grid_functions.cc File Reference

#include <protocols/ligand_docking/grid_functions.hh>
#include <utility/graph/Graph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random_permutation.hh>
#include <utility/vector1.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/pose/Pose.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::ligand_docking

Typedefs
using	protocols::ligand_docking::CartGridIntOP = utility::pointer::shared_ptr< core::grid::CartGrid< int > >

Functions
static basic::Tracer	protocols::ligand_docking::TR ("protocols.ligand_docking.grid_functions", basic::t_debug)
int	protocols::ligand_docking::grid_score (core::grid::CartGrid< int > const &grid, core::conformation::Residue const &rsd, int max_score=9999)
	Sum the grid values for all heavy atoms in the residue. More...
void	protocols::ligand_docking::grid_score_atr_rep (core::grid::CartGrid< int > const &grid, core::conformation::Residue const &rsd, int &atr_out, int &rep_out, int max_rep=9999)
	Sum the grid values for all heavy atoms in the residue. More...
void	protocols::ligand_docking::rb_grid_score_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose const &pose, core::Size begin, core::Size const end, int &atr_out, int &rep_out, int max_rep)
	Sum the grid values for all heavy atoms in the residue. More...
std::pair< int, int >	protocols::ligand_docking::get_rb_atr_and_rep_scores (core::grid::CartGrid< int > const &grid, core::pose::Pose const &pose, core::Size begin, core::Size end)
	a cleaner implementation of rb_grid_score_atr_rep More...
void	protocols::ligand_docking::grid_rotamer_trials (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no, core::pack::task::PackerTask const &packertask, int const min_score=0)
	Try all rotamers for the specified residue and install the first one that minimizes the grid score. Only tested with ligand residues w/ a conformer library. More...
void	protocols::ligand_docking::grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no, core::pack::task::PackerTask const &packertask)
	Try all rotamers for the specified residue and install the first one that minimizes the repulsive score, breaking ties by the attractive score. Only tested with ligand residues w/ a conformer library. More...
void	protocols::ligand_docking::rb_grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size begin, core::Size end, core::pack::task::PackerTask const &packertask)
void	protocols::ligand_docking::rotamers_for_trials (core::pose::Pose &pose, core::Size rsd_no, utility::vector1< core::conformation::ResidueOP > &conformers_out, core::pack::task::PackerTask const &packertask)
	Internal helper function for rotamer trials; fills conformers_out. More...
void	protocols::ligand_docking::set_sphere (core::grid::CartGrid< int > &grid, core::Vector const &center, core::Real radius, int value)
void	protocols::ligand_docking::set_repulsive_bb_cores (utility::pointer::shared_ptr< core::grid::CartGrid< int > >grid, core::pose::Pose const &pose, core::Real const rep_rad)
utility::pointer::shared_ptr< core::grid::CartGrid< int > >	protocols::ligand_docking::make_atr_rep_grid (core::pose::Pose const &pose, core::Vector const &center)
	@detail this function assumes there is only one ligand so it only considers protein residues More...
utility::pointer::shared_ptr< core::grid::CartGrid< int > >	protocols::ligand_docking::make_atr_rep_grid_without_ligand (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
	@detail this function assumes excludes one ligand from the grid More...
utility::pointer::shared_ptr< core::grid::CartGrid< int > >	protocols::ligand_docking::make_atr_rep_grid_without_ligands (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
	Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude. More...

Detailed Description

Author

Ian W. Davis