#include <FoldTreeHybridize.hh>

Inheritance diagram for protocols::hybridization::FoldTreeHybridize:

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

void	init ()

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_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_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	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)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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
	this function informs 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
	this function informs 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...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

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 ()

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_

bool	add_non_init_chunks_

bool	domain_assembly_

bool	add_hetatm_

core::Real	hetatm_cst_weight_

core::Real	frag_weight_aligned_

bool	auto_frag_insertion_weight_

core::Size	max_registry_shift_

std::string	cst_file_

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_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 66 of file FoldTreeHybridize.hh.

Constructor & Destructor Documentation

protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize ( )

Definition at line 130 of file FoldTreeHybridize.cc.

References init().

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
	)

Definition at line 136 of file FoldTreeHybridize.cc.

References core::fragment::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`
	)

Definition at line 298 of file FoldTreeHybridize.cc.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), gap_distance(), 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

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

private

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

virtual

Implements protocols::moves::Mover.

Definition at line 1162 of file FoldTreeHybridize.cc.

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

private

Definition at line 1567 of file FoldTreeHybridize.cc.

References auto_frag_insertion_weight_, big_frag_insertion_weight_, frag_1mer_insertion_weight_, small_frag_insertion_weight_, strand_pairings_template_indices_, 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)

Definition at line 468 of file FoldTreeHybridize.cc.

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

Referenced by translate_virt_to_CoM().

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

private

Definition at line 1039 of file FoldTreeHybridize.cc.

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

Referenced by add_strand_pairings().

Real protocols::hybridization::FoldTreeHybridize::gap_distance ( Size Seq_gap)

Definition at line 261 of file FoldTreeHybridize.cc.

Referenced by add_gap_constraints_to_pose().

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

private

Definition at line 577 of file FoldTreeHybridize.cc.

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.

Definition at line 1599 of file FoldTreeHybridize.cc.

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

private

Definition at line 1070 of file FoldTreeHybridize.cc.

References jump_frags_.

Referenced by add_strand_pairing(), and apply().

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

Definition at line 1082 of file FoldTreeHybridize.cc.

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)

Definition at line 592 of file FoldTreeHybridize.cc.

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

Referenced by apply().

utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags ( core::pose::Pose & pose)

Definition at line 507 of file FoldTreeHybridize.cc.

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(), 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)

Definition at line 625 of file FoldTreeHybridize.cc.

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

Referenced by apply().

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

inline

Definition at line 141 of file FoldTreeHybridize.hh.

void protocols::hybridization::FoldTreeHybridize::init ( void )

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

private

Definition at line 1028 of file FoldTreeHybridize.cc.

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

Definition at line 214 of file FoldTreeHybridize.cc.

References template_poses_, and template_wts_.

Referenced by filter_templates(), and FoldTreeHybridize().

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

Definition at line 658 of file FoldTreeHybridize.cc.

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
	)

Definition at line 243 of file FoldTreeHybridize.cc.

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

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

inline

Definition at line 111 of file FoldTreeHybridize.hh.

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

inline

Definition at line 109 of file FoldTreeHybridize.hh.

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

inline

Definition at line 116 of file FoldTreeHybridize.hh.

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

inline

Definition at line 114 of file FoldTreeHybridize.hh.

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

inline

Definition at line 103 of file FoldTreeHybridize.hh.

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

inline

Definition at line 110 of file FoldTreeHybridize.hh.

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

inline

Definition at line 125 of file FoldTreeHybridize.hh.

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

inline

Definition at line 112 of file FoldTreeHybridize.hh.

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

inline

Definition at line 115 of file FoldTreeHybridize.hh.

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

inline

Definition at line 104 of file FoldTreeHybridize.hh.

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

Definition at line 222 of file FoldTreeHybridize.cc.

References core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), 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

Definition at line 117 of file FoldTreeHybridize.hh.

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

inline

Definition at line 122 of file FoldTreeHybridize.hh.

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

inline

Definition at line 124 of file FoldTreeHybridize.hh.

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

inline

Definition at line 127 of file FoldTreeHybridize.hh.

Referenced by init().

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

inline

Definition at line 123 of file FoldTreeHybridize.hh.

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

inline

Definition at line 113 of file FoldTreeHybridize.hh.

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

inline

Definition at line 105 of file FoldTreeHybridize.hh.

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

inline

Definition at line 106 of file FoldTreeHybridize.hh.

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

inline

Definition at line 107 of file FoldTreeHybridize.hh.

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

inline

Definition at line 108 of file FoldTreeHybridize.hh.

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

inline

Definition at line 118 of file FoldTreeHybridize.hh.

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

inline

Definition at line 119 of file FoldTreeHybridize.hh.

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

Definition at line 323 of file FoldTreeHybridize.cc.

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(), 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(), and protocols::hybridization::TR().

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
	)