protocols::hybridization::HybridizeProtocol Class Reference

#include <HybridizeProtocol.hh>

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="NULL", 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	add_template (core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", 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), std::string filename="default")
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
	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 (TagCOP, 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...
void	set_batch_relax (core::Size newval)
void	add_big_fragments (core::fragment::FragSetOP newval)
void	add_small_fragments (core::fragment::FragSetOP newval)
void	set_stage1_scorefxn (core::scoring::ScoreFunctionOP newval)
void	set_stage2_scorefxn (core::scoring::ScoreFunctionOP newval)
void	set_stage1_increase_cycles (core::Real newval)
void	set_stage2_increase_cycles (core::Real newval)
void	set_fullatom_scorefxn (core::scoring::ScoreFunctionOP newval)
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
void	set_type (std::string const &setting)
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 Attributes
utility::vector1< core::Size >	starting_templates_
core::Real	stage1_probability_
core::Real	stage1_increase_cycles_
core::Real	stage2_increase_cycles_
core::Real	stage25_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	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_
bool	seqfrags_only_
bool	nofragbias_
bool	skip_long_min_
core::Real	hetatm_self_cst_weight_
core::Real	hetatm_prot_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_
core::pack::task::TaskFactoryOP	task_factory_
core::pack::task::PackerTaskOP	task_
utility::vector1< bool >	allowed_to_move_
bool	jump_move_
core::Size	jump_move_repeat_
bool	keep_pose_constraint_
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::HybridizeProtocol::HybridizeProtocol

(

)

References init(), option, read_template_structures(), cm::hybridize::template_list, and user.

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::hybridization::HybridizeProtocol::add_big_fragments ( core::fragment::FragSetOP  newval )

inline

References fragments_big_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::add_small_fragments ( core::fragment::FragSetOP  newval )

inline

References fragments_small_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::add_template	(	std::string	template_fn,
		std::string	cst_fn,
		std::string	symmdef_file = "NULL",
		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)
	)

References core::chemical::ChemicalManager::get_instance(), core::import_pose::pose_from_pdb(), and core::chemical::ChemicalManager::residue_type_set().

Referenced by protocols::hybridization::MRMover::apply(), parse_my_tag(), and read_template_structures().

void protocols::hybridization::HybridizeProtocol::add_template	(	core::pose::PoseOP	template_pose,
		std::string	cst_fn,
		std::string	symmdef_file = "NULL",
		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),
		std::string	filename = "default"
	)

References chunks, domain_assembly_weights_, protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::loops::Loops::num_loop(), symmdef_files_, template_chunks_, template_clusterID_, template_contigs_, template_cst_fn_, template_cst_reses_, template_fn_, template_weights_, templates_, and protocols::hybridization::TR.

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

Referenced by apply().

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

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::BOGUS_ATOM_ID, F, 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.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, add_hetatm_, add_non_init_chunks_, protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), align_by_domain(), allowed_to_move_, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::moves::Mover::apply(), protocols::relax::FastRelax::apply(), core::scoring::atom_pair_constraint, auto_frag_insertion_weight_, protocols::relax::FastRelax::batch_apply(), batch_relax_, core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::ResidueLevelTask::being_packed(), big_frag_insertion_weight_, cartfrag_overlap_, core::chemical::CENTROID, check_and_create_fragments(), chunk_insertion_weight_, core::scoring::ScoreFunction::clone(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::pose::Pose::data(), core::conformation::Conformation::detect_disulfides(), disulf_file_, domain_assembly_, domain_assembly_weights_, domains_, expand_domains_to_full_length(), core::pose::symmetry::extract_asymmetric_unit(), protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), F, fa_cst_fn_, fa_scorefxn_, core::chemical::FA_STANDARD, core::io::silent::SilentStruct::fill_struct(), filter_templates_, basic::options::OptionKeys::in::fix_disulf, frag_1mer_insertion_weight_, frag_weight_aligned_, fragments_big_, fragments_small_, gdtmm, protocols::hybridization::get_gdtmm(), protocols::hybridization::get_num_residues_nonvirt(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), hcut_, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, I, initialize_and_sample_loops(), core::pose::initialize_disulfide_bonds(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), jump_move_, jump_move_repeat_, keep_pose_constraint_, length_, linmin_only_, core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), max_registry_shift_, protocols::relax::RelaxProtocolBase::min_type(), native_, core::conformation::Residue::natoms(), no_global_frame_, nofragbias_, basic::options::option, option, pairings_file_, pcut_, pick_starting_template(), core::pack::task::TaskFactory::push_back(), numeric::random::RandomGenerator::random_range(), random_sheets_, realign_domains_, realign_domains_stage2_, relax_repeats_, core::scoring::constraints::remove_nonbb_constraints(), resi, core::pose::Pose::residue(), residue, core::pack::task::PackerTask::residue_task(), protocols::hybridization::RG, core::optimization::CartesianMinimizer::run(), protocols::hybridization::DomainAssembly::run(), runtime_assert, seqfrags_only_, basic::datacache::BasicDataCache::set(), core::kinematics::MoveMap::set_bb(), core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear(), core::kinematics::MoveMap::set_chi(), protocols::relax::FastRelax::set_force_nonideal(), core::kinematics::MoveMap::set_jump(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScore(), protocols::hybridization::setup_centroid_constraints(), protocols::hybridization::setup_fullatom_constraints(), protocols::hybridization::setup_interface_atompair_constraints(), protocols::hybridization::setup_interface_coordinate_constraints(), protocols::hybridization::setup_user_coordinate_constraints(), sheets_, skip_long_min_, cm::hybridize::skip_stage2, 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_, stage25_increase_cycles_, stage2_increase_cycles_, stage2_scorefxn_, protocols::loops::start, protocols::loops::stop, strand_pairs_, symmdef_files_, basic::options::OptionKeys::symmetry::symmetry_definition, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), task_, task_factory_, template_chunks_, template_clusterID_, template_contigs_, template_cst_fn_, template_fn_, template_weights_, templates_, core::pose::Pose::total_residue(), protocols::hybridization::TR, numeric::random::RandomGenerator::uniform(), user, user_csts_, and core::conformation::Residue::xyz().

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::check_and_create_fragments

(

Pose &

pose

)

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

Referenced by apply().

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

virtual

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 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
	)

References numeric::random::RandomGenerator::random_range(), protocols::hybridization::RG, size(), and protocols::loops::start.

Referenced by apply().

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

virtual

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 HybridizeProtocol().

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

virtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::HybridizeProtocol::init

(

void

)

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), 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_, batch_relax_, cm::hybridize::big_frag_insertion_weight, big_frag_insertion_weight_, cartfrag_overlap_, corrections::score::cenrot, chunk_insertion_weight_, core::scoring::ScoreFunctionFactory::create_score_function(), basic::options::OptionKeys::relax::default_repeats, disulf_file_, domain_assembly_, fa_cst_fn_, fa_scorefxn_, jumps::filter_templates, filter_templates_, in::fix_disulf, in::file::frag3, in::file::frag9, cm::hybridize::frag_1mer_insertion_weight, frag_1mer_insertion_weight_, cm::hybridize::frag_weight_aligned, frag_weight_aligned_, fragments_big_, fragments_small_, frags, in::file::fullatom, core::chemical::ChemicalManager::get_instance(), core::scoring::get_score_function(), corrections::score::hb_fade_energy, corrections::score::hb_sp2_chipen, corrections::score::hb_sp2_outer_width, corrections::score::hbond_measure_sp3acc_BAH_from_hvy, score::hbond_params, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, jump_move_, jump_move_repeat_, keep_pose_constraint_, cm::hybridize::linmin_only, linmin_only_, cm::hybridize::max_registry_shift, max_registry_shift_, in::file::native, native_, cm::hybridize::no_global_frame, no_global_frame_, nofragbias_, option, jumps::pairing_file, pairings_file_, core::scoring::hbonds::HBondOptions::params_database_tag(), core::import_pose::pose_from_pdb(), numeric::random::RandomGenerator::random_range(), jumps::random_sheets, random_sheets_, core::fragment::FragmentIO::read_data(), cm::hybridize::realign_domains, realign_domains_, cm::hybridize::realign_domains_stage2, realign_domains_stage2_, cm::hybridize::relax, relax_repeats_, core::chemical::ChemicalManager::residue_type_set(), mistakes::restore_pre_talaris_2013_behavior, protocols::hybridization::RG, seqfrags_only_, jumps::sheets, sheets_, skip_long_min_, cm::hybridize::small_frag_insertion_weight, 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, stage1_increase_cycles_, cm::hybridize::stage1_patch, cm::hybridize::stage1_probability, stage1_probability_, stage1_scorefxn_, cm::hybridize::stage1_weights, stage25_increase_cycles_, cm::hybridize::stage2_increase_cycles, stage2_increase_cycles_, cm::hybridize::stage2_patch, stage2_scorefxn_, cm::hybridize::stage2_weights, cm::hybridize::stage2min_increase_cycles, cm::hybridize::starting_template, starting_templates_, protocols::hybridization::TR, and user.

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
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::loops::add_cutpoint_variants(), allowed_to_move_, protocols::simple_moves::ClassicFragmentMover::apply(), core::pose::Pose::conformation(), protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), fragments_big_, fragments_small_, core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, loops, core::conformation::Residue::natoms(), option, core::pose::Pose::pdb_info(), numeric::random::RandomGenerator::random_range(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), protocols::hybridization::RG, core::kinematics::MoveMap::set_bb(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), core::kinematics::MoveMap::set_chi(), protocols::loops::set_extended_torsions(), core::pose::Pose::set_xyz(), cm::hybridize::stage1_increase_cycles, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), protocols::hybridization::TR, and core::pose::Pose::xyz().

Referenced by apply().

void protocols::hybridization::HybridizeProtocol::parse_my_tag ( TagCOP  tag, basic::datacache::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.

References add_hetatm_, add_non_init_chunks_, add_template(), auto_frag_insertion_weight_, batch_relax_, big_frag_insertion_weight_, cartfrag_overlap_, chunk_insertion_weight_, core::scoring::ScoreFunction::clone(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), disulf_file_, domain_assembly_, fa_cst_fn_, fa_scorefxn_, filter_templates_, frag_1mer_insertion_weight_, frag_files, frag_weight_aligned_, fragments_big_, fragments_small_, frags, basic::datacache::DataMap::get(), core::pose::get_resnum_list_ordered(), hcut_, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, jump_move_, jump_move_repeat_, keep_pose_constraint_, length_, linmin_only_, max_registry_shift_, no_global_frame_, nofragbias_, pairings_file_, protocols::rosetta_scripts::parse_task_operations(), pcut_, random_sheets, random_sheets_, core::fragment::FragmentIO::read_data(), read_template_structures(), realign_domains_, realign_domains_stage2_, relax_repeats_, runtime_assert, seqfrags_only_, sheets, sheets_, skip_long_min_, small_frag_insertion_weight_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, stage1_increase_cycles_, stage1_probability_, stage1_scorefxn_, stage25_increase_cycles_, stage2_increase_cycles_, stage2_scorefxn_, starting_templates_, utility::string_split(), task_, task_factory_, user_csts_, and weight.

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
	)

References numeric::random::WeightedSampler::add_weight(), numeric::random::WeightedSampler::random_sample(), protocols::hybridization::RG, starting_templates_, template_chunks_, template_clusterID_, template_contigs_, template_weights_, templates_, and numeric::random::WeightedSampler::weights().

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.

References add_template(), utility::io::izstream::close(), utility::io::izstream::eof(), getline(), utility::string_split(), protocols::hybridization::TR, and weight.

Referenced by HybridizeProtocol(), and parse_my_tag().

void protocols::hybridization::HybridizeProtocol::read_template_structures

(

utility::vector1< utility::file::FileName > const &

template_filenames

)

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_.

void protocols::hybridization::HybridizeProtocol::set_batch_relax ( core::Size  newval )

inline

References batch_relax_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::set_fullatom_scorefxn ( core::scoring::ScoreFunctionOP  newval )

inline

References fa_scorefxn_.

void protocols::hybridization::HybridizeProtocol::set_stage1_increase_cycles ( core::Real  newval )

inline

References stage1_increase_cycles_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::set_stage1_scorefxn ( core::scoring::ScoreFunctionOP  newval )

inline

References stage1_scorefxn_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::set_stage2_increase_cycles ( core::Real  newval )

inline

References stage2_increase_cycles_.

Referenced by protocols::hybridization::MRMover::apply().

void protocols::hybridization::HybridizeProtocol::set_stage2_scorefxn ( core::scoring::ScoreFunctionOP  newval )

inline

References stage2_scorefxn_.

Referenced by protocols::hybridization::MRMover::apply().

Member Data Documentation

bool protocols::hybridization::HybridizeProtocol::add_hetatm_

private

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

bool protocols::hybridization::HybridizeProtocol::add_non_init_chunks_

private

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

utility::vector1<bool> protocols::hybridization::HybridizeProtocol::allowed_to_move_

private

Referenced by apply(), and initialize_and_sample_loops().

core::sequence::SequenceAlignmentOP protocols::hybridization::HybridizeProtocol::aln_

private

bool protocols::hybridization::HybridizeProtocol::auto_frag_insertion_weight_

private

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

core::Size protocols::hybridization::HybridizeProtocol::batch_relax_

private

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

core::Real protocols::hybridization::HybridizeProtocol::big_frag_insertion_weight_

private

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

core::Size protocols::hybridization::HybridizeProtocol::cartfrag_overlap_

private

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

core::Real protocols::hybridization::HybridizeProtocol::chunk_insertion_weight_

private

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

std::map< Size, utility::vector1 < Size > > protocols::hybridization::HybridizeProtocol::clusterID_map_

private

std::string protocols::hybridization::HybridizeProtocol::disulf_file_

private

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

bool protocols::hybridization::HybridizeProtocol::domain_assembly_

private

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

utility::vector1< core::Real > protocols::hybridization::HybridizeProtocol::domain_assembly_weights_

private

Referenced by add_template(), and apply().

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

private

Referenced by apply().

std::string protocols::hybridization::HybridizeProtocol::fa_cst_fn_

private

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

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::fa_scorefxn_

private

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

bool protocols::hybridization::HybridizeProtocol::filter_templates_

private

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

core::Real protocols::hybridization::HybridizeProtocol::frag_1mer_insertion_weight_

private

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

core::Real protocols::hybridization::HybridizeProtocol::frag_weight_aligned_

private

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

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeProtocol::fragments_big_

private

Referenced by add_big_fragments(), apply(), check_and_create_fragments(), init(), initialize_and_sample_loops(), and parse_my_tag().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeProtocol::fragments_small_

private

Referenced by add_small_fragments(), apply(), check_and_create_fragments(), init(), initialize_and_sample_loops(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::hcut_

private

Referenced by apply(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::hetatm_prot_cst_weight_

private

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

core::Real protocols::hybridization::HybridizeProtocol::hetatm_self_cst_weight_

private

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

bool protocols::hybridization::HybridizeProtocol::jump_move_

private

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

core::Size protocols::hybridization::HybridizeProtocol::jump_move_repeat_

private

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

bool protocols::hybridization::HybridizeProtocol::keep_pose_constraint_

private

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

core::Size protocols::hybridization::HybridizeProtocol::length_

private

Referenced by apply(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::linmin_only_

private

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

core::Size protocols::hybridization::HybridizeProtocol::max_registry_shift_

private

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

core::pose::PoseOP protocols::hybridization::HybridizeProtocol::native_

private

Referenced by apply(), and init().

bool protocols::hybridization::HybridizeProtocol::no_global_frame_

private

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

bool protocols::hybridization::HybridizeProtocol::nofragbias_

private

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

std::string protocols::hybridization::HybridizeProtocol::pairings_file_

private

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

core::Real protocols::hybridization::HybridizeProtocol::pcut_

private

Referenced by apply(), and parse_my_tag().

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

private

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

bool protocols::hybridization::HybridizeProtocol::realign_domains_

private

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

bool protocols::hybridization::HybridizeProtocol::realign_domains_stage2_

private

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

core::Size protocols::hybridization::HybridizeProtocol::relax_repeats_

private

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

bool protocols::hybridization::HybridizeProtocol::seqfrags_only_

private

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

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

private

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

bool protocols::hybridization::HybridizeProtocol::skip_long_min_

private

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

core::Real protocols::hybridization::HybridizeProtocol::small_frag_insertion_weight_

private

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

core::Size protocols::hybridization::HybridizeProtocol::stage1_1_cycles_

private

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

core::Size protocols::hybridization::HybridizeProtocol::stage1_2_cycles_

private

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

core::Size protocols::hybridization::HybridizeProtocol::stage1_3_cycles_

private

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

core::Size protocols::hybridization::HybridizeProtocol::stage1_4_cycles_

private

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

core::Real protocols::hybridization::HybridizeProtocol::stage1_increase_cycles_

private

Referenced by apply(), init(), parse_my_tag(), and set_stage1_increase_cycles().

core::Real protocols::hybridization::HybridizeProtocol::stage1_probability_

private

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

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage1_scorefxn_

private

Referenced by apply(), init(), parse_my_tag(), and set_stage1_scorefxn().

core::Real protocols::hybridization::HybridizeProtocol::stage25_increase_cycles_

private

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

core::Real protocols::hybridization::HybridizeProtocol::stage2_increase_cycles_

private

Referenced by apply(), init(), parse_my_tag(), and set_stage2_increase_cycles().

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2_scorefxn_

private

Referenced by apply(), init(), parse_my_tag(), and set_stage2_scorefxn().

utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::starting_templates_

private

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

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

private

Referenced by apply().

utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::symmdef_files_

private

Referenced by add_template(), and apply().

core::pack::task::PackerTaskOP protocols::hybridization::HybridizeProtocol::task_

private

Referenced by apply(), and parse_my_tag().

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

private

Referenced by apply(), and parse_my_tag().

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

private

Referenced by add_template(), apply(), and pick_starting_template().

utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::template_clusterID_

private

Referenced by add_template(), apply(), and pick_starting_template().

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

private

Referenced by add_template(), apply(), and pick_starting_template().

utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_cst_fn_

private

Referenced by add_template(), and apply().

utility::vector1< utility::vector1<core::Size> > protocols::hybridization::HybridizeProtocol::template_cst_reses_

private

Referenced by add_template().

utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_fn_

private

Referenced by add_template(), and apply().

utility::vector1< core::Real > protocols::hybridization::HybridizeProtocol::template_weights_

private

Referenced by add_template(), apply(), and pick_starting_template().

core::Real protocols::hybridization::HybridizeProtocol::template_weights_sum_

private

utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeProtocol::templates_

private

Referenced by add_template(), apply(), check_and_create_fragments(), pick_starting_template(), and read_template_structures().

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

private

Referenced by apply(), and parse_my_tag().

---

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

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