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Public Member Functions | List of all members
protocols::qsar::scoring_grid::GridBase Class Referenceabstract

#include <GridBase.hh>

Inheritance diagram for protocols::qsar::scoring_grid::GridBase:
Inheritance graph
[legend]

Public Member Functions

 GridBase ()
 
 ~GridBase () override
 
virtual GridBaseOP clone () const =0
 Make a copy of the grid, respecting the subclassing. More...
 
virtual void initialize (core::Vector const &center, core::Real width, core::Real resolution)=0
 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)=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 core::Real score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const =0
 return the current scoer of an UltraLightResidue using the current grid More...
 
virtual core::Real atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const =0
 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, qsarMapCOP qsar_map) const =0
 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, qsarMapCOP qsar_map) const =0
 return the current score of an atom using the current grid More...
 
virtual std::string get_type () const =0
 get the type of the grid More...
 
virtual void set_chain (char chain)=0
 set the chain the grid applies to More...
 
virtual void dump_BRIX (std::string const &prefix) const =0
 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 () const =0
 Serialize the GridBase object into a json_spirit Value. More...
 
virtual void deserialize (utility::json_spirit::mObject data)=0
 deserialize a json spirit Value into a GridBase object More...
 
virtual bool is_in_grid (core::conformation::UltraLightResidue const &residue) const =0
 determine if all residue atoms are in a grid More...
 
virtual bool is_in_grid (core::conformation::Residue const &residue) const =0
 determine if all residue atoms are in a grid More...
 
virtual void show (std::ostream &out) const =0
 Print a brief summary about this grid to the provided output stream. More...
 
virtual std::string hash_fingerprint () const =0
 Return a string representing the settings which don't change based on reinitialization. More...
 

Constructor & Destructor Documentation

◆ GridBase()

protocols::qsar::scoring_grid::GridBase::GridBase ( )
inline

◆ ~GridBase()

protocols::qsar::scoring_grid::GridBase::~GridBase ( )
inlineoverride

Member Function Documentation

◆ atom_score() [1/2]

virtual core::Real protocols::qsar::scoring_grid::GridBase::atom_score ( core::conformation::Residue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
pure virtual

◆ atom_score() [2/2]

virtual core::Real protocols::qsar::scoring_grid::GridBase::atom_score ( core::conformation::UltraLightResidue const &  residue,
core::Size  atomno,
qsarMapCOP  qsar_map 
) const
pure virtual

◆ clone()

virtual GridBaseOP protocols::qsar::scoring_grid::GridBase::clone ( ) const
pure virtual

◆ deserialize()

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

◆ dump_BRIX()

virtual void protocols::qsar::scoring_grid::GridBase::dump_BRIX ( std::string const &  prefix) const
pure virtual

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

Implemented in protocols::qsar::scoring_grid::SolvationMetaGrid, protocols::qsar::scoring_grid::SingleGrid, protocols::qsar::scoring_grid::PCSMultiGrid, and protocols::qsar::scoring_grid::ConstantScoreBase.

◆ get_type()

virtual std::string protocols::qsar::scoring_grid::GridBase::get_type ( ) const
pure virtual

◆ hash_fingerprint()

virtual std::string protocols::qsar::scoring_grid::GridBase::hash_fingerprint ( ) const
pure virtual

◆ initialize()

virtual void protocols::qsar::scoring_grid::GridBase::initialize ( core::Vector const &  center,
core::Real  width,
core::Real  resolution 
)
pure virtual

◆ is_in_grid() [1/2]

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

◆ is_in_grid() [2/2]

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

◆ parse_my_tag()

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

◆ refresh() [1/3]

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

◆ refresh() [2/3]

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

◆ refresh() [3/3]

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

◆ score() [1/2]

virtual core::Real protocols::qsar::scoring_grid::GridBase::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
pure virtual

◆ score() [2/2]

virtual core::Real protocols::qsar::scoring_grid::GridBase::score ( core::conformation::UltraLightResidue const &  residue,
core::Real const  max_score,
qsarMapCOP  qsar_map 
) const
pure virtual

◆ serialize()

virtual utility::json_spirit::Value protocols::qsar::scoring_grid::GridBase::serialize ( ) const
pure virtual

◆ set_chain()

virtual void protocols::qsar::scoring_grid::GridBase::set_chain ( char  chain)
pure virtual

◆ show()

virtual void protocols::qsar::scoring_grid::GridBase::show ( std::ostream &  out) const
pure virtual

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