#include <FlexbbRotamerSet.hh>

Inheritance diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSet:

Collaboration diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSet:

Public Types
typedef core::pack::rotamer_set::RotamerSet_	parent

Public Types inherited from core::pack::rotamer_set::RotamerSet_
typedef conformation::ResidueOP	ResidueOP

typedef conformation::ResidueCOP	ResidueCOP

typedef pack::dunbrack::ChiSetOP	ChiSetOP

typedef scoring::trie::RotamerTrieBaseOP	RotamerTrieBaseOP

Public Member Functions
	FlexbbRotamerSet ()

virtual	~FlexbbRotamerSet ()

void	set_owner (FlexbbRotamerSetsCAP owner)

virtual void	build_dependent_rotamers (core::pack::rotamer_set::RotamerSets const &rotamer_sets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, core::graph::GraphCOP packer_neighbor_graph)
	Build rotamers that depend on positions of rotamers built in a previous pass This function won't work... More...

void	set_existing_residue (core::conformation::ResidueCOP residue)

Public Member Functions inherited from core::pack::rotamer_set::RotamerSet_
	RotamerSet_ ()

virtual	~RotamerSet_ ()

virtual void	build_rotamers (pose::Pose const &the_pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)

virtual void	add_rotamer (conformation::Residue const &rotamer)

virtual Size	get_n_residue_types () const
	Return the number of different residue types; two residue types are considered different if they have a different address. More...

virtual Size	get_n_residue_groups () const
	Return the number of different residue groups. Two residue types are considered to be part of the same block of residues if 1. they have the same address or 2. they have the same "name3" and the same neighbor radius. More...

virtual Size	get_residue_type_begin (Size which_restype) const
	Return the first rotamer of a particular residue type. More...

virtual Size	get_residue_group_begin (Size which_resgroup) const
	Return the first rotamer that belongs to a particular rotamer group. More...

virtual Size	get_n_rotamers_for_residue_type (Size which_resgroup) const

virtual Size	get_n_rotamers_for_residue_group (Size which_resgroup) const

virtual Size	get_residue_type_index_for_rotamer (Size which_rotamer) const
	Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7. More...

virtual Size	get_residue_group_index_for_rotamer (Size which_rotamer) const
	Return the index of the rotamer group for a particular rotamer. More...

virtual void	compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, utility::vector1< core::PackerEnergy > &energies) const
	Computes the packers "one body energies" for the set of rotamers. More...

virtual void	compute_one_body_energy_maps (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, utility::vector1< scoring::EnergyMap > &energies) const
	for OPTE More...

virtual Size	num_rotamers () const

virtual Size	id_for_current_rotamer () const

virtual conformation::ResidueCOP	rotamer (Size rot_id) const

virtual Rotamers::const_iterator	begin () const

virtual Rotamers::const_iterator	end () const

virtual conformation::ResidueOP	nonconst_rotamer (Size rot_id)

virtual void	store_trie (Size method_enum_id, conformation::AbstractRotamerTrieOP trie)

virtual conformation::AbstractRotamerTrieCOP	get_trie (Size method_enum_id) const

virtual void	drop_rotamer (Size rot_id)
	removes a single rotamer and causes a rotamer index update More...

virtual void	drop_rotamers (utility::vector1< bool > const &rotamers_to_delete)
	rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers More...

virtual void	drop_rotamers_by_index (utility::vector1< Size > const &rotamer_indices_to_delete)
	deletes the rotamers in the list with the given indices. The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2. More...

void	set_extra_samples (task::PackerTask const &task, int num_10A_neighbors, int chi, chemical::ResidueTypeCOP concrete_residue, utility::vector1< Real > &extra_chi_steps) const
	Pushes standard-deviation multiples that should be sampled for this residue – if this residue has more neighbors within 10A than the task-specified cutoff for buriedness, then extra rotamer samples are added to the extra_chi_steps vector, otherwise, the vector is not modified. More...

Public Member Functions inherited from core::pack::rotamer_set::RotamerSet
	RotamerSet ()

virtual	~RotamerSet ()

void	set_resid (Size resid)

virtual Size	resid () const

Public Member Functions inherited from core::conformation::RotamerSetBase
	RotamerSetBase ()

virtual	~RotamerSetBase ()

BasicDataCache &	data ()
	BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh. More...

BasicDataCache const &	data () const
	BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh. More...

Protected Member Functions
virtual void	build_rotamers_for_concrete_virt (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, core::chemical::ResidueTypeCOP concrete_residue, core::graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
	Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue. More...

virtual core::PackerEnergy	bump_check (core::conformation::ResidueCOP rotamer, core::scoring::ScoreFunction const &sf, core::pose::Pose const &pose, core::pack::task::PackerTask const &task, core::graph::GraphCOP packer_neighbor_graph) const
	Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization. More...

Protected Member Functions inherited from core::pack::rotamer_set::RotamerSet_
void	build_rotamers_for_concrete (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
	Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. More...

void	build_dependent_rotamers_for_concrete (RotamerSets const &rotamer_sets, pose::Pose const &pose, scoring::ScoreFunction const &, task::PackerTask const &task, conformation::Residue const &existing_residue, chemical::ResidueTypeCOP concrete_residue, graph::GraphCOP packer_neighbor_graph)
	Build rotamers of a specific type that depend on positions of rotamers built in a previous pass Use an input "existing residue" which may or may not reflect the coordinates of the residue at pose.residue( resid_ );. More...

void	build_optimize_H_rotamers (pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue)
	Creates a sets of rotamers for an "optimize H" repacking. More...

Private Attributes
ResidueCOP	existing_residue_

FlexbbRotamerSetsCAP	owner_

Detailed Description

Definition at line 34 of file FlexbbRotamerSet.hh.

Member Typedef Documentation

typedef core::pack::rotamer_set::RotamerSet_ protocols::flexpack::rotamer_set::FlexbbRotamerSet::parent

Definition at line 38 of file FlexbbRotamerSet.hh.

Constructor & Destructor Documentation

protocols::flexpack::rotamer_set::FlexbbRotamerSet::FlexbbRotamerSet ( )

Definition at line 32 of file FlexbbRotamerSet.cc.

protocols::flexpack::rotamer_set::FlexbbRotamerSet::~FlexbbRotamerSet ( )

virtual

Definition at line 36 of file FlexbbRotamerSet.cc.

Member Function Documentation

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_dependent_rotamers	(	core::pack::rotamer_set::RotamerSets const &	rotamer_sets,
		core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	scorefxn,
		core::pack::task::PackerTask const &	task,
		core::graph::GraphCOP	packer_neighbor_graph
	)

virtual

Build rotamers that depend on positions of rotamers built in a previous pass This function won't work...

Reimplemented from core::pack::rotamer_set::RotamerSet_.

Definition at line 47 of file FlexbbRotamerSet.cc.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_rotamers_for_concrete_virt	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	scorefxn,
		core::pack::task::PackerTask const &	task,
		core::chemical::ResidueTypeCOP	concrete_residue,
		core::graph::GraphCOP	packer_neighbor_graph,
		bool	use_neighbor_context = `true`
	)

protectedvirtual

Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

Definition at line 66 of file FlexbbRotamerSet.cc.

References core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and existing_residue_.

core::PackerEnergy protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check	(	core::conformation::ResidueCOP	rotamer,
		core::scoring::ScoreFunction const &	sf,
		core::pose::Pose const &	pose,
		core::pack::task::PackerTask const &	task,
		core::graph::GraphCOP	packer_neighbor_graph
	)		const

protectedvirtual

Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

Definition at line 86 of file FlexbbRotamerSet.cc.

References core::scoring::ScoreFunction::bump_check_backbone(), core::scoring::ScoreFunction::bump_check_full(), core::scoring::EMapVector::dot(), owner_, core::pack::task::PackerTask::pack_residue(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), and core::scoring::ScoreFunction::weights().

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_existing_residue ( core::conformation::ResidueCOP residue)

Definition at line 59 of file FlexbbRotamerSet.cc.

References existing_residue_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_owner ( FlexbbRotamerSetsCAP owner)

Definition at line 40 of file FlexbbRotamerSet.cc.

References owner_.