ClashBasedShellSelector.cc File Reference

The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position. More...

#include <core/pack/task/residue_selector/ClashBasedShellSelector.hh>
#include <core/pack/task/residue_selector/ClashBasedShellSelectorCreator.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/find_neighbors.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/PointGraph.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/task/xml_util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/selection.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/xml_util.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/select/residue_selector/util.hh>
#include <core/select/residue_selector/ResidueSelectorCreators.hh>
#include <core/types.hh>
#include <basic/datacache/DataMap.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/tag/Tag.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <utility/vector1.hh>
#include <utility/assert.hh>
#include <boost/format.hpp>

Namespaces
	core
	A class for reading in the atom type properties.
	core::pack
	core::pack::task
	core::pack::task::residue_selector

Functions
static basic::Tracer	core::pack::task::residue_selector::TR ("core.pack.task.residue_selector.ClashBasedShellSelector")
set< Size >	core::pack::task::residue_selector::find_clashing_shells (PackerTaskCOP const focus_task, Pose const &pose, ScoreFunction const &scorefxn, Size const num_shells, bool const include_focus, Real const bump_factor)
set< Size >	core::pack::task::residue_selector::find_clashing_shell (PackerTaskCOP task, Pose const &const_pose, ScoreFunction const &scorefxn, Real const bump_factor)
void	core::pack::task::residue_selector::add_clashes_to_shell (Pose const &pose, Residue const &rot1, set< Size > const &focus, set< Size > &shell)
void	core::pack::task::residue_selector::add_clashes_to_shell (Pose const &pose, Residue const &rot1, Real const bump_factor, set< Size > const &focus, set< Size > &shell)
bool	core::pack::task::residue_selector::is_sc_sc_clash (Residue const &rsd1, Residue const &rsd2, Real bump_factor)
bool	core::pack::task::residue_selector::is_sc_bb_clash (Residue const &sc_rsd, Residue const &bb_rsd, Real bump_factor)
set< Size >	core::pack::task::residue_selector::resnums_from_bool_mask (vector1< bool > mask)
	Return a set containing the indices with true values in the given boolean mask. More...
set< Size >	core::pack::task::residue_selector::resnums_from_task (core::pack::task::PackerTaskCOP task)
	Return a set containing the positions that are not fixed (i.e. that are packable or designable) in the given PackerTask. More...
vector1< bool >	core::pack::task::residue_selector::bool_mask_from_resnums (Pose const &pose, set< Size > const &resnums)
vector1< bool >	core::pack::task::residue_selector::bool_mask_from_task (core::pack::task::PackerTaskCOP task)
	Return a boolean mask where the indices that are not fixed (i.e. that are packable or designable) in the given PackerTask are true and all others are false. More...
PackerTaskOP	core::pack::task::residue_selector::task_from_resnums (Pose const &pose, set< Size > resnums)
PackerTaskOP	core::pack::task::residue_selector::task_from_bool_mask (Pose const &pose, vector1< bool > mask)
	Return a PackerTask where the indices that are true in the given boolean mask are repackable and all others are frozen. More...
void	core::pack::task::residue_selector::freeze_repack_positions (PackerTaskOP task)

Detailed Description

The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position.

Detailed: The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position. There are two recommended ways to use this selector.

Detailed: (Usage 1) identify all residues that could clash with residues designated as design positions by the packer. The constructor for this usage takes (a) task, (b) scorefxn, and (c) pose.

Detailed: (Usage 2) identify all residues that could clash with an arbitrary set of residues. The constructor for this usage takes one argument of type std::set<core::Size>.

Detailed: In either usage, once you create the residue selector object, you then get result of which positions could clash using the apply function e.g. utility::vector1< bool > clashing_residues = ClashBasedShellSelector_object->apply( *pose_copy );

Author

Noah Ollikainen (nolli.nosp@m.kai@.nosp@m.gmail.nosp@m..com)

Roland A. Pache, PhD

Amanda Loshbaugh (alosh.nosp@m.bau@.nosp@m.gmail.nosp@m..com)

Kale Kundert (kale@.nosp@m.thek.nosp@m.under.nosp@m.ts.n.nosp@m.et)