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

#include <SolvationMetaGrid.hh>

Public Member Functions

 SolvationMetaGrid ()
 
virtual ~SolvationMetaGrid ()
 
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 refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
 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)
 populate the grid with values based on a passed pose More...
 
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center)
 populate the grid with values based on a passed pose More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag)
 a grid based on RosettaScripts input 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...
 
virtual std::string get_type ()
 get the type of the grid More...
 
virtual void set_chain (char chain)
 set the chain the grid applies to More...
 
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...
 
virtual utility::json_spirit::Value serialize ()
 Serialize the GridBase object into a json_spirit Value. More...
 
virtual void deserialize (utility::json_spirit::mObject data)
 deserialize a json spirit Value into a GridBase object More...
 
virtual bool is_in_grid (core::conformation::UltraLightResidue const &residue)
 determine if all residue atoms are in a grid More...
 
virtual bool is_in_grid (core::conformation::Residue const &residue)
 determine if all residue atoms are in a grid More...
 
- Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
 GridBase ()
 
virtual ~GridBase ()
 

Private Attributes

std::string type_
 
std::map< core::ShortSize,
SingleGridOP
grid_map_
 

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::SolvationMetaGrid::SolvationMetaGrid ( )
protocols::qsar::scoring_grid::SolvationMetaGrid::~SolvationMetaGrid ( )
virtual

Member Function Documentation

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score ( core::conformation::UltraLightResidue const &  residue,
core::Size  atomno,
qsarMapOP  qsar_map 
)
virtual

return the current score of an atom using the current grid

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

References grid_map_, core::conformation::UltraLightResidue::residue(), and utility_exit_with_message.

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score ( core::conformation::Residue const &  residue,
core::Size  atomno,
qsarMapOP  qsar_map 
)
virtual

return the current score of an atom using the current grid

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

References core::conformation::Residue::atom(), grid_map_, and utility_exit_with_message.

void protocols::qsar::scoring_grid::SolvationMetaGrid::deserialize ( utility::json_spirit::mObject  data)
virtual

deserialize a json spirit Value into a GridBase object

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

References grid, grid_map_, and type_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::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 utility_exit_with_message.

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

get the type of the grid

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

void protocols::qsar::scoring_grid::SolvationMetaGrid::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 core::chemical::ChemicalManager::get_instance(), and grid_map_.

bool protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid ( core::conformation::UltraLightResidue const &  residue)
virtual

determine if all residue atoms are in a grid

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

References grid_map_.

bool protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid ( core::conformation::Residue const &  residue)
virtual

determine if all residue atoms are in a grid

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

References grid_map_.

void protocols::qsar::scoring_grid::SolvationMetaGrid::parse_my_tag ( utility::tag::TagCOP  tag)
virtual

a grid based on RosettaScripts input

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

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

populate the grid with values based on a passed pose

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

Referenced by refresh().

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

populate the grid with values based on a passed pose

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

References refresh().

void protocols::qsar::scoring_grid::SolvationMetaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center 
)
virtual

populate the grid with values based on a passed pose

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

References grid_map_.

core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
)
virtual
core::Real protocols::qsar::scoring_grid::SolvationMetaGrid::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
)
virtual
utility::json_spirit::Value protocols::qsar::scoring_grid::SolvationMetaGrid::serialize ( )
virtual

Serialize the GridBase object into a json_spirit Value.

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

References grid_map_, utility::tools::make_vector(), and type_.

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

set the chain the grid applies to

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

References grid_map_.

Member Data Documentation

std::map<core::ShortSize,SingleGridOP> protocols::qsar::scoring_grid::SolvationMetaGrid::grid_map_
private
std::string protocols::qsar::scoring_grid::SolvationMetaGrid::type_
private

Referenced by deserialize(), and serialize().


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