference

#include <GridBase.hh>

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List of all members.

Public Member Functions

 GridBase (std::string type, core::Real weight)
void initialize (core::Vector const &center, core::Real width, core::Real resolution)
 initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)=0
 populate the grid with values based on a passed pose
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)=0
 populate the grid with values based on a passed pose
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center)=0
 populate the grid with values based on a passed pose
virtual void parse_my_tag (utility::tag::TagPtr const tag)=0
 a grid based on RosettaScripts input
core::grid::CartGrid
< core::Real > const & 
get_grid ()
 return a constant reference to the grid
void set_type (std::string type)
 set the grid type
std::string get_type ()
 return the grids type
void set_weight (core::Real weight)
 set the weight of the grid
core::Real get_weight ()
 get the weight of the grid
void set_center (core::Vector center)
 set the center of the grid
core::Vector get_center ()
 get the center of the grid
core::Real get_min_value () const
 get the max score value in the grid
core::Real get_max_value () const
 get the minimum score value in the grid
core::Real get_point (core::Real x, core::Real y, core::Real z)
 get the value of a single point in the grid
numeric::xyzVector< core::Sizeget_dimensions ()
 get dimensions of the grid
virtual core::Real score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapOP qsar_map)
 return the current score of a residue using the current grid
void grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride)
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)
void dump_BRIX (std::string const &prefix)
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_distance_sphere (core::Vector const &coords, core::Real cutoff)
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 fill_with_value (core::Real)
 the entire grid with some value

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::GridBase::GridBase ( std::string  type,
core::Real  weight 
)

Member Function Documentation

void protocols::qsar::scoring_grid::GridBase::diffuse_ring ( core::Vector const &  coords,
core::Real  radius,
core::Real  width,
core::Real  magnitude 
)
void protocols::qsar::scoring_grid::GridBase::dump_BRIX ( std::string const &  prefix)
void protocols::qsar::scoring_grid::GridBase::fill_with_value ( core::Real  value)

the entire grid with some value

References core::grid::CartGrid< T >::setFullOccupied().

Referenced by protocols::qsar::scoring_grid::VdwGrid::refresh().

core::Vector protocols::qsar::scoring_grid::GridBase::get_center ( )

get the center of the grid

numeric::xyzVector< core::Size > protocols::qsar::scoring_grid::GridBase::get_dimensions ( )

get dimensions of the grid

References core::grid::CartGrid< T >::getNumberOfPoints().

core::grid::CartGrid< core::Real > const & protocols::qsar::scoring_grid::GridBase::get_grid ( )

return a constant reference to the grid

Referenced by protocols::qsar::scoring_grid::VdwGrid::score().

core::Real protocols::qsar::scoring_grid::GridBase::get_max_value ( ) const

get the minimum score value in the grid

References core::grid::CartGrid< T >::getMaxValue().

core::Real protocols::qsar::scoring_grid::GridBase::get_min_value ( ) const

get the max score value in the grid

References core::grid::CartGrid< T >::getMinValue().

core::Real protocols::qsar::scoring_grid::GridBase::get_point ( core::Real  x,
core::Real  y,
core::Real  z 
)

get the value of a single point in the grid

References core::grid::CartGrid< T >::getValue().

Referenced by protocols::qsar::scoring_grid::VdwGrid::score().

std::list< std::pair< core::Vector, core::Real > > protocols::qsar::scoring_grid::GridBase::get_point_value_list_within_range ( core::Real  lower_bound,
core::Real  upper_bound,
core::Size  stride 
)
std::string protocols::qsar::scoring_grid::GridBase::get_type ( )

return the grids type

core::Real protocols::qsar::scoring_grid::GridBase::get_weight ( )

get the weight of the grid

void protocols::qsar::scoring_grid::GridBase::grid_to_kin ( utility::io::ozstream &  out,
core::Real  min_val,
core::Real  max_val,
core::Size  stride 
)
void protocols::qsar::scoring_grid::GridBase::initialize ( core::Vector const &  center,
core::Real  width,
core::Real  resolution 
)

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

References core::grid::CartGrid< T >::setBase(), core::grid::CartGrid< T >::setDimensions(), core::grid::CartGrid< T >::setupZones(), and core::grid::CartGrid< T >::zero().

virtual void protocols::qsar::scoring_grid::GridBase::parse_my_tag ( utility::tag::TagPtr const  tag) [pure virtual]
virtual void protocols::qsar::scoring_grid::GridBase::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center 
) [pure virtual]
virtual void protocols::qsar::scoring_grid::GridBase::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
) [pure virtual]
virtual void protocols::qsar::scoring_grid::GridBase::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
utility::vector1< core::Size ligand_chain_ids_to_exclude 
) [pure virtual]
core::Real protocols::qsar::scoring_grid::GridBase::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
) [virtual]
void protocols::qsar::scoring_grid::GridBase::set_center ( core::Vector  center)

set the center of the grid

void protocols::qsar::scoring_grid::GridBase::set_distance_sphere ( core::Vector const &  coords,
core::Real  cutoff 
)
void protocols::qsar::scoring_grid::GridBase::set_distance_sphere_for_atom ( core::Real const &  atom_shell,
core::Vector const &  coords,
core::Real  cutoff 
)
void protocols::qsar::scoring_grid::GridBase::set_point ( core::Vector const &  coords,
core::Real  value 
)
void protocols::qsar::scoring_grid::GridBase::set_ring ( core::Vector const &  coords,
core::Real  inner_radius,
core::Real  outer_radius,
core::Real  value 
)
void protocols::qsar::scoring_grid::GridBase::set_sphere ( core::Vector const &  coords,
core::Real  radius,
core::Real  value 
)
void protocols::qsar::scoring_grid::GridBase::set_type ( std::string  type)

set the grid type

void protocols::qsar::scoring_grid::GridBase::set_weight ( core::Real  weight)

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