#include <HybridizeProtocol.hh>

Inheritance diagram for protocols::hybridization::HybridizeProtocol:

Public Member Functions
	HybridizeProtocol ()

	HybridizeProtocol (utility::vector1< core::pose::PoseOP > templates_in, utility::vector1< core::Real > template_weights_in, core::scoring::ScoreFunctionOP stage1_scorefxn_in, core::scoring::ScoreFunctionOP stage2_scorefxn_in, core::scoring::ScoreFunctionOP fa_scorefxn_in, std::string frag3_fn, std::string frag9_fn, std::string &cen_cst_in, std::string &fa_cst_in)

void	init ()

void	update_template (core::Size const template_idx)

void	add_template (std::string const &template_fn, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), bool const align_pdb_info=true)

void	add_null_template (core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1.)

void	add_template (core::pose::PoseOP template_pose, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), std::string const &filename="default", bool const align_pdb_info=true)

void	validate_template (std::string const &filename, std::string const &fasta, core::pose::PoseOP template_pose, bool &align_pdb_info)

core::Size	pick_starting_template ()

void	do_intrastage_docking (core::pose::Pose &pose)

void	align_templates_by_domain (core::pose::PoseOP &ref_pose, utility::vector1< protocols::loops::Loops > domains=utility::vector1< protocols::loops::Loops >())

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

void	domain_parse_templates (core::Size nres)

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	add_fragment_csts (core::pose::Pose &pose)

void	check_and_create_fragments (Pose &)

void	setup_templates_and_sampling_options (core::pose::Pose const &pose)

void	apply (Pose &) override
	Main Method. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	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_stage2pack_scorefxn (core::scoring::ScoreFunctionOP newval)

void	set_stage2min_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)

void	set_add_hetatm (bool add_hetatm)

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Attributes
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	stage2_temperature_

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	add_hetatm_

bool	realign_domains_

bool	realign_domains_stage2_

bool	no_global_frame_

bool	linmin_only_

core::Real	add_non_init_chunks_

bool	seqfrags_only_

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_

core::scoring::ScoreFunctionOP	stage2pack_scorefxn_

core::scoring::ScoreFunctionOP	stage2min_scorefxn_

std::string	fa_cst_fn_

std::string	fa_cst_in_

std::string	disulf_file_

core::Size	cartfrag_overlap_

bool	csts_from_frags_

int	max_contig_insertion_

bool	min_after_stage1_

core::Real	fragprob_stage2_

core::Real	randfragprob_stage2_

bool	include_loop_ss_chunks_

bool	cenrot_

core::Real	pcut_

core::Real	hcut_

core::Size	length_

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

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::Size >	non_null_template_indices_

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

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

utility::vector1< std::string >	template_fns_

utility::vector1< std::string >	template_cst_fn_

utility::vector1< std::string >	symmdef_files_

utility::vector1< core::Real >	template_weights_

utility::vector1< bool >	should_align_pdb_infos_

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

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

utility::vector1 < utility::vector1< char > >	randomize_chains_

utility::vector1 < detailedControlsTagSetting >	detailed_controls_settings_

std::string	cen_cst_in_

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_

utility::vector1< bool >	residue_sample_template_

utility::vector1< bool >	residue_sample_abinitio_

utility::vector1< core::Size >	residue_max_registry_shift_

bool	jump_move_

core::Size	jump_move_repeat_

bool	keep_pose_constraint_

std::string	coord_cst_res_

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

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 core::init::init().

protocols::hybridization::HybridizeProtocol::HybridizeProtocol	(	utility::vector1< core::pose::PoseOP >	templates_in,
		utility::vector1< core::Real >	template_weights_in,
		core::scoring::ScoreFunctionOP	stage1_scorefxn_in,
		core::scoring::ScoreFunctionOP	stage2_scorefxn_in,
		core::scoring::ScoreFunctionOP	fa_scorefxn_in,
		std::string	frag3_fn,
		std::string	frag9_fn,
		std::string &	cen_cst_in,
		std::string &	fa_cst_in
	)

References core::fragment::FragmentIO::read_data().

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_fragment_csts ( core::pose::Pose & pose )

References core::pose::Pose::add_constraint(), core::conformation::Residue::is_protein(), core::chemical::element::N, core::pose::Pose::residue(), and protocols::hybridization::TR().

void protocols::hybridization::HybridizeProtocol::add_null_template	(	core::pose::PoseOP	template_pose,
		std::string	cst_fn,
		std::string	symmdef_file = `"NULL"`,
		core::Real	weight = `1.`
	)

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 const &	template_fn,
		std::string const &	cst_fn,
		std::string const &	symmdef_file = `"NULL"`,
		core::Real const	weight = `1.`,
		utility::vector1< char > const &	rand_chains = `utility::vector1<core::Size>(0)`,
		bool const	align_pdb_info = `true`
	)

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::hybridization::TR().

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

void protocols::hybridization::HybridizeProtocol::add_template	(	core::pose::PoseOP	template_pose,
		std::string const &	cst_fn,
		std::string const &	symmdef_file = `"NULL"`,
		core::Real const	weight = `1.`,
		utility::vector1< char > const &	rand_chains = `utility::vector1<core::Size>(0)`,
		std::string const &	filename = `"default"`,
		bool const	align_pdb_info = `true`
	)

References protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::loops::Loops::num_loop(), protocols::loops::Loops::push_back(), and protocols::hybridization::TR().

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

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::element::F, core::pose::initialize_atomid_map(), core::chemical::ResidueTypeBase::is_protein(), protocols::constraint_generator::last_protein_residue(), protocols::hybridization::partial_align(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, protocols::hybridization::TMalign::TMscore(), protocols::hybridization::TR(), and core::conformation::Residue::xyz().

void protocols::hybridization::HybridizeProtocol::align_templates_by_domain	(	core::pose::PoseOP &	ref_pose,
		utility::vector1< protocols::loops::Loops >	domains = `utility::vector1 <protocols::loops::Loops>()`
	)

References core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), and protocols::hybridization::DDomainParse::split().

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::relax::FastRelax::apply(), core::scoring::atom_pair_constraint, protocols::relax::FastRelax::batch_apply(), core::chemical::CENTROID, core::conformation::Residue::chain(), core::conformation::Conformation::chains_from_termini(), core::conformation::change_cys_state(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::kinematics::FoldTree::cutpoints(), core::pose::Pose::data(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::sequence::end, core::chemical::element::F, core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), protocols::hybridization::get_gdtmm(), core::chemical::element::I, core::pose::initialize_disulfide_bonds(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::is_fullatom(), core::pose::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::is_upper_terminus(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), protocols::relax::RelaxProtocolBase::min_type(), core::conformation::Residue::natoms(), protocols::loops::Loops::num_loop(), protocols::loops::Loops::push_back(), core::chemical::rings::q, protocols::geometry::random_reorientation_matrix(), core::scoring::constraints::remove_nonbb_constraints(), core::pose::Pose::residue(), core::scoring::rg, core::optimization::CartesianMinimizer::run(), core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear(), protocols::relax::FastRelax::set_force_nonideal(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::loops::Loop::set_start(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScore(), protocols::hybridization::setup_centroid_constraints(), protocols::hybridization::setup_constraints(), protocols::hybridization::setup_fullatom_constraints(), protocols::hybridization::setup_user_coordinate_constraints(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, protocols::hybridization::TR(), core::conformation::Residue::type(), core::scoring::vdw, 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::chop_fragments(), core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), protocols::mean_field::min(), 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(), and core::pose::Pose::size().

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

overridevirtual

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.

void protocols::hybridization::HybridizeProtocol::do_intrastage_docking ( core::pose::Pose & pose )

References core::pose::symmetry::is_symmetric(), and core::pose::symmetry::make_symmetric_movemap().

void protocols::hybridization::HybridizeProtocol::domain_parse_templates ( core::Size nres )

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::num_loop(), protocols::loops::Loops::sequential_order(), protocols::hybridization::DDomainParse::split(), protocols::loops::start, protocols::loops::stop, and protocols::hybridization::TR().

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

overridevirtual

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.

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

overridevirtual

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(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::get_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::fragment::FragmentIO::read_data(), protocols::antibody::design::relax, core::scoring::rg, and protocols::hybridization::TR().

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(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::scoring::rg, protocols::loops::set_extended_torsions(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and protocols::hybridization::TR().

std::string protocols::hybridization::HybridizeProtocol::mover_name ( )

static

Referenced by protocols::hybridization::HybridizeProtocolCreator::keyname().

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

overridevirtual

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 core::scoring::coordinate_constraint, protocols::hybridization::off, protocols::hybridization::on, core::pack::task::parse_task_operations(), core::fragment::FragmentIO::read_data(), protocols::hybridization::TR(), and protocols::hybridization::unset.

core::Size protocols::hybridization::HybridizeProtocol::pick_starting_template ( )

References core::scoring::rg.

void protocols::hybridization::HybridizeProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pose::attributes_for_get_resnum_selector(), core::pack::task::attributes_for_parse_task_operations(), protocols::hybridization::hybridize_subelement_ct_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::hybridization::HybridizeProtocolCreator::provide_xml_schema().

void protocols::hybridization::HybridizeProtocol::set_add_hetatm ( bool add_hetatm )

inline

References add_hetatm_.

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().

void protocols::hybridization::HybridizeProtocol::set_stage2min_scorefxn ( core::scoring::ScoreFunctionOP newval )

inline

References stage2min_scorefxn_.

void protocols::hybridization::HybridizeProtocol::set_stage2pack_scorefxn ( core::scoring::ScoreFunctionOP newval )

inline

References stage2pack_scorefxn_.

void protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options ( core::pose::Pose const & pose )

References protocols::hybridization::get_num_residues_nonvirt(), core::pose::get_resnum_list_ordered(), protocols::hybridization::off, core::pose::Pose::sequence(), and protocols::hybridization::unset.

void protocols::hybridization::HybridizeProtocol::update_template ( core::Size const template_idx )

References protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), core::scoring::dssp::Dssp::insert_ss_into_pose(), and protocols::loops::Loops::num_loop().

void protocols::hybridization::HybridizeProtocol::validate_template	(	std::string const &	filename,
		std::string const &	fasta,
		core::pose::PoseOP	template_pose,
		bool &	align_pdb_info
	)

References core::sequence::SWAligner::align(), core::pose::symmetry::extract_asymmetric_unit(), protocols::magnesium::is_ligand(), core::id::SequenceMapping::reverse(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), and protocols::hybridization::TR().

Member Data Documentation

bool protocols::hybridization::HybridizeProtocol::add_hetatm_

private

Referenced by set_add_hetatm().

core::Real protocols::hybridization::HybridizeProtocol::add_non_init_chunks_

private

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

private

bool protocols::hybridization::HybridizeProtocol::auto_frag_insertion_weight_

private

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

private

Referenced by set_batch_relax().

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

private

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

private

std::string protocols::hybridization::HybridizeProtocol::cen_cst_in_

private

bool protocols::hybridization::HybridizeProtocol::cenrot_

private

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

private

std::string protocols::hybridization::HybridizeProtocol::coord_cst_res_

private

bool protocols::hybridization::HybridizeProtocol::csts_from_frags_

private

utility::vector1< detailedControlsTagSetting > protocols::hybridization::HybridizeProtocol::detailed_controls_settings_

private

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

private

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

private

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

private

std::string protocols::hybridization::HybridizeProtocol::fa_cst_in_

private

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

private

Referenced by set_fullatom_scorefxn().

bool protocols::hybridization::HybridizeProtocol::filter_templates_

private

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

private

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

private

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

private

Referenced by add_big_fragments().

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

private

Referenced by add_small_fragments().

core::Real protocols::hybridization::HybridizeProtocol::fragprob_stage2_

private

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

private

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

private

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

private

bool protocols::hybridization::HybridizeProtocol::include_loop_ss_chunks_

private

bool protocols::hybridization::HybridizeProtocol::jump_move_

private

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

private

bool protocols::hybridization::HybridizeProtocol::keep_pose_constraint_

private

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

private

bool protocols::hybridization::HybridizeProtocol::linmin_only_

private

int protocols::hybridization::HybridizeProtocol::max_contig_insertion_

private

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

private

bool protocols::hybridization::HybridizeProtocol::min_after_stage1_

private

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

private

bool protocols::hybridization::HybridizeProtocol::no_global_frame_

private

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

private

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

private

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

private

core::Real protocols::hybridization::HybridizeProtocol::randfragprob_stage2_

private

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

private

utility::vector1< utility::vector1<char> > protocols::hybridization::HybridizeProtocol::randomize_chains_

private

bool protocols::hybridization::HybridizeProtocol::realign_domains_

private

bool protocols::hybridization::HybridizeProtocol::realign_domains_stage2_

private

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

private

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

private

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

private

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

private

bool protocols::hybridization::HybridizeProtocol::seqfrags_only_

private

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

private

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

private

bool protocols::hybridization::HybridizeProtocol::skip_long_min_

private

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

private

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

private

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

private

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

private

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

private

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

private

Referenced by set_stage1_increase_cycles().

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

private

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

private

Referenced by set_stage1_scorefxn().

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

private

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

private

Referenced by set_stage2_increase_cycles().

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

private

Referenced by set_stage2_scorefxn().

core::Real protocols::hybridization::HybridizeProtocol::stage2_temperature_

private

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2min_scorefxn_

private

Referenced by set_stage2min_scorefxn().

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2pack_scorefxn_

private

Referenced by set_stage2pack_scorefxn().

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation