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ClashBasedShellSelector.hh 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.fwd.hh>
#include <core/types.hh>
#include <core/select/residue_selector/ResidueSelector.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/tag/XMLSchemaGeneration.fwd.hh>
#include <utility/vector1.hh>
#include <set>

Classes

class  core::pack::task::residue_selector::ClashBasedShellSelector
 Define a shell based on potential sidechain clashes with a set of residues being repacked or designed. More...
 

Namespaces

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

Functions

std::set< core::Sizecore::pack::task::residue_selector::find_clashing_shells (core::pack::task::PackerTaskCOP const focus, core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::Size const num_shells=ClashBasedShellSelector::DEFAULT_NUM_SHELLS, bool const include_focus=ClashBasedShellSelector::DEFAULT_INCLUDE_FOCUS, core::Real const bump_factor=ClashBasedShellSelector::DEFAULT_BUMP_FACTOR)
 Return the indices of any residues that clash with any of the rotamers allowed by the given PackerTask. More...
 
std::set< core::Sizecore::pack::task::residue_selector::find_clashing_shell (core::pack::task::PackerTaskCOP const focus, core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::Real const bump_factor=ClashBasedShellSelector::DEFAULT_BUMP_FACTOR)
 Find a single shell of clashing residues. More...
 
void core::pack::task::residue_selector::add_clashes_to_shell (core::pose::Pose const &pose, core::conformation::Residue const &rot1, std::set< core::Size > const &focus, std::set< core::Size > &shell)
 Add any residue that clashes with the given rotamer to the given shell, unless the given rotamer also clashes with the backbone somewhere. More...
 
void core::pack::task::residue_selector::add_clashes_to_shell (core::pose::Pose const &pose, core::conformation::Residue const &rot1, core::Real const bump_factor, std::set< core::Size > const &focus, std::set< core::Size > &shell)
 
bool core::pack::task::residue_selector::is_sc_sc_clash (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, core::Real bump_factor=ClashBasedShellSelector::DEFAULT_BUMP_FACTOR)
 Return true if there is a sidechain clash between the two given residues. More...
 
bool core::pack::task::residue_selector::is_sc_bb_clash (core::conformation::Residue const &sc_rsd, core::conformation::Residue const &bb_rsd, core::Real bump_factor=ClashBasedShellSelector::DEFAULT_BUMP_FACTOR)
 Return true if a sidechain atom in the first residue clashes with a backbone atom in the second residue. More...
 
std::set< core::Sizecore::pack::task::residue_selector::resnums_from_bool_mask (utility::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...
 
utility::vector1< bool > core::pack::task::residue_selector::bool_mask_from_resnums (core::pose::Pose const &pose, std::set< core::Size > const &resis)
 Return a boolean mask where the indices in the given set are true and all others are false. More...
 
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...
 
core::pack::task::PackerTaskOP core::pack::task::residue_selector::task_from_bool_mask (core::pose::Pose const &pose, utility::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...
 
core::pack::task::PackerTaskOP core::pack::task::residue_selector::task_from_resnums (core::pose::Pose const &pose, std::set< core::Size > resnums)
 Return a PackerTask where the indices that in the given set are repackable and all others are frozen. More...
 

Detailed Description

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

Author
Noah Ollikainen (nolli.nosp@m.kai@.nosp@m.gmail.nosp@m..com)
Roland A. Pache, PhD
Kale Kundert (kale@.nosp@m.thek.nosp@m.under.nosp@m.ts.n.nosp@m.et)