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core::pack::task::residue_selector Namespace Reference

Classes

class  ClashBasedShellSelector
 Define a shell based on potential sidechain clashes with a set of residues being repacked or designed. More...
 
class  ClashBasedShellSelectorCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< ClashBasedShellSelector
ClashBasedShellSelectorOP
 
typedef
utility::pointer::shared_ptr
< ClashBasedShellSelector
const > 
ClashBasedShellSelectorCOP
 

Functions

static basic::Tracer TR ("core.pack.task.residue_selector.ClashBasedShellSelector")
 
set< Sizefind_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< Sizefind_clashing_shell (PackerTaskCOP task, Pose const &const_pose, ScoreFunction const &scorefxn, Real const bump_factor)
 
void add_clashes_to_shell (Pose const &pose, Residue const &rot1, set< Size > const &focus, set< Size > &shell)
 
void add_clashes_to_shell (Pose const &pose, Residue const &rot1, Real const bump_factor, set< Size > const &focus, set< Size > &shell)
 
bool is_sc_sc_clash (Residue const &rsd1, Residue const &rsd2, Real bump_factor)
 
bool is_sc_bb_clash (Residue const &sc_rsd, Residue const &bb_rsd, Real bump_factor)
 
set< Sizeresnums_from_bool_mask (vector1< bool > mask)
 Return a set containing the indices with true values in the given boolean mask. More...
 
set< Sizeresnums_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< boolbool_mask_from_resnums (Pose const &pose, set< Size > const &resnums)
 
vector1< boolbool_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 task_from_resnums (Pose const &pose, set< Size > resnums)
 
PackerTaskOP 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 freeze_repack_positions (PackerTaskOP task)
 
std::set< core::Sizefind_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::Sizefind_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 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 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 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 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::Sizeresnums_from_bool_mask (utility::vector1< bool > mask)
 Return a set containing the indices with true values in the given boolean mask. More...
 
utility::vector1< boolbool_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...
 
core::pack::task::PackerTaskOP 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 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...
 

Typedef Documentation

Function Documentation

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 
)
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.

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 
)
vector1<bool> core::pack::task::residue_selector::bool_mask_from_resnums ( Pose const &  pose,
set< Size > const &  resnums 
)
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.

utility::vector1< bool > core::pack::task::residue_selector::bool_mask_from_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.

Referenced by resnums_from_task().

set<Size> core::pack::task::residue_selector::find_clashing_shell ( PackerTaskCOP  task,
Pose const &  const_pose,
ScoreFunction const &  scorefxn,
Real const  bump_factor 
)
std::set<core::Size> core::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.

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 
)
std::set<core::Size> core::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.

See ClashBasedShellSelector for more details about how clash-based shell selection works, although most of the logic is implemented in this function.

void core::pack::task::residue_selector::freeze_repack_positions ( PackerTaskOP  task)
bool core::pack::task::residue_selector::is_sc_bb_clash ( Residue const &  sc_rsd,
Residue const &  bb_rsd,
Real  bump_factor 
)
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.

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_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.

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.

Referenced by resnums_from_task().

std::set<core::Size> core::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.

Referenced by resnums_from_task().

std::set< core::Size > core::pack::task::residue_selector::resnums_from_task ( PackerTaskCOP  task)

Return a set containing the positions that are not fixed (i.e. that are packable or designable) in the given PackerTask.

References bool_mask_from_task(), and resnums_from_bool_mask().

Referenced by find_clashing_shell(), and find_clashing_shells().

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.

References core::pack::task::TaskFactory::push_back(), and core::pose::Pose::size().

Referenced by core::pack::task::residue_selector::ClashBasedShellSelector::apply(), and task_from_resnums().

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.

References core::pack::task::TaskFactory::push_back(), and core::pose::Pose::size().

Referenced by core::pack::task::residue_selector::ClashBasedShellSelector::apply(), and task_from_resnums().

PackerTaskOP core::pack::task::residue_selector::task_from_resnums ( Pose const &  pose,
set< Size >  resnums 
)
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.

static basic::Tracer core::pack::task::residue_selector::TR ( "core.pack.task.residue_selector.ClashBasedShellSelector"  )
static