protocols::hybridization::FoldTreeHybridize Class Reference

#include <FoldTreeHybridize.hh>

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, utility::vector1< protocols::loops::Loops > const &template_contigs, core::fragment::FragSetOP fragments_small_in, core::fragment::FragSetOP fragments_big_in)
void	init ()
void	setup_for_parser ()
	Extract information from a setup mover. More...
void	revert_loops_to_original (core::pose::Pose &pose, Loops loops)
void	set_loops_to_virt_ala (core::pose::Pose &pose, Loops loops)
Real	gap_distance (Size Seq_gap)
void	add_gap_constraints_to_pose (core::pose::Pose &pose, Loops const &chunks, int gap_edge_shift=0, Real stdev=0.1)
void	restore_original_foldtree (core::pose::Pose &pose)
void	setup_foldtree (core::pose::Pose &pose)
numeric::xyzVector< Real >	center_of_mass (core::pose::Pose const &pose)
void	translate_virt_to_CoM (core::pose::Pose &pose)
utility::vector1< core::Real >	get_residue_weights_for_1mers (core::pose::Pose &pose)
utility::vector1< core::Real >	get_residue_weights_for_small_frags (core::pose::Pose &pose)
utility::vector1< core::Real >	get_residue_weights_for_big_frags (core::pose::Pose &pose)
void	set_constraint_file (std::string cst_file_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 (bool add_non_init_chunks_in)
void	set_domain_assembly (bool domain_assembly_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 const scorefxn)
void	set_task_factory (core::pack::task::TaskFactoryOP task_factory_in)
void	set_user_csts (utility::vector1< core::Size > user_csts_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)
std::string	get_name () const
	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	~Mover ()
virtual MoverSP	create ()
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	parse_state (SerializableState const &state)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void	save_state (SerializableState &state)
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
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...
void	set_current_tag (std::string const &new_tag)
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	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...
void	type (const std::string &type_in)
std::string	get_type () const
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...
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 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...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 ()
virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
virtual void	parse_my_tag (utility::tag::TagCOP const, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Private Attributes
HybridizeSetupOP	hybridize_setup_
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_
bool	add_non_init_chunks_
bool	domain_assembly_
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_
std::string	cst_file_
bool	initialize_pose_by_templates_
bool	realign_domains_
core::Size	initial_template_index_
core::scoring::ScoreFunctionOP	scorefxn_
utility::vector1< core::Real >	template_wts_
utility::vector1 < core::pose::PoseOP >	template_poses_
utility::vector1 < protocols::loops::Loops >	template_chunks_
utility::vector1 < protocols::loops::Loops >	template_contigs_
utility::vector1 < core::fragment::FragSetOP >	frag_libs_1mer_
utility::vector1 < core::fragment::FragSetOP >	frag_libs_small_
utility::vector1 < core::fragment::FragSetOP >	frag_libs_big_
Loops	ss_chunks_pose_
core::Size	top_n_big_frag_
core::Size	top_n_small_frag_
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 >	residue_max_registry_shift_
core::pack::task::TaskFactoryOP	task_factory_
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 protocols::filters::Filters_map	Filters_map
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

protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize

(

)

References init().

Referenced by clone(), protocols::hybridization::FoldTreeHybridizeCreator::create_mover(), and fresh_instance().

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,
		utility::vector1< protocols::loops::Loops > const &	template_contigs,
		core::fragment::FragSetOP	fragments_small_in,
		core::fragment::FragSetOP	fragments_big_in
	)

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

Member Function Documentation

void protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose	(	core::pose::Pose &	pose,
		Loops const &	chunks,
		int	gap_edge_shift = 0,
		Real	stdev = 0.1
	)

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), gap_distance(), protocols::abinitio::abscript::I, core::chemical::ResidueType::is_protein(), protocols::loops::Loops::num_loop(), core::pose::Pose::residue_type(), and protocols::hybridization::TR.

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

private

References protocols::simple_moves::ExtendedPoseMover::apply(), protocols::simple_moves::FragmentMover::apply_at_all_positions(), core::pose::create_subpose(), protocols::loops::extract_continuous_chunks(), core::pose::Pose::fold_tree(), protocols::jumping::JumpSample::fold_tree(), get_pairings_jump_mover(), jump_sample_, jumps, core::pose::Pose::pdb_info(), core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), protocols::loops::Loops::push_back(), core::pose::Pose::set_secstruct(), strand_pairings_template_indices_, target_sequence_, template_chunks_, template_contigs_, template_poses_, template_wts_, core::pose::Pose::total_residue(), protocols::hybridization::TR, and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by 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_, jumps, protocols::jumping::JumpSample::jumps(), movemap, pairings, pairings_file_, core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), random_sheets_, protocols::jumping::read_pairing_list(), protocols::hybridization::renumber_with_pdb_info(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), sheets_, protocols::jumping::JumpSample::size(), template_chunks_, template_poses_, templates_with_incorrect_strand_pairings_, protocols::hybridization::TR, and utility_exit_with_message.

Referenced by apply().

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

virtual

Implements protocols::moves::Mover.

References protocols::moves::accept_reject, add_hetatm_, protocols::moves::MoverContainer::add_mover(), protocols::hybridization::add_non_protein_cst(), add_strand_pairings(), protocols::hybridization::all_chunks, protocols::moves::RepeatMover::apply(), protocols::moves::WhileMover::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::moves::Mover::apply(), protocols::moves::RandomMover::apply(), protocols::simple_moves::FragmentMover::apply_at_all_positions(), core::scoring::atom_pair_constraint, auto_frag_insertion_weight(), big_frag_insertion_weight_, core::chemical::CENTROID_ROT, core::scoring::ScoreFunction::clone(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), cst_file_, floating_pairs_, frag_1mer_insertion_weight_, frag_libs_1mer_, frag_libs_big_, frag_libs_small_, gdtmm, protocols::hybridization::get_gdtmm(), get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), get_pairings_jump_mover(), get_pairings_residues(), get_residue_weights_for_1mers(), get_residue_weights_for_big_frags(), get_residue_weights_for_small_frags(), core::conformation::Residue::has(), hetatm_prot_cst_weight_, hetatm_self_cst_weight_, hybridize_setup_, protocols::abinitio::abscript::I, jumps::increase_chainbreak, increase_cycles_, initial_template_index_, initialize_pose_by_templates_, jumps::invrate_jump_move, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), protocols::moves::TrialMover::keep_stats_type(), core::scoring::linear_chainbreak, max_registry_shift_, numeric::mod(), native_, option, core::scoring::overlap_chainbreak, protocols::forge::methods::overlap_chainbreak(), overlap_chainbreaks_, pack_rotamers(), core::pack::task::TaskFactory::push_back(), protocols::hybridization::random_chunk, protocols::moves::MonteCarlo::recover_low(), core::pose::Pose::remove_constraints(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), residue_max_registry_shift_, residue_sample_abinitio_, residue_sample_template_, restore_original_foldtree(), protocols::moves::MonteCarlo::score_function(), scorefxn_, core::pose::Pose::sequence(), protocols::moves::MonteCarlo::set_autotemp(), protocols::moves::MonteCarlo::set_temperature(), protocols::hybridization::ChunkTrialMover::set_template(), core::pose::setPoseExtraScores(), protocols::hybridization::setup_centroid_constraints(), setup_foldtree(), setup_for_parser(), setup_scorefunctions(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::moves::MonteCarlo::show_counters(), protocols::moves::MonteCarlo::show_scores(), protocols::hybridization::AllResiduesChanged::show_unmoved(), abinitio::skip_convergence_check, small_frag_insertion_weight_, ss_chunks_pose_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, cm::hybridize::stage1_4_cenrot_score, stage1_4_cycles_, strand_pairings_template_indices_, superimpose_strand_pairings_to_templates(), target_sequence_, template_chunks_, template_poses_, template_wts_, top_n_big_frag_, core::pose::Pose::total_residue(), protocols::hybridization::TR, translate_virt_to_CoM(), user, and user_csts_.

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_, frag_1mer_insertion_weight_, small_frag_insertion_weight_, strand_pairings_template_indices_, sum(), template_chunks_, top_n_big_frag_, top_n_small_frag_, and protocols::hybridization::TR.

Referenced by apply().

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

(

core::pose::Pose const &

pose

)

References core::chemical::aa_vrt, j, nres, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

Referenced by translate_virt_to_CoM().

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

privatevirtual

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.

References FoldTreeHybridize().

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_contigs_, template_poses_, template_wts_, and protocols::hybridization::TR.

Referenced by add_strand_pairings().

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

privatevirtual

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.

References FoldTreeHybridize().

Real protocols::hybridization::FoldTreeHybridize::gap_distance

(

Size

Seq_gap

)

Referenced by add_gap_constraints_to_pose().

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(), get_residue_weights_for_1mers(), and get_residue_weights_for_small_frags().

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

virtual

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

Implements protocols::moves::Mover.

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

private

References protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), jump_frags_, movemap, core::kinematics::MoveMap::set_bb(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), core::kinematics::MoveMap::set_jump(), and protocols::moves::Mover::type().

Referenced by add_strand_pairing(), and apply().

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

(

)

References strand_pairs_.

Referenced by apply(), and get_jump_anchors().

utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_1mers

(

core::pose::Pose &

pose

)

References frag_libs_small_, get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), get_residue_weights_for_big_frags(), residue_sample_abinitio_, and protocols::hybridization::TR.

Referenced by apply().

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

(

core::pose::Pose &

pose

)

References domain_assembly_, frag_weight_aligned_, protocols::hybridization::get_num_residues_nonvirt(), protocols::loops::Loops::has(), initial_template_index_, protocols::hybridization::renumber_with_pdb_info(), residue_sample_abinitio_, template_contigs_, template_poses_, and protocols::hybridization::TR.

Referenced by apply(), get_residue_weights_for_1mers(), and get_residue_weights_for_small_frags().

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

(

core::pose::Pose &

pose

)

References frag_libs_big_, get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), get_residue_weights_for_big_frags(), residue_sample_abinitio_, and protocols::hybridization::TR.

Referenced by apply().

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

inline

void protocols::hybridization::FoldTreeHybridize::init

(

void

)

References add_hetatm_, cm::hybridize::add_non_init_chunks, add_non_init_chunks_, evaluation::align_rmsd_target, align_rmsd_target, cm::hybridize::auto_frag_insertion_weight, auto_frag_insertion_weight_, big_frag_insertion_weight_, chunk_insertion_weight_, core::scoring::ScoreFunctionFactory::create_score_function(), domain_assembly_, filter_templates_, frag_1mer_insertion_weight_, cm::hybridize::frag_weight_aligned, frag_weight_aligned_, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, increase_cycles_, initialize_pose_by_templates_, cm::hybridize::max_registry_shift, max_registry_shift_, in::file::native, native_, option, jumps::overlap_chainbreak, overlap_chainbreaks_, pairings_file_, core::import_pose::pose_from_pdb(), random_sheets_, realign_domains_, set_scorefunction(), sheets_, small_frag_insertion_weight_, cm::hybridize::stage1_1_cycles, stage1_1_cycles_, cm::hybridize::stage1_2_cycles, stage1_2_cycles_, cm::hybridize::stage1_3_cycles, stage1_3_cycles_, cm::hybridize::stage1_4_cycles, stage1_4_cycles_, cm::hybridize::stage1_increase_cycles, top_n_big_frag_, top_n_small_frag_, and user.

Referenced by FoldTreeHybridize().

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::total_residue().

Referenced by superimpose_strand_pairings_to_templates().

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

private

References template_poses_, and template_wts_.

Referenced by filter_templates(), FoldTreeHybridize(), and setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::parse_my_tag ( utility::tag::TagCOP const  tag, basic::datacache::DataMap &  data, filters::Filters_map const &  filters, moves::Movers_map const &  movers, Pose const &  pose  )

privatevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References add_non_init_chunks_, auto_frag_insertion_weight_, core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::ResidueLevelTask::being_packed(), big_frag_insertion_weight_, core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), filter_templates_, frag_1mer_insertion_weight_, frag_weight_aligned_, basic::datacache::DataMap::get(), hybridize_setup_, initialize_pose_by_templates_, max_registry_shift, max_registry_shift_, pairings_file_, protocols::rosetta_scripts::parse_task_operations(), random_sheets, random_sheets_, realign_domains_, residue_max_registry_shift_, residue_sample_abinitio_, residue_sample_template_, core::pack::task::PackerTask::residue_task(), set_increase_cycles(), set_scorefunction(), sheets, sheets_, small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, protocols::hybridization::TR, and utility_exit_with_message.

void protocols::hybridization::FoldTreeHybridize::restore_original_foldtree

(

core::pose::Pose &

pose

)

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

Referenced by apply().

void protocols::hybridization::FoldTreeHybridize::revert_loops_to_original	(	core::pose::Pose &	pose,
		Loops	loops
	)

References core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::MutateResidue::apply(), in::file::fasta, protocols::loops::Loops::num_loop(), option, core::sequence::read_fasta_file(), core::pose::Pose::residue_type(), sequence, protocols::loops::start, and core::chemical::ResidueType::variant_types().

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

Referenced by setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::set_add_non_init_chunks ( bool  add_non_init_chunks_in )

inline

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

inline

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

inline

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

inline

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

inline

Referenced by setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::set_domain_assembly ( bool  domain_assembly_in )

inline

Referenced by setup_for_parser().

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

inline

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

inline

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

inline

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

inline

Referenced by parse_my_tag().

void protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala	(	core::pose::Pose &	pose,
		Loops	loops
	)

References core::pose::Pose::conformation(), protocols::loops::Loops::num_loop(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), and protocols::loops::start.

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

inline

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

inline

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

inline

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

inline

Referenced by init(), and parse_my_tag().

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

void protocols::hybridization::FoldTreeHybridize::set_task_factory

(

core::pack::task::TaskFactoryOP

task_factory_in

)

References task_factory_.

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

inline

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

inline

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

inline

void protocols::hybridization::FoldTreeHybridize::setup_foldtree

(

core::pose::Pose &

pose

)

References protocols::loops::Loops::add_loop(), add_non_init_chunks_, core::pose::Pose::conformation(), domain_assembly_, 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(), j, nres, option, core::fragment::SecondaryStructure::secstruct(), 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(), protocols::loops::start, protocols::loops::stop, strand_pairings_template_indices_, strand_pairs_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), template_chunks_, template_poses_, template_wts_, core::pose::Pose::total_residue(), protocols::hybridization::TR, numeric::random::uniform(), and user.

Referenced by apply().

void protocols::hybridization::FoldTreeHybridize::setup_for_parser

(

)

Extract information from a setup mover.

References chop_fragments(), frag_libs_1mer_, frag_libs_big_, frag_libs_small_, hybridize_setup_, initial_template_index_, normalize_template_wts(), realign_domains_, set_add_hetatm(), set_constraint_file(), set_domain_assembly(), template_chunks_, template_contigs_, template_poses_, and template_wts_.

Referenced by apply().

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::ScoreFunction::clone(), 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().

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

private

References atom_names, core::id::BOGUS_ATOM_ID, floating_pairs_, fold_tree, core::pose::Pose::fold_tree(), initial_template_index_, core::pose::initialize_atomid_map(), j, map_pdb_info_number(), residue, rms, strand_pairings_template_indices_, core::scoring::superimpose_pose(), template_poses_, templates_with_incorrect_strand_pairings_, and protocols::hybridization::TR.

Referenced by apply().

void protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM

(

core::pose::Pose &

pose

)

References core::pose::Pose::batch_set_xyz(), center_of_mass(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), protocols::hybridization::TR, translation, numeric::xyzVector< class >::x(), core::pose::Pose::xyz(), protocols::kinmatch::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by apply().

Member Data Documentation

bool protocols::hybridization::FoldTreeHybridize::add_hetatm_

private

Referenced by apply(), and init().

bool protocols::hybridization::FoldTreeHybridize::add_non_init_chunks_

private

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

bool protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight_

private

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

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

private

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

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

private

Referenced by auto_frag_insertion_weight(), and init().

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

private

Referenced by apply().

bool protocols::hybridization::FoldTreeHybridize::domain_assembly_

private

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

bool protocols::hybridization::FoldTreeHybridize::filter_templates_

private

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

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

private

Referenced by apply(), and superimpose_strand_pairings_to_templates().

HybridizeFoldtreeDynamic protocols::hybridization::FoldTreeHybridize::foldtree_mover_

private

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

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

private

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

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

private

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

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

private

Referenced by apply(), FoldTreeHybridize(), get_residue_weights_for_small_frags(), and setup_for_parser().

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

private

Referenced by add_strand_pairings(), apply(), FoldTreeHybridize(), get_residue_weights_for_1mers(), setup_foldtree(), and setup_for_parser().

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

private

Referenced by get_residue_weights_for_big_frags(), init(), and parse_my_tag().

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

private

Referenced by apply(), and init().

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

private

Referenced by apply(), and init().

HybridizeSetupOP protocols::hybridization::FoldTreeHybridize::hybridize_setup_

private

Referenced by apply(), parse_my_tag(), and setup_for_parser().

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

private

Referenced by apply(), and init().

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

private

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

bool protocols::hybridization::FoldTreeHybridize::initialize_pose_by_templates_

private

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

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

private

Referenced by add_strand_pairings(), and get_pairings_jump_mover().

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

private

Referenced by add_strand_pairing(), and add_strand_pairings().

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

private

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

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

private

Referenced by apply(), and init().

bool protocols::hybridization::FoldTreeHybridize::overlap_chainbreaks_

private

Referenced by apply(), and init().

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

private

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

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

private

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

bool protocols::hybridization::FoldTreeHybridize::realign_domains_

private

Referenced by init(), parse_my_tag(), and setup_for_parser().

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

private

Referenced by apply(), and parse_my_tag().

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

private

Referenced by apply(), get_residue_weights_for_1mers(), get_residue_weights_for_big_frags(), get_residue_weights_for_small_frags(), and parse_my_tag().

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

private

Referenced by apply(), and parse_my_tag().

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

private

Referenced by apply(), and setup_scorefunctions().

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

private

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

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

private

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

Loops protocols::hybridization::FoldTreeHybridize::ss_chunks_pose_

private

Referenced by apply().

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

private

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

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

private

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

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

private

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

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

private

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

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().

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

private

Referenced by get_pairings_residues(), and setup_foldtree().

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

private

Referenced by add_strand_pairing(), and apply().

core::pack::task::TaskFactoryOP protocols::hybridization::FoldTreeHybridize::task_factory_

private

Referenced by set_task_factory().

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(), setup_foldtree(), and setup_for_parser().

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

private

Referenced by add_strand_pairing(), filter_templates(), FoldTreeHybridize(), get_residue_weights_for_big_frags(), and setup_for_parser().

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_for_big_frags(), normalize_template_wts(), setup_foldtree(), setup_for_parser(), and superimpose_strand_pairings_to_templates().

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

private

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

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

private

Referenced by add_strand_pairings(), and superimpose_strand_pairings_to_templates().

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

private

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

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

private

Referenced by auto_frag_insertion_weight(), and init().

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

private

Referenced by apply().

---

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

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