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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/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/Pose.hh>
#include <core/scoring/xml_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/select/residue_selector/util.hh>
#include <core/types.hh>
#include <basic/datacache/DataMap.fwd.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/tag/Tag.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <utility/vector1.hh>
#include <boost/format.hpp>
#include <utility/stream_util.hh>

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)
 
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)
 
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)