Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::qsar::scoring_grid::SingleGrid Class Referenceabstract

#include <SingleGrid.hh>

Public Member Functions

 SingleGrid (std::string type)
 
virtual ~SingleGrid ()
 
virtual 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). More...
 
virtual void set_chain (char chain)
 set the chain around which to calculate the grid More...
 
char get_chain ()
 get the chain around which the grid is calculated More...
 
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 More...
 
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 More...
 
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center)=0
 populate the grid with values based on a passed pose More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag)=0
 setup a grid based on RosettaScripts input More...
 
virtual utility::json_spirit::Value serialize ()
 serialize the SingleGrid to a json_spirit object More...
 
virtual void deserialize (utility::json_spirit::mObject data)
 deserialize a json_spirit object to a SingleGrid More...
 
core::grid::CartGrid
< core::Real > const & 
get_grid ()
 return a constant reference to the grid More...
 
void set_type (std::string type)
 set the grid type More...
 
virtual std::string get_type ()
 return the grids type More...
 
void set_center (core::Vector center)
 set the center of the grid More...
 
core::Vector get_center ()
 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)
 get the value of a single point in the grid based on pdb coordinates More...
 
core::Real get_point (core::Vector coords)
 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...
 
virtual core::Real score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapOP qsar_map)
 return the current score of an UltraLightResidue using the current grid More...
 
virtual core::Real atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapOP qsar_map)
 return the current score of an atom using the current grid More...
 
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 More...
 
virtual core::Real atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapOP qsar_map)
 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)
 
virtual bool is_in_grid (core::conformation::UltraLightResidue const &residue)
 check to see if residue is in grid More...
 
virtual bool is_in_grid (core::conformation::Residue const &residue)
 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)
 
virtual void dump_BRIX (std::string const &prefix)
 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_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 set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorOP lj_spline, core::Vector const &coords, core::Real cutoff)
 
void fill_with_value (core::Real)
 the entire grid with some value More...
 
- Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
 GridBase ()
 
virtual ~GridBase ()
 

Private Attributes

core::grid::CartGrid< core::Realgrid_
 
std::string type_
 
core::Vector center_
 
char chain_
 

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::SingleGrid::SingleGrid ( std::string  type)
protocols::qsar::scoring_grid::SingleGrid::~SingleGrid ( )
virtual

Member Function Documentation

core::Real protocols::qsar::scoring_grid::SingleGrid::atom_score ( core::conformation::UltraLightResidue const &  residue,
core::Size  atomno,
qsarMapOP  qsar_map 
)
virtual
core::Real protocols::qsar::scoring_grid::SingleGrid::atom_score ( core::conformation::Residue const &  residue,
core::Size  atomno,
qsarMapOP  qsar_map 
)
virtual
void protocols::qsar::scoring_grid::SingleGrid::deserialize ( utility::json_spirit::mObject  data)
virtual
void protocols::qsar::scoring_grid::SingleGrid::diffuse_ring ( core::Vector const &  coords,
core::Real  radius,
core::Real  width,
core::Real  magnitude 
)
void protocols::qsar::scoring_grid::SingleGrid::dump_BRIX ( std::string const &  prefix)
virtual

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

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

References grid_, and type_.

void protocols::qsar::scoring_grid::SingleGrid::fill_with_value ( core::Real  value)
core::Vector protocols::qsar::scoring_grid::SingleGrid::get_center ( )

get the center of the grid

References center_.

char protocols::qsar::scoring_grid::SingleGrid::get_chain ( )
numeric::xyzVector< core::Size > protocols::qsar::scoring_grid::SingleGrid::get_dimensions ( )
core::grid::CartGrid< core::Real > const & protocols::qsar::scoring_grid::SingleGrid::get_grid ( )
core::Real protocols::qsar::scoring_grid::SingleGrid::get_max_value ( ) const

get the minimum score value in the grid

References grid_.

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

get the max score value in the grid

References grid_.

core::Vector protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords ( int  x,
int  y,
int  z 
)
core::Vector protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords ( core::grid::CartGrid< core::Real >::GridPt  gridpt)

get the pdb coordinates based on grid point coordinates

References grid_.

core::Real protocols::qsar::scoring_grid::SingleGrid::get_point ( core::Real  x,
core::Real  y,
core::Real  z 
)
core::Real protocols::qsar::scoring_grid::SingleGrid::get_point ( core::Vector  coords)

get the value of a single point in the grid based on pdb coordinates

References grid_.

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

References grid_.

std::string protocols::qsar::scoring_grid::SingleGrid::get_type ( )
virtual

return the grids type

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

References type_.

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

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

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

References center_, grid_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

bool protocols::qsar::scoring_grid::SingleGrid::is_in_grid ( core::conformation::UltraLightResidue const &  residue)
virtual
bool protocols::qsar::scoring_grid::SingleGrid::is_in_grid ( core::conformation::Residue const &  residue)
virtual
virtual void protocols::qsar::scoring_grid::SingleGrid::parse_my_tag ( utility::tag::TagCOP  tag)
pure virtual
virtual void protocols::qsar::scoring_grid::SingleGrid::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::SingleGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
utility::vector1< core::Size ligand_chain_ids_to_exclude 
)
pure virtual
virtual void protocols::qsar::scoring_grid::SingleGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center 
)
pure virtual
core::Real protocols::qsar::scoring_grid::SingleGrid::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
)
virtual
core::Real protocols::qsar::scoring_grid::SingleGrid::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
)
virtual
utility::json_spirit::Value protocols::qsar::scoring_grid::SingleGrid::serialize ( )
virtual
void protocols::qsar::scoring_grid::SingleGrid::set_center ( core::Vector  center)

set the center of the grid

References center_.

void protocols::qsar::scoring_grid::SingleGrid::set_chain ( char  chain)
virtual

set the chain around which to calculate the grid

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

References chain_.

void protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere ( core::Vector const &  coords,
core::Real  cutoff 
)
void protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom ( core::Real const &  atom_shell,
core::Vector const &  coords,
core::Real  cutoff 
)
void protocols::qsar::scoring_grid::SingleGrid::set_point ( core::Vector const &  coords,
core::Real  value 
)
void protocols::qsar::scoring_grid::SingleGrid::set_ring ( core::Vector const &  coords,
core::Real  inner_radius,
core::Real  outer_radius,
core::Real  value 
)
void protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom ( numeric::interpolation::spline::InterpolatorOP  lj_spline,
core::Vector const &  coords,
core::Real  cutoff 
)
void protocols::qsar::scoring_grid::SingleGrid::set_sphere ( core::Vector const &  coords,
core::Real  radius,
core::Real  value 
)
void protocols::qsar::scoring_grid::SingleGrid::set_type ( std::string  type)

set the grid type

References type_.

Member Data Documentation

core::Vector protocols::qsar::scoring_grid::SingleGrid::center_
private
char protocols::qsar::scoring_grid::SingleGrid::chain_
private

Referenced by get_chain(), serialize(), and set_chain().

core::grid::CartGrid<core::Real> protocols::qsar::scoring_grid::SingleGrid::grid_
private
std::string protocols::qsar::scoring_grid::SingleGrid::type_
private

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