#include <HybridizeProtocol.hh>

Inheritance diagram for protocols::hybridization::HybridizeProtocol:

Collaboration diagram for protocols::hybridization::HybridizeProtocol:

Public Member Functions
	HybridizeProtocol ()

void	init ()

void	read_template_structures (utility::file::FileName template_list)
	Old way of parsing hybrid config files; RosettaScripts is now preferred. More...

void	read_template_structures (utility::vector1< utility::file::FileName > const &template_filenames)

void	add_template (std::string template_fn, std::string cst_fn, std::string symmdef_file, core::Real weight=1., core::Real domain_assembly_weight=0., core::Size cluster_id=1, utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0))

void	pick_starting_template (core::Size &initial_template_index, core::Size &initial_template_index_icluster, utility::vector1< core::Size > &template_index_icluster, utility::vector1< core::pose::PoseOP > &templates_icluster, utility::vector1< core::Real > &weights_icluster, utility::vector1< protocols::loops::Loops > &template_chunks_icluster, utility::vector1< protocols::loops::Loops > &template_contigs_icluster)

utility::vector1< Loops >	expand_domains_to_full_length (utility::vector1< utility::vector1< Loops > > all_domains, Size ref_domains_index, Size n_residues)

void	align_by_domain (utility::vector1< core::pose::PoseOP > &poses, utility::vector1< Loops > domains, core::pose::PoseOP &ref_pose)

void	align_by_domain (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< Loops > domains)

void	initialize_and_sample_loops (core::pose::Pose &pose, core::pose::PoseOP chosen_templ, protocols::loops::Loops template_contigs_icluster, core::scoring::ScoreFunctionOP scorefxn)

void	check_and_create_fragments (Pose &)

virtual void	apply (Pose &)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

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

virtual protocols::moves::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...

virtual void	parse_my_tag (TagPtr const, 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...

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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Attributes
utility::vector1< core::Size >	starting_templates_

core::Real	stage1_probability_

core::Real	stage1_increase_cycles_

core::Real	stage2_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	frag_weight_aligned_

bool	auto_frag_insertion_weight_

core::Size	max_registry_shift_

bool	domain_assembly_

bool	add_hetatm_

bool	realign_domains_

bool	realign_domains_stage2_

bool	add_non_init_chunks_

bool	no_global_frame_

bool	linmin_only_

core::Real	hetatm_cst_weight_

core::scoring::ScoreFunctionOP	stage1_scorefxn_

core::scoring::ScoreFunctionOP	stage2_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

std::string	fa_cst_fn_

std::string	disulf_file_

core::Size	cartfrag_overlap_

core::Real	pcut_

core::Real	hcut_

core::Size	length_

core::Size	batch_relax_

core::Size	relax_repeats_

utility::vector1 < core::fragment::FragSetOP >	fragments_big_

utility::vector1 < core::fragment::FragSetOP >	fragments_small_

core::pose::PoseOP	native_

core::sequence::SequenceAlignmentOP	aln_

utility::vector1 < core::pose::PoseOP >	templates_

utility::vector1< std::string >	template_fn_

utility::vector1< std::string >	template_cst_fn_

utility::vector1< std::string >	symmdef_files_

utility::vector1< core::Real >	template_weights_

utility::vector1< core::Real >	domain_assembly_weights_

utility::vector1< core::Size >	template_clusterID_

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

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

utility::vector1 < utility::vector1< core::Size > >	template_cst_reses_

core::Real	template_weights_sum_

std::map< Size, utility::vector1< Size > >	clusterID_map_

utility::vector1 < protocols::loops::Loops >	domains_

std::string	pairings_file_

utility::vector1< core::Size >	sheets_

utility::vector1< core::Size >	random_sheets_

bool	filter_templates_

utility::vector1< std::pair < core::Size, core::Size > >	strand_pairs_

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 36 of file HybridizeProtocol.hh.

Constructor & Destructor Documentation

protocols::hybridization::HybridizeProtocol::HybridizeProtocol ( )

Definition at line 181 of file HybridizeProtocol.cc.

References init(), and read_template_structures().

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::hybridization::HybridizeProtocol::add_template	(	std::string	template_fn,
		std::string	cst_fn,
		std::string	symmdef_file,
		core::Real	weight = `1.`,
		core::Real	domain_assembly_weight = `0.`,
		core::Size	cluster_id = `1`,
		utility::vector1< core::Size >	cst_reses = `utility::vector1<core::Size>(0)`
	)

void protocols::hybridization::HybridizeProtocol::align_by_domain	(	utility::vector1< core::pose::PoseOP > &	poses,
		utility::vector1< Loops >	domains,
		core::pose::PoseOP &	ref_pose
	)

Definition at line 1107 of file HybridizeProtocol.cc.

Referenced by apply().

void protocols::hybridization::HybridizeProtocol::align_by_domain	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		utility::vector1< Loops >	domains
	)

Definition at line 1120 of file HybridizeProtocol.cc.

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::chemical::ResidueType::is_protein(), protocols::hybridization::partial_align(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), protocols::loops::stop, protocols::hybridization::TMalign::TMscore(), core::pose::Pose::total_residue(), and protocols::hybridization::TR().

void protocols::hybridization::HybridizeProtocol::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 669 of file HybridizeProtocol.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), add_hetatm_, add_non_init_chunks_, protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::pose::addVirtualResAsRoot(), align_by_domain(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom_index(), auto_frag_insertion_weight_, protocols::relax::FastRelax::batch_apply(), batch_relax_, big_frag_insertion_weight_, core::scoring::cart_bonded, cartfrag_overlap_, core::chemical::CENTROID, check_and_create_fragments(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pose::Pose::data(), disulf_file_, domain_assembly_, domain_assembly_weights_, domains_, expand_domains_to_full_length(), protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), fa_cst_fn_, fa_scorefxn_, core::chemical::FA_STANDARD, filter_templates_, core::pose::Pose::fold_tree(), frag_1mer_insertion_weight_, frag_weight_aligned_, fragments_big_, fragments_small_, protocols::hybridization::get_gdtmm(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), hcut_, hetatm_cst_weight_, initialize_and_sample_loops(), core::pose::initialize_disulfide_bonds(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), length_, linmin_only_, core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), max_registry_shift_, native_, no_global_frame_, pairings_file_, pcut_, pick_starting_template(), random_sheets_, realign_domains_, realign_domains_stage2_, relax_repeats_, core::pose::Pose::residue(), protocols::hybridization::RG(), core::kinematics::FoldTree::root(), core::optimization::CartesianMinimizer::run(), protocols::hybridization::DomainAssembly::run(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::relax::FastRelax::set_force_nonideal(), core::kinematics::MoveMap::set_jump(), protocols::relax::RelaxProtocolBase::set_min_type(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::pose::setPoseExtraScores(), protocols::hybridization::setup_centroid_constraints(), protocols::hybridization::setup_fullatom_constraints(), sheets_, small_frag_insertion_weight_, protocols::hybridization::DDomainParse::split(), stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, stage1_increase_cycles_, stage1_probability_, stage1_scorefxn_, stage2_increase_cycles_, stage2_scorefxn_, protocols::loops::start, protocols::loops::stop, strand_pairs_, symmdef_files_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), template_chunks_, template_clusterID_, template_contigs_, template_cst_fn_, template_cst_reses_, template_fn_, template_weights_, templates_, core::pose::Pose::total_residue(), protocols::hybridization::TR(), and core::pose::Pose::xyz().

void protocols::hybridization::HybridizeProtocol::check_and_create_fragments ( Pose & pose)

Definition at line 294 of file HybridizeProtocol.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::fragment::chop_fragments(), core::pose::Pose::conformation(), fragments_big_, fragments_small_, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), core::pose::read_psipred_ss2_file(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), templates_, and core::pose::Pose::total_residue().

Referenced by apply().

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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 1178 of file HybridizeProtocol.cc.

References HybridizeProtocol().

utility::vector1< Loops > protocols::hybridization::HybridizeProtocol::expand_domains_to_full_length	(	utility::vector1< utility::vector1< Loops > >	all_domains,
		Size	ref_domains_index,
		Size	n_residues
	)

Definition at line 1047 of file HybridizeProtocol.cc.

References protocols::hybridization::RG(), core::io::serialization::size(), and protocols::loops::start.

Referenced by apply().

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

virtual

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).

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.

Definition at line 1179 of file HybridizeProtocol.cc.

References HybridizeProtocol().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 1182 of file HybridizeProtocol.cc.

void protocols::hybridization::HybridizeProtocol::init ( void )

Definition at line 205 of file HybridizeProtocol.cc.

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), add_hetatm_, add_non_init_chunks_, auto_frag_insertion_weight_, batch_relax_, big_frag_insertion_weight_, cartfrag_overlap_, core::scoring::ScoreFunctionFactory::create_score_function(), disulf_file_, domain_assembly_, fa_cst_fn_, fa_scorefxn_, filter_templates_, frag_1mer_insertion_weight_, frag_weight_aligned_, fragments_big_, fragments_small_, core::scoring::getScoreFunction(), hetatm_cst_weight_, linmin_only_, max_registry_shift_, native_, no_global_frame_, pairings_file_, core::import_pose::pose_from_pdb(), random_sheets_, core::fragment::FragmentIO::read_data(), realign_domains_, realign_domains_stage2_, relax_repeats_, protocols::hybridization::RG(), sheets_, small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, stage1_increase_cycles_, stage1_probability_, stage1_scorefxn_, stage2_increase_cycles_, stage2_scorefxn_, starting_templates_, and protocols::hybridization::TR().

Referenced by HybridizeProtocol().

void protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops	(	core::pose::Pose &	pose,
		core::pose::PoseOP	chosen_templ,
		protocols::loops::Loops	template_contigs_icluster,
		core::scoring::ScoreFunctionOP	scorefxn
	)

void protocols::hybridization::HybridizeProtocol::parse_my_tag	(	TagPtr const	tag,
		moves::DataMap &	data,
		filters::Filters_map const &	filters,
		moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

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.

Definition at line 1187 of file HybridizeProtocol.cc.

References add_hetatm_, add_non_init_chunks_, add_template(), auto_frag_insertion_weight_, batch_relax_, big_frag_insertion_weight_, cartfrag_overlap_, disulf_file_, domain_assembly_, fa_cst_fn_, fa_scorefxn_, filter_templates_, frag_1mer_insertion_weight_, frag_weight_aligned_, fragments_big_, fragments_small_, protocols::moves::DataMap::get(), core::pose::get_resnum_list_ordered(), hcut_, hetatm_cst_weight_, length_, linmin_only_, max_registry_shift_, no_global_frame_, pairings_file_, pcut_, random_sheets_, core::fragment::FragmentIO::read_data(), read_template_structures(), realign_domains_, realign_domains_stage2_, relax_repeats_, sheets_, small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, stage1_increase_cycles_, stage1_probability_, stage1_scorefxn_, stage2_increase_cycles_, stage2_scorefxn_, and starting_templates_.

void protocols::hybridization::HybridizeProtocol::pick_starting_template	(	core::Size &	initial_template_index,
		core::Size &	initial_template_index_icluster,
		utility::vector1< core::Size > &	template_index_icluster,
		utility::vector1< core::pose::PoseOP > &	templates_icluster,
		utility::vector1< core::Real > &	weights_icluster,
		utility::vector1< protocols::loops::Loops > &	template_chunks_icluster,
		utility::vector1< protocols::loops::Loops > &	template_contigs_icluster
	)

Definition at line 621 of file HybridizeProtocol.cc.

References protocols::hybridization::RG(), starting_templates_, template_chunks_, template_clusterID_, template_contigs_, template_weights_, and templates_.

Referenced by apply().

void protocols::hybridization::HybridizeProtocol::read_template_structures ( utility::file::FileName template_list)

Old way of parsing hybrid config files; RosettaScripts is now preferred.

Definition at line 563 of file HybridizeProtocol.cc.

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

Referenced by HybridizeProtocol(), and parse_my_tag().

void protocols::hybridization::HybridizeProtocol::read_template_structures ( utility::vector1< utility::file::FileName > const & template_filenames)

Definition at line 603 of file HybridizeProtocol.cc.

References core::chemical::ChemicalManager::get_instance(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::moves::Mover::name(), core::import_pose::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), and templates_.