protocols::hybridization::FoldTreeHybridize Class Reference

#include <FoldTreeHybridize.hh>

Inheritance diagram for protocols::hybridization::FoldTreeHybridize:

Public Member Functions
	FoldTreeHybridize ()
	FoldTreeHybridize (core::Size const initial_template_index, utility::vector1< core::pose::PoseOP > const &template_poses, utility::vector1< core::Real > const &template_weights, utility::vector1< protocols::loops::Loops > const &template_chunks, core::fragment::FragSetOP fragments_small_in, core::fragment::FragSetOP fragments_big_in)
void	init ()
void	restore_original_foldtree (core::pose::Pose &pose)
void	setup_foldtree (core::pose::Pose &pose)
numeric::xyzVector< core::Real >	center_of_mass (core::pose::Pose const &pose)
void	translate_virt_to_CoM (core::pose::Pose &pose)
void	get_residue_weights (core::pose::Pose &pose, utility::vector1< core::Real > &wt1, utility::vector1< core::Real > &wt3, utility::vector1< core::Real > &wt9)
void	set_constraint_file (std::string cst_file_in)
void	set_constraint (std::string &cst_in)
void	set_increase_cycles (core::Real increase_cycles_in)
void	set_stage1_1_cycles (core::Size stage1_1_cycles_in)
void	set_stage1_2_cycles (core::Size stage1_2_cycles_in)
void	set_stage1_3_cycles (core::Size stage1_3_cycles_in)
void	set_stage1_4_cycles (core::Size stage1_4_cycles_in)
void	set_add_non_init_chunks (core::Real add_non_init_chunks_in)
void	set_add_hetatm (bool add_hetatm_in, core::Real hetatm_self_cst_weight_in, core::Real hetatm_prot_cst_weight_in)
void	set_frag_1mer_insertion_weight (core::Real frag_1mer_insertion_weight_in)
void	set_small_frag_insertion_weight (core::Real small_frag_insertion_weight_in)
void	set_big_frag_insertion_weight (core::Real big_frag_insertion_weight_in)
void	set_chunk_insertion_weight (core::Real chunk_insertion_weight_in)
void	set_frag_weight_aligned (core::Real frag_weight_aligned_in)
void	set_auto_frag_insertion_weight (bool auto_frag_insertion_weight_in)
void	set_max_registry_shift (core::Size max_registry_shift_in)
void	set_top_n_big_frag (core::Size top_n_big_frag_in)
void	set_top_n_small_frag (core::Size top_n_small_frag_in)
void	set_pairings_file (std::string pairings_file_in)
void	set_sheets (utility::vector1< core::Size > sheets_in)
void	set_random_sheets (utility::vector1< core::Size > random_sheets_in)
void	set_filter_templates (bool filter_templates_in)
void	set_scorefunction (core::scoring::ScoreFunctionOP scorefxn)
void	set_minimize_at_end (bool min_at_end_in)
void	set_minimize_sf (core::scoring::ScoreFunctionOP minscorefxn_in)
void	set_max_insertion (int max_in)
void	set_user_csts (utility::vector1< core::Size > user_csts_in)
void	set_per_residue_controls (utility::vector1< bool > const &residue_sample_template_in, utility::vector1< bool > const &residue_sample_abinitio_in)
void	setup_scorefunctions (core::scoring::ScoreFunctionOP score0, core::scoring::ScoreFunctionOP score1, core::scoring::ScoreFunctionOP score2, core::scoring::ScoreFunctionOP score5, core::scoring::ScoreFunctionOP score3)
void	apply (core::pose::Pose &pose) override
	Main Method. More...
std::string	get_name () const override
	Each derived class must specify its name. The class name. More...
utility::vector1< std::pair< core::Size, core::Size > >	get_strand_pairs ()
std::set< core::Size >	get_pairings_residues ()
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual MoverOP	create ()
MoverCOP	get_self_ptr () const
MoverOP	get_self_ptr ()
MoverCAP	get_self_weak_ptr () const
MoverAP	get_self_weak_ptr ()
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
void	set_type (std::string const &setting)
	Set the 'type' string. More...
std::string	get_type () const
void	type (const std::string &type_in)
	Set the 'type' string. More...
std::string const &	type () const
	Get the set 'type' string. More...
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	set_current_tag (std::string const &new_tag)
std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...
virtual core::Real	last_proposal_density_ratio ()
virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	normalize_template_wts ()
void	auto_frag_insertion_weight (WeightedFragmentTrialMoverOP &frag_1mer_trial_mover, WeightedFragmentTrialMoverOP &small_frag_trial_mover, WeightedFragmentTrialMoverOP &big_frag_trial_mover)
utility::vector1< core::Size >	get_jump_anchors ()
void	add_strand_pairings ()
void	add_strand_pairing (core::scoring::dssp::Pairing const &pairing)
void	filter_templates (std::set< core::Size > const &templates_to_remove)
void	superimpose_strand_pairings_to_templates (core::pose::Pose &pose)
core::Size	map_pdb_info_number (const core::pose::Pose &pose, core::Size pdb_res)
protocols::simple_moves::ClassicFragmentMoverOP	get_pairings_jump_mover ()
protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

Private Attributes
core::Real	increase_cycles_
core::Size	stage1_1_cycles_
core::Size	stage1_2_cycles_
core::Size	stage1_3_cycles_
core::Size	stage1_4_cycles_
core::Real	frag_1mer_insertion_weight_
core::Real	small_frag_insertion_weight_
core::Real	big_frag_insertion_weight_
core::Real	chunk_insertion_weight_
core::Real	add_non_init_chunks_
bool	add_hetatm_
core::Real	hetatm_self_cst_weight_
core::Real	hetatm_prot_cst_weight_
core::Real	frag_weight_aligned_
bool	auto_frag_insertion_weight_
core::Size	max_registry_shift_
core::Size	max_contig_insertion_
std::string	cst_file_
std::string	cst_in_
bool	min_at_end_
bool	realign_domains_
core::Size	initial_template_index_
core::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreFunctionOP	minscorefxn_
utility::vector1< core::Real >	template_wts_
utility::vector1< core::pose::PoseOP >	template_poses_
utility::vector1< protocols::loops::Loops >	template_chunks_
utility::vector1< core::fragment::FragSetOP >	frag_libs_1mer_
utility::vector1< core::fragment::FragSetOP >	frag_libs_small_
utility::vector1< core::fragment::FragSetOP >	frag_libs_big_
protocols::loops::Loops	ss_chunks_pose_
core::Size	top_n_big_frag_
core::Size	top_n_small_frag_
core::Real	temp_stage1_
std::string	pairings_file_
utility::vector1< core::Size >	sheets_
utility::vector1< core::Size >	random_sheets_
bool	filter_templates_
std::string	target_sequence_
utility::vector1< std::pair< core::Size, core::Size > >	strand_pairs_
std::set< core::Size >	strand_pairings_template_indices_
std::set< core::Size >	templates_with_incorrect_strand_pairings_
protocols::jumping::JumpSample	jump_sample_
core::fragment::FragSetOP	jump_frags_
std::set< core::Size >	floating_pairs_
bool	overlap_chainbreaks_
HybridizeFoldtreeDynamic	foldtree_mover_
core::pose::PoseOP	native_
utility::vector1< bool >	residue_sample_template_
utility::vector1< bool >	residue_sample_abinitio_
utility::vector1< core::Size >	user_csts_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef std::list< std::string >	Strings
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	Overload this static method if you access options within the mover. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

FoldTreeHybridize() [1/2]

protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize

(

)

References init().

FoldTreeHybridize() [2/2]

protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize	(	core::Size const	initial_template_index,
		utility::vector1< core::pose::PoseOP > const &	template_poses,
		utility::vector1< core::Real > const &	template_weights,
		utility::vector1< protocols::loops::Loops > const &	template_chunks,
		core::fragment::FragSetOP	fragments_small_in,
		core::fragment::FragSetOP	fragments_big_in
	)

References core::fragment::chop_fragments(), frag_libs_1mer_, frag_libs_big_, frag_libs_small_, init(), initial_template_index_, normalize_template_wts(), template_chunks_, template_poses_, and template_wts_.

Member Function Documentation

add_strand_pairing()

void protocols::hybridization::FoldTreeHybridize::add_strand_pairing ( core::scoring::dssp::Pairing const &  pairing )

private

References protocols::pose_creation::ExtendedPoseMover::apply(), core::pose::create_subpose(), protocols::loops::extract_continuous_chunks(), protocols::jumping::JumpSample::fold_tree(), get_pairings_jump_mover(), jump_sample_, core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), protocols::loops::Loops::push_back(), strand_pairings_template_indices_, target_sequence_, template_chunks_, template_poses_, template_wts_, protocols::hybridization::TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by add_strand_pairings().

add_strand_pairings()

void protocols::hybridization::FoldTreeHybridize::add_strand_pairings ( )

private

References add_strand_pairing(), filter_templates(), filter_templates_, frag_libs_small_, protocols::jumping::JumpSample::get_pairing(), protocols::loops::Loops::has(), core::scoring::dssp::StrandPairingSet::has_pairing(), protocols::jumping::JumpSample::is_valid(), jump_frags_, jump_sample_, protocols::jumping::JumpSample::jumps(), pairings_file_, core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), random_sheets_, core::scoring::dssp::read_pairing_list(), protocols::hybridization::renumber_with_pdb_info(), sheets_, protocols::jumping::JumpSample::size(), template_chunks_, template_poses_, templates_with_incorrect_strand_pairings_, and protocols::hybridization::TR().

Referenced by apply().

apply()

void protocols::hybridization::FoldTreeHybridize::apply ( core::pose::Pose &  )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::moves::accept_reject, add_hetatm_, protocols::loops::Loops::add_loop(), protocols::hybridization::add_non_protein_cst(), add_strand_pairings(), protocols::hybridization::all_chunks, protocols::hybridization::ChunkTrialMover::apply(), protocols::moves::RepeatMover::apply(), protocols::moves::WhileMover::apply(), core::scoring::atom_pair_constraint, auto_frag_insertion_weight(), big_frag_insertion_weight_, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::scoring::coordinate_constraint, cst_file_, core::chemical::element::F, floating_pairs_, frag_1mer_insertion_weight_, frag_libs_1mer_, frag_libs_big_, frag_libs_small_, protocols::hybridization::get_gdtmm(), get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), get_pairings_jump_mover(), get_pairings_residues(), get_residue_weights(), core::conformation::Residue::has(), protocols::hybridization::ChunkTrialMover::has_valid_moves(), hetatm_prot_cst_weight_, hetatm_self_cst_weight_, core::chemical::element::I, increase_cycles_, initial_template_index_, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, core::pose::symmetry::make_symmetric_movemap(), max_contig_insertion_, max_registry_shift_, min_at_end_, minscorefxn_, core::scoring::name_from_score_type(), native_, core::scoring::overlap_chainbreak, overlap_chainbreaks_, protocols::hybridization::random_chunk, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), residue_sample_abinitio_, residue_sample_template_, restore_original_foldtree(), core::scoring::rg, core::optimization::AtomTreeMinimizer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), scorefxn_, core::pose::Pose::sequence(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::hybridization::ChunkTrialMover::set_template(), core::pose::setPoseExtraScore(), protocols::hybridization::setup_centroid_constraints(), setup_foldtree(), setup_scorefunctions(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::hybridization::AllResiduesChanged::show_unmoved(), core::pose::Pose::size(), small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, strand_pairings_template_indices_, superimpose_strand_pairings_to_templates(), target_sequence_, temp_stage1_, template_chunks_, template_poses_, template_wts_, top_n_big_frag_, protocols::hybridization::TR(), translate_virt_to_CoM(), and user_csts_.

auto_frag_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight ( WeightedFragmentTrialMoverOP &  frag_1mer_trial_mover, WeightedFragmentTrialMoverOP &  small_frag_trial_mover, WeightedFragmentTrialMoverOP &  big_frag_trial_mover  )

private

References auto_frag_insertion_weight_, big_frag_insertion_weight_, chunk_insertion_weight_, core::chemical::element::F, frag_1mer_insertion_weight_, small_frag_insertion_weight_, strand_pairings_template_indices_, core::simple_metrics::metrics::sum, template_chunks_, top_n_big_frag_, top_n_small_frag_, and protocols::hybridization::TR().

Referenced by apply().

center_of_mass()

numeric::xyzVector< Real > protocols::hybridization::FoldTreeHybridize::center_of_mass

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by translate_virt_to_CoM().

clone()

protocols::moves::MoverOP protocols::hybridization::FoldTreeHybridize::clone ( ) const

overrideprivatevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

filter_templates()

void protocols::hybridization::FoldTreeHybridize::filter_templates ( std::set< core::Size > const &  templates_to_remove )

private

References initial_template_index_, normalize_template_wts(), template_chunks_, template_poses_, template_wts_, and protocols::hybridization::TR().

Referenced by add_strand_pairings().

fresh_instance()

protocols::moves::MoverOP protocols::hybridization::FoldTreeHybridize::fresh_instance ( ) const

overrideprivatevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

get_jump_anchors()

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::get_jump_anchors ( )

private

References foldtree_mover_, protocols::hybridization::HybridizeFoldtreeDynamic::get_anchors(), and get_pairings_residues().

Referenced by apply(), and get_residue_weights().

get_name()

std::string protocols::hybridization::FoldTreeHybridize::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

get_pairings_jump_mover()

protocols::simple_moves::ClassicFragmentMoverOP protocols::hybridization::FoldTreeHybridize::get_pairings_jump_mover ( )

private

References jump_frags_.

Referenced by add_strand_pairing(), and apply().

get_pairings_residues()

std::set< core::Size > protocols::hybridization::FoldTreeHybridize::get_pairings_residues

(

)

References strand_pairs_.

Referenced by apply(), and get_jump_anchors().

get_residue_weights()

void protocols::hybridization::FoldTreeHybridize::get_residue_weights	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > &	wt1,
		utility::vector1< core::Real > &	wt3,
		utility::vector1< core::Real > &	wt9
	)

References frag_libs_big_, frag_libs_small_, frag_weight_aligned_, get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), initial_template_index_, residue_sample_abinitio_, template_poses_, and protocols::hybridization::TR().

Referenced by apply().

get_strand_pairs()

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::FoldTreeHybridize::get_strand_pairs ( )

inline

References strand_pairs_.

init()

void protocols::hybridization::FoldTreeHybridize::init

(

void

)

References add_hetatm_, add_non_init_chunks_, auto_frag_insertion_weight_, big_frag_insertion_weight_, chunk_insertion_weight_, core::scoring::ScoreFunctionFactory::create_score_function(), filter_templates_, frag_1mer_insertion_weight_, frag_weight_aligned_, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, increase_cycles_, max_contig_insertion_, max_registry_shift_, min_at_end_, native_, core::scoring::overlap_chainbreak, overlap_chainbreaks_, pairings_file_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), random_sheets_, realign_domains_, set_minimize_sf(), set_scorefunction(), sheets_, small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, temp_stage1_, top_n_big_frag_, and top_n_small_frag_.

Referenced by FoldTreeHybridize().

map_pdb_info_number()

core::Size protocols::hybridization::FoldTreeHybridize::map_pdb_info_number ( const core::pose::Pose &  pose, core::Size  pdb_res  )

private

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by superimpose_strand_pairings_to_templates().

normalize_template_wts()

void protocols::hybridization::FoldTreeHybridize::normalize_template_wts ( )

private

References template_poses_, and template_wts_.

Referenced by filter_templates(), and FoldTreeHybridize().

restore_original_foldtree()

void protocols::hybridization::FoldTreeHybridize::restore_original_foldtree

(

core::pose::Pose &

pose

)

References foldtree_mover_, and protocols::hybridization::HybridizeFoldtreeDynamic::reset().

Referenced by apply().

set_add_hetatm()

void protocols::hybridization::FoldTreeHybridize::set_add_hetatm ( bool  add_hetatm_in, core::Real  hetatm_self_cst_weight_in, core::Real  hetatm_prot_cst_weight_in  )

inline

References add_hetatm_, hetatm_prot_cst_weight_, and hetatm_self_cst_weight_.

set_add_non_init_chunks()

void protocols::hybridization::FoldTreeHybridize::set_add_non_init_chunks ( core::Real  add_non_init_chunks_in )

inline

References add_non_init_chunks_.

set_auto_frag_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::set_auto_frag_insertion_weight ( bool  auto_frag_insertion_weight_in )

inline

References auto_frag_insertion_weight_.

set_big_frag_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::set_big_frag_insertion_weight ( core::Real  big_frag_insertion_weight_in )

inline

References big_frag_insertion_weight_.

set_chunk_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::set_chunk_insertion_weight ( core::Real  chunk_insertion_weight_in )

inline

References chunk_insertion_weight_.

set_constraint()

void protocols::hybridization::FoldTreeHybridize::set_constraint ( std::string &  cst_in )

inline

References cst_in_.

set_constraint_file()

void protocols::hybridization::FoldTreeHybridize::set_constraint_file ( std::string  cst_file_in )

inline

References cst_file_.

set_filter_templates()

void protocols::hybridization::FoldTreeHybridize::set_filter_templates ( bool  filter_templates_in )

inline

References filter_templates_.

set_frag_1mer_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::set_frag_1mer_insertion_weight ( core::Real  frag_1mer_insertion_weight_in )

inline

References frag_1mer_insertion_weight_.

set_frag_weight_aligned()

void protocols::hybridization::FoldTreeHybridize::set_frag_weight_aligned ( core::Real  frag_weight_aligned_in )

inline

References frag_weight_aligned_.

set_increase_cycles()

void protocols::hybridization::FoldTreeHybridize::set_increase_cycles ( core::Real  increase_cycles_in )

inline

References increase_cycles_.

set_max_insertion()

void protocols::hybridization::FoldTreeHybridize::set_max_insertion ( int  max_in )

inline

References max_contig_insertion_.

set_max_registry_shift()

void protocols::hybridization::FoldTreeHybridize::set_max_registry_shift ( core::Size  max_registry_shift_in )

inline

References max_registry_shift_.

set_minimize_at_end()

void protocols::hybridization::FoldTreeHybridize::set_minimize_at_end ( bool  min_at_end_in )

inline

References min_at_end_.

set_minimize_sf()

void protocols::hybridization::FoldTreeHybridize::set_minimize_sf ( core::scoring::ScoreFunctionOP  minscorefxn_in )

inline

References minscorefxn_.

Referenced by init().

set_pairings_file()

void protocols::hybridization::FoldTreeHybridize::set_pairings_file ( std::string  pairings_file_in )

inline

References pairings_file_.

set_per_residue_controls()

void protocols::hybridization::FoldTreeHybridize::set_per_residue_controls ( utility::vector1< bool > const &  residue_sample_template_in, utility::vector1< bool > const &  residue_sample_abinitio_in  )

inline

References residue_sample_abinitio_, and residue_sample_template_.

set_random_sheets()

void protocols::hybridization::FoldTreeHybridize::set_random_sheets ( utility::vector1< core::Size >  random_sheets_in )

inline

References random_sheets_.

set_scorefunction()

void protocols::hybridization::FoldTreeHybridize::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn )

inline

References scorefxn_.

Referenced by init().

set_sheets()

void protocols::hybridization::FoldTreeHybridize::set_sheets ( utility::vector1< core::Size >  sheets_in )

inline

References sheets_.

set_small_frag_insertion_weight()

void protocols::hybridization::FoldTreeHybridize::set_small_frag_insertion_weight ( core::Real  small_frag_insertion_weight_in )

inline

References small_frag_insertion_weight_.

set_stage1_1_cycles()

void protocols::hybridization::FoldTreeHybridize::set_stage1_1_cycles ( core::Size  stage1_1_cycles_in )

inline

References stage1_1_cycles_.

set_stage1_2_cycles()

void protocols::hybridization::FoldTreeHybridize::set_stage1_2_cycles ( core::Size  stage1_2_cycles_in )

inline

References stage1_2_cycles_.

set_stage1_3_cycles()

void protocols::hybridization::FoldTreeHybridize::set_stage1_3_cycles ( core::Size  stage1_3_cycles_in )

inline

References stage1_3_cycles_.

set_stage1_4_cycles()

void protocols::hybridization::FoldTreeHybridize::set_stage1_4_cycles ( core::Size  stage1_4_cycles_in )

inline

References stage1_4_cycles_.

set_top_n_big_frag()

void protocols::hybridization::FoldTreeHybridize::set_top_n_big_frag ( core::Size  top_n_big_frag_in )

inline

References top_n_big_frag_.

set_top_n_small_frag()

void protocols::hybridization::FoldTreeHybridize::set_top_n_small_frag ( core::Size  top_n_small_frag_in )

inline

References top_n_small_frag_.

set_user_csts()

void protocols::hybridization::FoldTreeHybridize::set_user_csts ( utility::vector1< core::Size >  user_csts_in )

inline

References user_csts_.

setup_foldtree()

void protocols::hybridization::FoldTreeHybridize::setup_foldtree

(

core::pose::Pose &

pose

)

References protocols::loops::Loops::add_loop(), add_non_init_chunks_, core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), foldtree_mover_, frag_libs_small_, protocols::hybridization::get_num_residues_nonvirt(), initial_template_index_, protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::pose::symmetry::is_symmetric(), core::scoring::rg, core::pose::Pose::secstruct(), protocols::loops::Loops::sequential_order(), core::pose::Pose::set_secstruct(), protocols::loops::set_secstruct_from_psipred_ss2(), protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, strand_pairings_template_indices_, strand_pairs_, template_chunks_, template_poses_, and protocols::hybridization::TR().

Referenced by apply().

setup_scorefunctions()

void protocols::hybridization::FoldTreeHybridize::setup_scorefunctions	(	core::scoring::ScoreFunctionOP	score0,
		core::scoring::ScoreFunctionOP	score1,
		core::scoring::ScoreFunctionOP	score2,
		core::scoring::ScoreFunctionOP	score5,
		core::scoring::ScoreFunctionOP	score3
	)

References core::scoring::atom_pair_constraint, core::scoring::cbeta, core::scoring::cbeta_smooth, core::scoring::cen_env_smooth, core::scoring::cen_pair_smooth, core::scoring::cenpack, core::scoring::cenpack_smooth, core::scoring::coordinate_constraint, core::scoring::elec_dens_fast, core::scoring::env, core::scoring::hs_pair, core::scoring::linear_chainbreak, core::scoring::pair, scorefxn_, core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights(), core::scoring::sheet, core::scoring::ss_pair, and core::scoring::vdw.

Referenced by apply().

superimpose_strand_pairings_to_templates()

void protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates ( core::pose::Pose &  pose )

private

References core::kinematics::FoldTree::begin(), core::id::AtomID::BOGUS_ATOM_ID(), core::kinematics::FoldTree::end(), core::chemical::element::F, floating_pairs_, core::pose::Pose::fold_tree(), initial_template_index_, core::pose::initialize_atomid_map(), map_pdb_info_number(), core::scoring::rg, core::scoring::rms, core::kinematics::FoldTree::root(), strand_pairings_template_indices_, core::scoring::superimpose_pose(), template_poses_, templates_with_incorrect_strand_pairings_, and protocols::hybridization::TR().

Referenced by apply().

translate_virt_to_CoM()

void protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM

(

core::pose::Pose &

pose

)

References core::pose::Pose::batch_set_xyz(), center_of_mass(), core::chemical::element::F, core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::hybridization::TR(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by apply().

Member Data Documentation

add_hetatm_

bool protocols::hybridization::FoldTreeHybridize::add_hetatm_

private

Referenced by apply(), init(), and set_add_hetatm().

add_non_init_chunks_

core::Real protocols::hybridization::FoldTreeHybridize::add_non_init_chunks_

private

Referenced by init(), set_add_non_init_chunks(), and setup_foldtree().

auto_frag_insertion_weight_

bool protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight_

private

Referenced by auto_frag_insertion_weight(), init(), and set_auto_frag_insertion_weight().

big_frag_insertion_weight_

core::Real protocols::hybridization::FoldTreeHybridize::big_frag_insertion_weight_

private

Referenced by apply(), auto_frag_insertion_weight(), init(), and set_big_frag_insertion_weight().

chunk_insertion_weight_

core::Real protocols::hybridization::FoldTreeHybridize::chunk_insertion_weight_

private

Referenced by auto_frag_insertion_weight(), init(), and set_chunk_insertion_weight().

cst_file_

std::string protocols::hybridization::FoldTreeHybridize::cst_file_

private

Referenced by apply(), and set_constraint_file().

cst_in_

std::string protocols::hybridization::FoldTreeHybridize::cst_in_

private

Referenced by set_constraint().

filter_templates_

bool protocols::hybridization::FoldTreeHybridize::filter_templates_

private

Referenced by add_strand_pairings(), init(), and set_filter_templates().

floating_pairs_

std::set< core::Size > protocols::hybridization::FoldTreeHybridize::floating_pairs_

private

Referenced by apply(), and superimpose_strand_pairings_to_templates().

foldtree_mover_

HybridizeFoldtreeDynamic protocols::hybridization::FoldTreeHybridize::foldtree_mover_

private

Referenced by get_jump_anchors(), restore_original_foldtree(), and setup_foldtree().

frag_1mer_insertion_weight_

core::Real protocols::hybridization::FoldTreeHybridize::frag_1mer_insertion_weight_

private

Referenced by apply(), auto_frag_insertion_weight(), init(), and set_frag_1mer_insertion_weight().

frag_libs_1mer_

utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_1mer_

private

Referenced by apply(), and FoldTreeHybridize().

frag_libs_big_

utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_big_

private

Referenced by apply(), FoldTreeHybridize(), and get_residue_weights().

frag_libs_small_

utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_small_

private

Referenced by add_strand_pairings(), apply(), FoldTreeHybridize(), get_residue_weights(), and setup_foldtree().

frag_weight_aligned_

core::Real protocols::hybridization::FoldTreeHybridize::frag_weight_aligned_

private

Referenced by get_residue_weights(), init(), and set_frag_weight_aligned().

hetatm_prot_cst_weight_

core::Real protocols::hybridization::FoldTreeHybridize::hetatm_prot_cst_weight_

private

Referenced by apply(), init(), and set_add_hetatm().

hetatm_self_cst_weight_

core::Real protocols::hybridization::FoldTreeHybridize::hetatm_self_cst_weight_

private

Referenced by apply(), init(), and set_add_hetatm().

increase_cycles_

core::Real protocols::hybridization::FoldTreeHybridize::increase_cycles_

private

Referenced by apply(), init(), and set_increase_cycles().

initial_template_index_

core::Size protocols::hybridization::FoldTreeHybridize::initial_template_index_

private

Referenced by apply(), filter_templates(), FoldTreeHybridize(), get_residue_weights(), setup_foldtree(), and superimpose_strand_pairings_to_templates().

jump_frags_

core::fragment::FragSetOP protocols::hybridization::FoldTreeHybridize::jump_frags_

private

Referenced by add_strand_pairings(), and get_pairings_jump_mover().

jump_sample_

protocols::jumping::JumpSample protocols::hybridization::FoldTreeHybridize::jump_sample_

private

Referenced by add_strand_pairing(), and add_strand_pairings().

max_contig_insertion_

core::Size protocols::hybridization::FoldTreeHybridize::max_contig_insertion_

private

Referenced by apply(), init(), and set_max_insertion().

max_registry_shift_

core::Size protocols::hybridization::FoldTreeHybridize::max_registry_shift_

private

Referenced by apply(), init(), and set_max_registry_shift().

min_at_end_

bool protocols::hybridization::FoldTreeHybridize::min_at_end_

private

Referenced by apply(), init(), and set_minimize_at_end().

minscorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::FoldTreeHybridize::minscorefxn_

private

Referenced by apply(), and set_minimize_sf().

native_

core::pose::PoseOP protocols::hybridization::FoldTreeHybridize::native_

private

Referenced by apply(), and init().

overlap_chainbreaks_

bool protocols::hybridization::FoldTreeHybridize::overlap_chainbreaks_

private

Referenced by apply(), and init().

pairings_file_

std::string protocols::hybridization::FoldTreeHybridize::pairings_file_

private

Referenced by add_strand_pairings(), init(), and set_pairings_file().

random_sheets_

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::random_sheets_

private

Referenced by add_strand_pairings(), init(), and set_random_sheets().

realign_domains_

bool protocols::hybridization::FoldTreeHybridize::realign_domains_

private

Referenced by init().

residue_sample_abinitio_

utility::vector1<bool> protocols::hybridization::FoldTreeHybridize::residue_sample_abinitio_

private

Referenced by apply(), get_residue_weights(), and set_per_residue_controls().

residue_sample_template_

utility::vector1<bool> protocols::hybridization::FoldTreeHybridize::residue_sample_template_

private

Referenced by apply(), and set_per_residue_controls().

scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::FoldTreeHybridize::scorefxn_

private

Referenced by apply(), set_scorefunction(), and setup_scorefunctions().

sheets_

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::sheets_

private

Referenced by add_strand_pairings(), init(), and set_sheets().

small_frag_insertion_weight_

core::Real protocols::hybridization::FoldTreeHybridize::small_frag_insertion_weight_

private

Referenced by apply(), auto_frag_insertion_weight(), init(), and set_small_frag_insertion_weight().

ss_chunks_pose_

protocols::loops::Loops protocols::hybridization::FoldTreeHybridize::ss_chunks_pose_

private

stage1_1_cycles_

core::Size protocols::hybridization::FoldTreeHybridize::stage1_1_cycles_

private

Referenced by apply(), init(), and set_stage1_1_cycles().

stage1_2_cycles_

core::Size protocols::hybridization::FoldTreeHybridize::stage1_2_cycles_

private

Referenced by apply(), init(), and set_stage1_2_cycles().

stage1_3_cycles_

core::Size protocols::hybridization::FoldTreeHybridize::stage1_3_cycles_

private

Referenced by apply(), init(), and set_stage1_3_cycles().

stage1_4_cycles_

core::Size protocols::hybridization::FoldTreeHybridize::stage1_4_cycles_

private

Referenced by apply(), init(), and set_stage1_4_cycles().

strand_pairings_template_indices_

std::set< core::Size > protocols::hybridization::FoldTreeHybridize::strand_pairings_template_indices_

private

Referenced by add_strand_pairing(), apply(), auto_frag_insertion_weight(), setup_foldtree(), and superimpose_strand_pairings_to_templates().

strand_pairs_

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::FoldTreeHybridize::strand_pairs_

private

Referenced by get_pairings_residues(), get_strand_pairs(), and setup_foldtree().

target_sequence_

std::string protocols::hybridization::FoldTreeHybridize::target_sequence_

private

Referenced by add_strand_pairing(), and apply().

temp_stage1_

core::Real protocols::hybridization::FoldTreeHybridize::temp_stage1_

private

Referenced by apply(), and init().

template_chunks_

utility::vector1< protocols::loops::Loops > protocols::hybridization::FoldTreeHybridize::template_chunks_

private

Referenced by add_strand_pairing(), add_strand_pairings(), apply(), auto_frag_insertion_weight(), filter_templates(), FoldTreeHybridize(), and setup_foldtree().

template_poses_

utility::vector1< core::pose::PoseOP > protocols::hybridization::FoldTreeHybridize::template_poses_

private

Referenced by add_strand_pairing(), add_strand_pairings(), apply(), filter_templates(), FoldTreeHybridize(), get_residue_weights(), normalize_template_wts(), setup_foldtree(), and superimpose_strand_pairings_to_templates().

template_wts_

utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::template_wts_

private

Referenced by add_strand_pairing(), apply(), filter_templates(), FoldTreeHybridize(), and normalize_template_wts().

templates_with_incorrect_strand_pairings_

std::set< core::Size > protocols::hybridization::FoldTreeHybridize::templates_with_incorrect_strand_pairings_

private

Referenced by add_strand_pairings(), and superimpose_strand_pairings_to_templates().

top_n_big_frag_

core::Size protocols::hybridization::FoldTreeHybridize::top_n_big_frag_

private

Referenced by apply(), auto_frag_insertion_weight(), init(), and set_top_n_big_frag().

top_n_small_frag_

core::Size protocols::hybridization::FoldTreeHybridize::top_n_small_frag_

private

Referenced by auto_frag_insertion_weight(), init(), and set_top_n_small_frag().

user_csts_

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::user_csts_

private

Referenced by apply(), and set_user_csts().

---

The documentation for this class was generated from the following files:

• src/protocols/hybridization/FoldTreeHybridize.hh
• src/protocols/hybridization/FoldTreeHybridize.cc