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< Size >	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 >	find_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< Size >	resnums_from_bool_mask (vector1< bool > mask)
	Return a set containing the indices with true values in the given boolean mask. More...
set< Size >	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 >	bool_mask_from_resnums (Pose const &pose, set< Size > const &resnums)
vector1< bool >	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	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::Size >	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::Size >	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	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::Size >	resnums_from_bool_mask (utility::vector1< bool > mask)
	Return a set containing the indices with true values in the given boolean mask. More...
utility::vector1< bool >	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...
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

typedef utility::pointer::shared_ptr< ClashBasedShellSelector const > core::pack::task::residue_selector::ClashBasedShellSelectorCOP

typedef utility::pointer::shared_ptr< ClashBasedShellSelector > core::pack::task::residue_selector::ClashBasedShellSelectorOP

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
	)

References core::pack::task::residue_selector::ClashBasedShellSelector::DEFAULT_BUMP_FACTOR.

Referenced by find_clashing_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
	)

References is_sc_bb_clash(), is_sc_sc_clash(), core::conformation::Residue::name1(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), and core::pose::Pose::size().

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
	)

References core::pose::Pose::size().

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

References add_clashes_to_shell(), core::pack::create_packer_graph(), resnums_from_task(), and core::scoring::ScoreFunction::setup_for_packing().

Referenced by find_clashing_shells().

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
	)

References find_clashing_shell(), resnums_from_task(), and task_from_resnums().

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

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

)

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

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

References core::conformation::Residue::atom_type(), core::kinematics::tree::distance_squared(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::last_backbone_atom(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::xyz().

Referenced by add_clashes_to_shell().

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
	)

References core::conformation::Residue::atom_type(), core::kinematics::tree::distance_squared(), core::conformation::Residue::first_sidechain_atom(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::xyz().

Referenced by add_clashes_to_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.

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
	)

References bool_mask_from_resnums(), and task_from_bool_mask().

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

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