container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well) More...

#include <Splice.hh>

Inheritance diagram for protocols::splice::Splice:

[legend]

Public Types
typedef core::pose::Pose	Pose

typedef utility::vector1< ResidueBBDofs >::const_iterator	dbase_const_iterator

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > >	DataccacheBoolDataOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	Splice ()

void	apply (Pose &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 (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

	~Splice () override

void	from_res (core::Size const f)

core::Size	from_res (core::pose::Pose const &pose) const

void	to_res (core::Size const t)

core::Size	to_res (core::pose::Pose const &pose) const

std::string	source_pdb () const

void	source_pdb (std::string const &s)

void	ccd (bool const c)

void	design_shell (core::Real const c)

void	repack_shell (core::Real const c)

bool	ccd () const

core::Real	dihedral_const () const

core::Real	coor_const () const

core::Real	design_shell () const

core::Real	repack_shell () const

void	scorefxn (core::scoring::ScoreFunctionOP sf)

core::scoring::ScoreFunctionOP	scorefxn () const

core::Real	rms_cutoff () const

void	rms_cutoff (core::Real const r)

core::Real	rms_cutoff_loop () const

void	rms_cutoff_loop (core::Real const r)

void	res_move (core::Size const r)

core::Size	res_move () const

void	randomize_cut (bool const r)

bool	randomize_cut () const

void	set_cut_res (core::Size const r)

core::Size	set_cut_res () const

void	cut_secondarystruc (bool const r)

bool	cut_secondarystruc () const

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::pack::task::TaskFactoryOP	design_task_factory () const

void	design_task_factory (core::pack::task::TaskFactoryOP tf)

void	set_segment_names_ordered (utility::vector1< std::string > SegNameOrder)

utility::vector1< std::string >	get_segment_names_ordered () const

void	set_dofs_pdb_name (std::string dofsPDBname)

std::string	get_dofs_pdb_name () const

std::string	torsion_database_fname () const

void	torsion_database_fname (std::string const &d)

core::Size	database_entry () const

void	database_entry (core::Size const d)

void	read_torsion_database ()

utility::vector1< ResidueBBDofs >	torsion_database () const

void	torsion_database (utility::vector1< ResidueBBDofs > const &d)

std::string	template_file () const

void	template_file (std::string const &s)

void	poly_ala (bool const p)

bool	poly_ala () const

void	equal_length (bool const e)

bool	equal_length () const

void	fold_tree (core::pose::Pose &pose, core::Size const start, core::Size const stop, core::Size const cut) const
	set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses More...

void	tail_fold_tree (core::pose::Pose &pose, core::Size const vl_vh_cut, core::Size chain_break, std::string segment_name) const
	Setup fold tree for segments at the termini of the protein, gdl, Apr2014. More...

void	set_fold_tree (core::pose::Pose &pose, core::Size const vl_vh_cut)
	@Set a general fold tree to use for all antibodies, gideon, Apr2014 More...

bool	design () const

void	design (bool const d)

void	delta_lengths (utility::vector1< int > const &dl)

utility::vector1< int >	delta_lengths ()

bool	dbase_iterate () const

void	dbase_iterate (bool const d)

utility::vector1< core::Size >::const_iterator	dbase_begin () const

utility::vector1< core::Size >::const_iterator	dbase_end () const

core::Size	find_dbase_entry (core::pose::Pose const &pose)
	controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset More...

core::Size	locked_res () const

void	locked_res (core::Size const r)

void	locked_res_id (char const c)

char	locked_res_id () const

std::string	checkpointing_file () const

void	checkpointing_file (std::string const &cf)

bool	rtmin () const

void	rtmin (bool const d)

bool	allow_all_aa () const

void	allow_all_aa (bool const d)

bool	thread_original_sequence () const

void	thread_original_sequence (bool const s)

void	load_from_checkpoint ()

void	save_to_checkpoint () const

std::string	loop_dbase_file_name () const

void	loop_dbase_file_name (std::string const &f)

void	loop_pdb_source (std::string const &l)

std::string	loop_pdb_source () const

protocols::filters::FilterOP	splice_filter () const

void	splice_filter (protocols::filters::FilterOP f)

void	database_pdb_entry (std::string const &s)

std::string	database_pdb_entry () const

void	read_splice_segments (std::string const &segment_type, std::string const &segment_name, std::string const &file_name)

core::sequence::SequenceProfileOP	generate_sequence_profile (core::pose::Pose &pose)

void	load_pdb_segments_from_pose_comments (core::pose::Pose const &p)

void	modify_pdb_segments_with_current_segment (std::string const &pdb_name)

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

void	add_dihedral_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to)
	add dihedral constraint to grafted loop according to source pdb dihedral angles More...

void	add_coordinate_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to, core::Size anchor, std::string atom_type="CA", core::pack::task::PackerTaskOP task=nullptr)
	apply coordinate constraints on the segment being inserted. "to" and "from" are residue number of the pose(!), anchor residue number is also on the pose More...

void	profile_weight_away_from_interface (core::Real const p)

core::Real	profile_weight_away_from_interface () const

bool	restrict_to_repacking_chain2 () const

void	restrict_to_repacking_chain2 (bool const r)

core::Size	get_current_seg ()

bool	add_sequence_constraints_only () const

void	add_sequence_constraints_only (bool const a)

bool	rb_sensitive () const

void	rb_sensitive (bool const r)

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

void	protein_family (std::string const &s)

core::Size	chain_num () const

void	chain_num (core::Size const c)

bool	skip_alignment () const

void	skip_alignment (bool const b)

bool	superimposed () const

void	superimposed (bool const b)

core::Size	source_pdb_from_res () const

void	source_pdb_from_res (core::Size const s)

core::Size	source_pdb_to_res () const

void	source_pdb_to_res (core::Size const s)

void	delete_hairpin (bool const b)

bool	delete_hairpin () const

core::Size	delete_hairpin_n () const

void	delete_hairpin_n (core::Size const c)

core::Size	delete_hairpin_c () const

void	delete_hairpin_c (core::Size const c)

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

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Member Functions
void	save_values (core::pose::Pose const &pose)

void	retrieve_values ()

std::string	parse_pdb_code (std::string pdb_file_name)
	This is helper function that cuts out a file name, removing the extension and the path. More...

void	copy_stretch (core::pose::Pose &target, core::pose::Pose const &source, core::Size const from_res, core::Size const to_res)
	copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs More...

core::Size	find_non_active_site_cut_site (core::pose::Pose const &pose)
	Since we want to minimally perturb the active site confirmation (whether it be binding or catalytic) the cut site should be placed farthest away. For each protein family we will probably need special definitions unless we find a more general way. For antibodies I go from the conserved Trp res at the base of CDR1 and then continue going to the C-ter until I find the distal loops. More...

void	superimpose_source_on_pose (core::pose::Pose const &, core::pose::Pose &)

void	chainbreak_check (core::pose::Pose const &pose, core::Real const tolerance, bool fail_retry_if_found, bool crash_if_found)

void	correct_bb_O_placements (core::pose::Pose Pose, core::Size cut_site)

Private Attributes
utility::vector1< std::string >	segment_names_ordered_

std::string	dofs_pdb_name

core::pose::ResidueIndexDescriptionCOP	from_res_

core::pose::ResidueIndexDescriptionCOP	to_res_

core::Size	saved_from_res_

core::Size	saved_to_res_

std::string	source_pdb_

bool	ccd_

core::Real	dihedral_const_

core::Real	coor_const_

core::Real	design_shell_

core::Real	repack_shell_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	rms_cutoff_

core::Real	rms_cutoff_loop_

core::Size	res_move_

bool	randomize_cut_

bool	cut_secondarystruc_

core::Size	set_cut_res_

core::pack::task::TaskFactoryOP	task_factory_

core::pack::task::TaskFactoryOP	design_task_factory_

std::string	torsion_database_fname_

core::Size	database_entry_

std::string	database_pdb_entry_

utility::vector1< ResidueBBDofs >	torsion_database_

utility::vector1< ResidueBBDofs >	tail_torsion_database_

std::string	template_file_

bool	poly_ala_

bool	equal_length_

core::pose::PoseCOP	template_pose_

core::pose::PoseCOP	start_pose_

core::pose::PoseOP	source_pose_

core::kinematics::FoldTreeOP	saved_fold_tree_

bool	design_

utility::vector1< int >	delta_lengths_

bool	dbase_iterate_

bool	allow_all_aa_

bool	thread_original_sequence_

bool	rtmin_

bool	first_pass_

utility::vector1< core::Size >	dbase_subset_

utility::vector1< core::Size >::const_iterator	current_dbase_entry_

DataccacheBoolDataOP	end_dbase_subset_

utility::pointer::shared_ptr< basic::datacache::DataMapObj< utility::vector1< core::Size > > >	locked_res_

char	locked_res_id_

std::string	checkpointing_file_

std::string	loop_dbase_file_name_

std::string	loop_pdb_source_

utility::pointer::shared_ptr< basic::datacache::DataMapObj< std::string > >	mover_tag_

protocols::filters::FilterOP	splice_filter_

std::string	Pdb4LetName_

std::string	protein_family_

std::map< std::string, utility::vector1< std::string > >	order_segments_

core::Size	chain_num_

bool	use_sequence_profiles_

std::string	segment_type_

core::Size	current_segment_pos

std::map< std::string, SpliceSegmentOP >	splice_segments_

std::map< std::string, std::string >	pdb_segments_

core::Real	profile_weight_away_from_interface_

bool	restrict_to_repacking_chain2_

bool	add_sequence_constraints_only_

bool	set_fold_tree_only_

bool	rb_sensitive_

std::map< std::string, std::string >	protein_family_to_database_

bool	skip_alignment_

std::map< std::string, std::string >	database_segment_map_

core::Size	vl_vh_cut

std::string	tail_segment_

bool	min_seg_

bool	CG_const_

bool	debug_

std::string	mover_name_

std::map< std::string, std::string >	pdb_to_H3_seq_map_

bool	superimposed_

core::Size	source_pdb_from_res_

core::Size	source_pdb_to_res_

bool	ignore_chain_break_

core::Real	tolerance_

bool	delete_hairpin_

core::Size	delete_hairpin_n_

core::Size	delete_hairpin_c_

core::Size	allowed_cuts_

bool	enzdes_

std::map< std::string, BBMatchingOP >	bb_comp_db_

Additional Inherited Members
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

container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well)

Member Typedef Documentation

◆ DataccacheBoolDataOP

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::splice::Splice::DataccacheBoolDataOP

◆ dbase_const_iterator

typedef utility::vector1< ResidueBBDofs >::const_iterator protocols::splice::Splice::dbase_const_iterator

◆ Pose

typedef core::pose::Pose protocols::splice::Splice::Pose

Constructor & Destructor Documentation

◆ Splice()

◆ ~Splice()

protocols::splice::Splice::~Splice ( )

overridedefault

Member Function Documentation

◆ add_coordinate_constraints()

void protocols::splice::Splice::add_coordinate_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	source_pose,
		core::Size	nearest_to_from,
		core::Size	nearest_to_to,
		core::Size	anchor,
		std::string	atom_type = `"CA"`,
		core::pack::task::PackerTaskOP	task = `nullptr`
	)

apply coordinate constraints on the segment being inserted. "to" and "from" are residue number of the pose(!), anchor residue number is also on the pose

References core::pose::Pose::aa(), core::pose::Pose::add_constraints(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::pose::Pose::chi(), core::conformation::Residue::chi_atoms(), core::kinematics::distance(), protocols::rosetta_scripts::find_nearest_res(), core::conformation::Residue::first_sidechain_atom(), core::pose::Pose::fold_tree(), core::membrane::intersect(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), protocols::splice::report_coordinate_constraints(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), protocols::splice::TR(), protocols::splice::TR_constraints(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ add_dihedral_constraints()

void protocols::splice::Splice::add_dihedral_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	source_pose,
		core::Size	nearest_to_from,
		core::Size	nearest_to_to
	)

add dihedral constraint to grafted loop according to source pdb dihedral angles

References core::pose::Pose::aa(), core::pose::Pose::add_constraints(), core::conformation::Residue::atom(), core::chemical::ResidueType::atom_index(), core::scoring::dihedral_constraint, protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), scorefxn(), tail_segment_, protocols::splice::TR_constraints(), and core::conformation::Atom::xyz().

Referenced by apply().

◆ add_sequence_constraints()

◆ add_sequence_constraints_only() [1/2]

bool protocols::splice::Splice::add_sequence_constraints_only ( ) const

inline

References add_sequence_constraints_only_.

Referenced by apply(), and parse_my_tag().

◆ add_sequence_constraints_only() [2/2]

void protocols::splice::Splice::add_sequence_constraints_only ( bool const a )

inline

References core::pose::motif::a(), and add_sequence_constraints_only_.

◆ allow_all_aa() [1/2]

bool protocols::splice::Splice::allow_all_aa ( ) const

inline

References allow_all_aa_.

Referenced by apply(), and parse_my_tag().

◆ allow_all_aa() [2/2]

void protocols::splice::Splice::allow_all_aa ( bool const d )

inline

References allow_all_aa_.

◆ apply()

void protocols::splice::Splice::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ ccd() [1/2]

bool protocols::splice::Splice::ccd ( ) const

inline

References ccd_.

Referenced by apply(), and parse_my_tag().

◆ ccd() [2/2]

void protocols::splice::Splice::ccd ( bool const c )

inline

References ccd_.

◆ chain_num() [1/2]

core::Size protocols::splice::Splice::chain_num ( ) const

inline

References chain_num_.

Referenced by copy_stretch(), fold_tree(), and Splice().

◆ chain_num() [2/2]

void protocols::splice::Splice::chain_num ( core::Size const c )

inline

References chain_num_.

◆ chainbreak_check()

void protocols::splice::Splice::chainbreak_check	(	core::pose::Pose const &	pose,
		core::Real const	tolerance,
		bool	fail_retry_if_found,
		bool	crash_if_found
	)

private

References allowed_cuts_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chain_num_, core::pose::Pose::conformation(), core::kinematics::distance(), core::pose::Pose::dump_pdb(), protocols::moves::FAIL_RETRY, mover_name_, core::pose::Pose::residue(), retrieve_values(), protocols::moves::Mover::set_last_move_status(), protocols::splice::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ checkpointing_file() [1/2]

std::string protocols::splice::Splice::checkpointing_file ( ) const

References checkpointing_file_.

Referenced by parse_my_tag().

◆ checkpointing_file() [2/2]

void protocols::splice::Splice::checkpointing_file ( std::string const & cf )

References checkpointing_file_.

◆ clone()

protocols::moves::MoverOP protocols::splice::Splice::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.

Referenced by apply().

◆ coor_const()

core::Real protocols::splice::Splice::coor_const ( ) const

inline

References coor_const_.

◆ copy_stretch()

void protocols::splice::Splice::copy_stretch	(	core::pose::Pose &	target,
		core::pose::Pose const &	source,
		core::Size const	from_res,
		core::Size const	to_res
	)

private

copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs

References protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::conformation::Conformation::chain_end(), chain_num(), chain_num_, core::pose::Pose::conformation(), core::pose::Pose::copy_segment(), debug_, protocols::protein_interface_design::movers::LoopLengthChange::delta(), core::pose::Pose::dump_pdb(), protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), from_res(), protocols::protein_interface_design::movers::LoopLengthChange::loop_end(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), mover_name_, segment_type_, protocols::protein_interface_design::movers::LoopLengthChange::tail(), to_res(), and protocols::splice::TR().

Referenced by apply().

◆ correct_bb_O_placements()

void protocols::splice::Splice::correct_bb_O_placements	(	core::pose::Pose	Pose,
		core::Size	cut_site
	)

private

◆ cut_secondarystruc() [1/2]

bool protocols::splice::Splice::cut_secondarystruc ( ) const

inline

References cut_secondarystruc_.

Referenced by apply(), and parse_my_tag().

◆ cut_secondarystruc() [2/2]

void protocols::splice::Splice::cut_secondarystruc ( bool const r )

inline

References cut_secondarystruc_.

◆ database_entry() [1/2]

core::Size protocols::splice::Splice::database_entry ( ) const

inline

References database_entry_.

Referenced by find_dbase_entry(), and parse_my_tag().

◆ database_entry() [2/2]

void protocols::splice::Splice::database_entry ( core::Size const d )

inline

References database_entry_.

◆ database_pdb_entry() [1/2]

std::string protocols::splice::Splice::database_pdb_entry ( ) const

inline

References database_pdb_entry_.

Referenced by parse_my_tag().

◆ database_pdb_entry() [2/2]

void protocols::splice::Splice::database_pdb_entry ( std::string const & s )

inline

References database_pdb_entry_.

◆ dbase_begin()

utility::vector1< core::Size >::const_iterator protocols::splice::Splice::dbase_begin ( ) const

References dbase_subset_.

◆ dbase_end()

utility::vector1< core::Size >::const_iterator protocols::splice::Splice::dbase_end ( ) const

References dbase_subset_.

Referenced by find_dbase_entry().

◆ dbase_iterate() [1/2]

bool protocols::splice::Splice::dbase_iterate ( ) const

inline

References dbase_iterate_.

Referenced by find_dbase_entry(), and parse_my_tag().

◆ dbase_iterate() [2/2]

void protocols::splice::Splice::dbase_iterate ( bool const d )

inline

References dbase_iterate_.

◆ delete_hairpin() [1/2]

bool protocols::splice::Splice::delete_hairpin ( ) const

inline

References delete_hairpin_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

◆ delete_hairpin() [2/2]

void protocols::splice::Splice::delete_hairpin ( bool const b )

inline

References protocols::match::upstream::b, and delete_hairpin_.

◆ delete_hairpin_c() [1/2]

core::Size protocols::splice::Splice::delete_hairpin_c ( ) const

inline

References delete_hairpin_c_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

◆ delete_hairpin_c() [2/2]

void protocols::splice::Splice::delete_hairpin_c ( core::Size const c )

inline

References delete_hairpin_c_.

◆ delete_hairpin_n() [1/2]

core::Size protocols::splice::Splice::delete_hairpin_n ( ) const

inline

References delete_hairpin_n_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

◆ delete_hairpin_n() [2/2]

void protocols::splice::Splice::delete_hairpin_n ( core::Size const c )

inline

References delete_hairpin_n_.

◆ delta_lengths() [1/2]

utility::vector1< int > protocols::splice::Splice::delta_lengths ( )

inline

References delta_lengths_.

◆ delta_lengths() [2/2]

void protocols::splice::Splice::delta_lengths ( utility::vector1< int > const & dl )

inline

References delta_lengths_.

◆ design() [1/2]

bool protocols::splice::Splice::design ( ) const

inline

References design_.

Referenced by apply(), and parse_my_tag().

◆ design() [2/2]

void protocols::splice::Splice::design ( bool const d )

inline

References design_.

◆ design_shell() [1/2]

core::Real protocols::splice::Splice::design_shell ( ) const

inline

References design_shell_.

Referenced by apply(), and parse_my_tag().

◆ design_shell() [2/2]

void protocols::splice::Splice::design_shell ( core::Real const c )

inline

References design_shell_.

◆ design_task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::splice::Splice::design_task_factory ( ) const

References design_task_factory_.

Referenced by apply(), and parse_my_tag().

◆ design_task_factory() [2/2]

void protocols::splice::Splice::design_task_factory ( core::pack::task::TaskFactoryOP tf )

References design_task_factory_.

◆ dihedral_const()

core::Real protocols::splice::Splice::dihedral_const ( ) const

inline

References dihedral_const_.

◆ equal_length() [1/2]

bool protocols::splice::Splice::equal_length ( ) const

inline

References equal_length_.

Referenced by find_dbase_entry(), and parse_my_tag().

◆ equal_length() [2/2]

void protocols::splice::Splice::equal_length ( bool const e )

inline

References equal_length_.

◆ find_dbase_entry()

core::Size protocols::splice::Splice::find_dbase_entry ( core::pose::Pose const & pose )

controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset

References bb_comp_db_, chain_num_, current_dbase_entry_, database_entry(), database_pdb_entry_, dbase_end(), dbase_iterate(), dbase_subset_, debug_, delta_lengths_, core::pose::Pose::dump_pdb(), end_dbase_subset_, equal_length(), protocols::rosetta_scripts::find_nearest_res(), first_pass_, load_from_checkpoint(), protocols::splice::load_pdb_segments_from_pose_comments(), locked_res(), protocols::splice::modify_dbase_with_compatible_backbones(), mover_name_, protocols::splice::nearest_to_entry_stop_on_pose(), pdb_segments_, protein_family_, retrieve_values(), core::scoring::rg, segment_names_ordered_, segment_type_, protocols::splice::ResidueBBDofs::size(), skip_alignment(), source_pdb(), protocols::splice::ResidueBBDofs::start_loop(), protocols::splice::ResidueBBDofs::stop_loop(), tail_segment_, template_pose_, core::id::to_string(), torsion_database_, and protocols::splice::TR().

Referenced by apply().

◆ find_non_active_site_cut_site()

core::Size protocols::splice::Splice::find_non_active_site_cut_site ( core::pose::Pose const & pose )

private

Since we want to minimally perturb the active site confirmation (whether it be binding or catalytic) the cut site should be placed farthest away. For each protein family we will probably need special definitions unless we find a more general way. For antibodies I go from the conserved Trp res at the base of CDR1 and then continue going to the C-ter until I find the distal loops.

References protocols::simple_filters::dssp(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), parse_pdb_code(), core::pose::Pose::pdb_info(), protein_family_, core::pose::Pose::residue(), segment_type_, splice_segments_, core::pose::Pose::total_residue(), protocols::splice::TR(), and protocols::splice::TR_pssm().

Referenced by apply().

◆ fold_tree()

void protocols::splice::Splice::fold_tree	(	core::pose::Pose &	pose,
		core::Size const	start,
		core::Size const	stop,
		core::Size const	cut
	)		const

set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::splice::Splice::fresh_instance ( ) const

inlineoverridevirtual

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.

◆ from_res() [1/2]

core::Size protocols::splice::Splice::from_res ( core::pose::Pose const & pose ) const

References from_res_.

◆ from_res() [2/2]

void protocols::splice::Splice::from_res ( core::Size const f )

References from_res_, and core::pose::make_rid_posenum().

Referenced by apply(), copy_stretch(), retrieve_values(), save_values(), and superimpose_source_on_pose().

◆ generate_sequence_profile()

◆ get_current_seg()

core::Size protocols::splice::Splice::get_current_seg ( )

inline

References current_segment_pos.

◆ get_dofs_pdb_name()

std::string protocols::splice::Splice::get_dofs_pdb_name ( ) const

inline

References dofs_pdb_name.

◆ get_name()

std::string protocols::splice::Splice::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References protocols::splice::SpliceCreator::mover_name().

◆ get_segment_names_ordered()

utility::vector1< std::string > protocols::splice::Splice::get_segment_names_ordered ( ) const

inline

References segment_names_ordered_.

◆ load_from_checkpoint()

void protocols::splice::Splice::load_from_checkpoint ( )

The checkpointing file has the following structure: the first line contains an ordered list of the dbase_subset_ for splice to iterate over the loop database. The second line contains the last element tested (the loop-entry number in the database; not the iterator to it!) and the third line contains the best element tested (again, the loop number from the database, not the iterator!). To recover from a checkpoint the following reads the dbase_subset_ then, if this is a first_pass_ the best entry becomes current, and if it is not a first_pass then the current entry is current.

References checkpointing_file_, current_dbase_entry_, dbase_subset_, and protocols::splice::TR().

Referenced by find_dbase_entry().

◆ load_pdb_segments_from_pose_comments()

void protocols::splice::Splice::load_pdb_segments_from_pose_comments ( core::pose::Pose const & p )

References core::pose::get_all_comments(), pdb_segments_, protocols::splice::TR(), and protocols::hybridization::val.

◆ locked_res() [1/2]

core::Size protocols::splice::Splice::locked_res ( ) const

References locked_res_.

Referenced by apply(), find_dbase_entry(), and fold_tree().

◆ locked_res() [2/2]

void protocols::splice::Splice::locked_res ( core::Size const r )

References locked_res_.

◆ locked_res_id() [1/2]

char protocols::splice::Splice::locked_res_id ( ) const

References locked_res_id_.

Referenced by apply().

◆ locked_res_id() [2/2]

void protocols::splice::Splice::locked_res_id ( char const c )

References locked_res_id_.

◆ loop_dbase_file_name() [1/2]

std::string protocols::splice::Splice::loop_dbase_file_name ( ) const

References loop_dbase_file_name_.

Referenced by parse_my_tag().

◆ loop_dbase_file_name() [2/2]

void protocols::splice::Splice::loop_dbase_file_name ( std::string const & f )

References loop_dbase_file_name_.

◆ loop_pdb_source() [1/2]

std::string protocols::splice::Splice::loop_pdb_source ( ) const

References loop_pdb_source_.

Referenced by parse_my_tag().

◆ loop_pdb_source() [2/2]

void protocols::splice::Splice::loop_pdb_source ( std::string const & l )

References loop_pdb_source_.

◆ modify_pdb_segments_with_current_segment()

void protocols::splice::Splice::modify_pdb_segments_with_current_segment ( std::string const & pdb_name )

References pdb_segments_, and segment_type_.

Referenced by apply().

◆ mover_name()

std::string protocols::splice::Splice::mover_name ( )

static

Referenced by parse_my_tag(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::splice::Splice::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_sequence_constraints_only(), allow_all_aa(), allowed_cuts_, bb_comp_db_, ccd(), CG_const_, chain_num_, checkpointing_file(), checkpointing_file_, cut_secondarystruc(), database_entry(), database_pdb_entry(), database_pdb_entry_, database_segment_map_, dbase_iterate(), debug_, delete_hairpin(), delete_hairpin_c(), delete_hairpin_n(), delta_lengths_, design(), design_shell(), design_task_factory(), end_dbase_subset_, enzdes_, equal_length(), protocols::rosetta_scripts::find_nearest_disulfide(), from_res_, ignore_chain_break_, protocols::rosetta_scripts::legacy_saved_pose_or_input(), locked_res_, loop_dbase_file_name(), loop_dbase_file_name_, loop_pdb_source(), min_seg_, mover_name(), mover_name_, mover_tag_, order_segments_, protocols::rosetta_scripts::parse_filter(), core::pose::parse_resnum(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), pdb_to_H3_seq_map_, poly_ala(), core::import_pose::pose_from_file(), profile_weight_away_from_interface(), protein_family(), protein_family_, protein_family_to_database_, randomize_cut(), rb_sensitive(), protocols::splice::read_H3_seq(), read_torsion_database(), repack_shell(), res_move(), restrict_to_repacking_chain2(), rms_cutoff(), rms_cutoff_loop(), rtmin(), scorefxn(), segment_names_ordered_, segment_type_, set_fold_tree_only_, skip_alignment(), source_pdb(), source_pdb_, source_pdb_from_res(), source_pdb_to_res(), source_pose_, splice_filter(), splice_segments_, start_pose_, superimposed(), tail_segment_, task_factory(), template_file(), template_file_, template_pose_, thread_original_sequence(), to_res_, tolerance_, torsion_database_, torsion_database_fname(), torsion_database_fname_, protocols::splice::TR(), and use_sequence_profiles_.

◆ parse_pdb_code()

std::string protocols::splice::Splice::parse_pdb_code ( std::string pdb_file_name )

private

This is helper function that cuts out a file name, removing the extension and the path.

Referenced by apply(), find_non_active_site_cut_site(), and generate_sequence_profile().

◆ poly_ala() [1/2]

bool protocols::splice::Splice::poly_ala ( ) const

inline

References poly_ala_.

Referenced by apply(), and parse_my_tag().

◆ poly_ala() [2/2]

void protocols::splice::Splice::poly_ala ( bool const p )

inline

References poly_ala_.

◆ profile_weight_away_from_interface() [1/2]

core::Real protocols::splice::Splice::profile_weight_away_from_interface ( ) const

References profile_weight_away_from_interface_.

Referenced by add_sequence_constraints(), and parse_my_tag().

◆ profile_weight_away_from_interface() [2/2]

void protocols::splice::Splice::profile_weight_away_from_interface ( core::Real const p )

References profile_weight_away_from_interface_.

◆ protein_family()

void protocols::splice::Splice::protein_family ( std::string const & s )

inline

References protein_family_.

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::splice::Splice::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), core::pose::attributes_for_saved_reference_pose_w_description(), protocols::splice::complex_type_name_for_subsubtag(), protocols::splice::complex_type_name_for_subtag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::splice::SpliceCreator::provide_xml_schema().

◆ randomize_cut() [1/2]

bool protocols::splice::Splice::randomize_cut ( ) const

inline

References randomize_cut_.

Referenced by apply(), and parse_my_tag().

◆ randomize_cut() [2/2]

void protocols::splice::Splice::randomize_cut ( bool const r )

inline

References randomize_cut_.

◆ rb_adjust_template()

void protocols::splice::Splice::rb_adjust_template ( core::pose::Pose const & pose )

References debug_, core::pose::Pose::dump_pdb(), protocols::splice::RBOutMover::get_disulf_jump(), mover_name_, rb_sensitive(), protocols::splice::RBInMover::set_fold_tree(), core::pose::Pose::split_by_chain(), template_pose_, and protocols::splice::TR().

Referenced by apply().

◆ rb_sensitive() [1/2]

bool protocols::splice::Splice::rb_sensitive ( ) const

inline

References rb_sensitive_.

Referenced by parse_my_tag(), and rb_adjust_template().

◆ rb_sensitive() [2/2]

void protocols::splice::Splice::rb_sensitive ( bool const r )

inline

References rb_sensitive_.

◆ read_splice_segments()

void protocols::splice::Splice::read_splice_segments	(	std::string const &	segment_type,
		std::string const &	segment_name,
		std::string const &	file_name
	)

sequence profiles Splice changes the backbone of the current pose and the following methods deal with dynamically constructing a sequence profile for the current backbone choices.

References segment_type_, splice_segments_, protocols::splice::TR(), and use_sequence_profiles_.

◆ read_torsion_database()

void protocols::splice::Splice::read_torsion_database ( )

the torsion dbase should have the following structure: each line represents a single loop. Each four values represent <phi> <psi> <omega> <3-let resid>; the last entry in a line represents <loop start> <loop stop> <cut site> cut; where cut signifies that this is the loop designator

References protocols::splice::ResidueBBDofs::clear(), protocols::splice::ResidueBBDofs::cut_site(), debug_, protocols::splice::ResidueBBDofs::disulfide(), core::scoring::omega, protocols::splice::ResidueBBDofs::push_back(), protocols::splice::ResidueBBDofs::size(), protocols::splice::ResidueBBDofs::source_pdb(), protocols::splice::ResidueBBDofs::start_loop(), protocols::splice::ResidueBBDofs::stop_loop(), protocols::splice::ResidueBBDofs::tail_segment(), tail_torsion_database_, torsion_database_, torsion_database_fname_, and protocols::splice::TR().

Referenced by parse_my_tag(), and set_fold_tree().

◆ remove_hairpin()

void protocols::splice::Splice::remove_hairpin ( core::pose::Pose & pose ) const

References core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), delete_hairpin(), delete_hairpin_c(), delete_hairpin_n(), core::pose::Pose::delete_polymer_residue(), core::sequence::end, protocols::rosetta_scripts::find_nearest_disulfide(), and protocols::loops::start.

Referenced by apply().

◆ repack_shell() [1/2]

core::Real protocols::splice::Splice::repack_shell ( ) const

inline

References repack_shell_.

Referenced by apply(), and parse_my_tag().

◆ repack_shell() [2/2]

void protocols::splice::Splice::repack_shell ( core::Real const c )

inline

References repack_shell_.

◆ res_move() [1/2]

core::Size protocols::splice::Splice::res_move ( ) const

inline

References res_move_.

Referenced by apply(), and parse_my_tag().

◆ res_move() [2/2]

void protocols::splice::Splice::res_move ( core::Size const r )

inline

References res_move_.

◆ restrict_to_repacking_chain2() [1/2]

bool protocols::splice::Splice::restrict_to_repacking_chain2 ( ) const

inline

References restrict_to_repacking_chain2_.

Referenced by apply(), and parse_my_tag().

◆ restrict_to_repacking_chain2() [2/2]

void protocols::splice::Splice::restrict_to_repacking_chain2 ( bool const r )

inline

References restrict_to_repacking_chain2_.

◆ retrieve_values()

void protocols::splice::Splice::retrieve_values ( )

private

References first_pass_, from_res(), save_to_checkpoint(), saved_from_res_, saved_to_res_, and to_res().

Referenced by apply(), chainbreak_check(), and find_dbase_entry().

◆ rms_cutoff() [1/2]

core::Real protocols::splice::Splice::rms_cutoff ( ) const

inline

References rms_cutoff_.

Referenced by apply(), and parse_my_tag().

◆ rms_cutoff() [2/2]

void protocols::splice::Splice::rms_cutoff ( core::Real const r )

inline

References rms_cutoff_.

◆ rms_cutoff_loop() [1/2]

core::Real protocols::splice::Splice::rms_cutoff_loop ( ) const

inline

References rms_cutoff_loop_.

Referenced by apply(), and parse_my_tag().

◆ rms_cutoff_loop() [2/2]

void protocols::splice::Splice::rms_cutoff_loop ( core::Real const r )

inline

References rms_cutoff_loop_.

◆ rtmin() [1/2]

bool protocols::splice::Splice::rtmin ( ) const

inline

References rtmin_.

Referenced by apply(), and parse_my_tag().

◆ rtmin() [2/2]

void protocols::splice::Splice::rtmin ( bool const d )

inline

References rtmin_.

◆ save_to_checkpoint()

void protocols::splice::Splice::save_to_checkpoint ( ) const

References checkpointing_file_, current_dbase_entry_, dbase_subset_, core::conformation::membrane::out, and protocols::splice::TR().

Referenced by retrieve_values().

◆ save_values()

void protocols::splice::Splice::save_values ( core::pose::Pose const & pose )

private

splice apply might change the from_res/to_res internals since they sometimes refer to the template file. If that happens, we want the values to revert to their original values before the end of the apply function (so retrieve_values) below must be called before return.

References from_res(), saved_from_res_, saved_to_res_, and to_res().

Referenced by apply().

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::splice::Splice::scorefxn ( ) const

References scorefxn_.

Referenced by add_dihedral_constraints(), add_sequence_constraints(), apply(), and parse_my_tag().

◆ scorefxn() [2/2]

void protocols::splice::Splice::scorefxn ( core::scoring::ScoreFunctionOP sf )

References scorefxn_.

◆ set_cut_res() [1/2]

core::Size protocols::splice::Splice::set_cut_res ( ) const

inline

References set_cut_res_.

◆ set_cut_res() [2/2]

void protocols::splice::Splice::set_cut_res ( core::Size const r )

inline

References set_cut_res_.

◆ set_dofs_pdb_name()

void protocols::splice::Splice::set_dofs_pdb_name ( std::string dofsPDBname )

inline

References dofs_pdb_name.

◆ set_fold_tree()

void protocols::splice::Splice::set_fold_tree	(	core::pose::Pose &	pose,
		core::Size const	vl_vh_cut
	)

@Set a general fold tree to use for all antibodies, gideon, Apr2014

References core::kinematics::FoldTree::add_edge(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), database_segment_map_, core::kinematics::FoldTree::delete_self_edges(), core::chemical::DISULFIDE, protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), protocols::rosetta_scripts::find_nearest_disulfide(), protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), core::pose::get_all_comments(), core::conformation::Residue::has_variant_type(), read_torsion_database(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), segment_names_ordered_, source_pdb(), template_pose_, core::id::to_string(), torsion_database_, torsion_database_fname_, core::pose::Pose::total_residue(), protocols::splice::TR(), and vl_vh_cut.

Referenced by apply().

◆ set_segment_names_ordered()

void protocols::splice::Splice::set_segment_names_ordered ( utility::vector1< std::string > SegNameOrder )

inline

References segment_names_ordered_.

◆ skip_alignment() [1/2]

bool protocols::splice::Splice::skip_alignment ( ) const

inline

References skip_alignment_.

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

◆ skip_alignment() [2/2]

void protocols::splice::Splice::skip_alignment ( bool const b )

inline

References protocols::match::upstream::b, and skip_alignment_.

◆ source_pdb() [1/2]

std::string protocols::splice::Splice::source_pdb ( ) const

inline

References source_pdb_.

Referenced by find_dbase_entry(), parse_my_tag(), and set_fold_tree().

◆ source_pdb() [2/2]

void protocols::splice::Splice::source_pdb ( std::string const & s )

inline

References source_pdb_.

◆ source_pdb_from_res() [1/2]

core::Size protocols::splice::Splice::source_pdb_from_res ( ) const

inline

References source_pdb_from_res_.

Referenced by apply(), parse_my_tag(), Splice(), and superimpose_source_on_pose().

◆ source_pdb_from_res() [2/2]

void protocols::splice::Splice::source_pdb_from_res ( core::Size const s )

inline

References source_pdb_from_res_.

◆ source_pdb_to_res() [1/2]

core::Size protocols::splice::Splice::source_pdb_to_res ( ) const

inline

References source_pdb_to_res_.

Referenced by apply(), parse_my_tag(), Splice(), and superimpose_source_on_pose().

◆ source_pdb_to_res() [2/2]

void protocols::splice::Splice::source_pdb_to_res ( core::Size const s )

inline

References source_pdb_to_res_.

◆ splice_filter() [1/2]

protocols::filters::FilterOP protocols::splice::Splice::splice_filter ( ) const

References splice_filter_.

Referenced by apply(), and parse_my_tag().

◆ splice_filter() [2/2]

void protocols::splice::Splice::splice_filter ( protocols::filters::FilterOP f )

References splice_filter_.

◆ superimpose_source_on_pose()

void protocols::splice::Splice::superimpose_source_on_pose	(	core::pose::Pose const &	pose,
		core::pose::Pose &	source_pose
	)

private

◆ superimposed() [1/2]

bool protocols::splice::Splice::superimposed ( ) const

inline

References superimposed_.

Referenced by apply(), parse_my_tag(), Splice(), and superimpose_source_on_pose().

◆ superimposed() [2/2]

void protocols::splice::Splice::superimposed ( bool const b )

inline

References protocols::match::upstream::b, and superimposed_.

◆ tail_fold_tree()

void protocols::splice::Splice::tail_fold_tree	(	core::pose::Pose &	pose,
		core::Size const	vl_vh_cut,
		core::Size	chain_break,
		std::string	segment_name
	)		const

Setup fold tree for segments at the termini of the protein, gdl, Apr2014.

References core::kinematics::FoldTree::add_edge(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::kinematics::FoldTree::delete_unordered_edge(), core::chemical::DISULFIDE, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), protocols::splice::TR(), and vl_vh_cut.

Referenced by apply().

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::splice::Splice::task_factory ( ) const

References task_factory_.

Referenced by apply(), and parse_my_tag().

◆ task_factory() [2/2]

void protocols::splice::Splice::task_factory ( core::pack::task::TaskFactoryOP tf )

References task_factory_.

◆ template_file() [1/2]

std::string protocols::splice::Splice::template_file ( ) const

inline

References template_file_.

Referenced by parse_my_tag().

◆ template_file() [2/2]

void protocols::splice::Splice::template_file ( std::string const & s )

inline

References template_file_.

◆ thread_original_sequence() [1/2]

bool protocols::splice::Splice::thread_original_sequence ( ) const

inline

References thread_original_sequence_.

Referenced by apply(), and parse_my_tag().

◆ thread_original_sequence() [2/2]

void protocols::splice::Splice::thread_original_sequence ( bool const s )

inline

References thread_original_sequence_.

◆ to_res() [1/2]

core::Size protocols::splice::Splice::to_res ( core::pose::Pose const & pose ) const

References to_res_.

◆ to_res() [2/2]

void protocols::splice::Splice::to_res ( core::Size const t )

References core::pose::make_rid_posenum(), protocols::hybridization::t, and to_res_.

Referenced by apply(), copy_stretch(), retrieve_values(), save_values(), and superimpose_source_on_pose().

◆ torsion_database() [1/2]

utility::vector1< ResidueBBDofs > protocols::splice::Splice::torsion_database ( ) const

inline

References torsion_database_.

◆ torsion_database() [2/2]

void protocols::splice::Splice::torsion_database ( utility::vector1< ResidueBBDofs > const & d )

inline

References torsion_database_.

◆ torsion_database_fname() [1/2]

std::string protocols::splice::Splice::torsion_database_fname ( ) const

inline

References torsion_database_fname_.

Referenced by parse_my_tag().

◆ torsion_database_fname() [2/2]

void protocols::splice::Splice::torsion_database_fname ( std::string const & d )

inline

References torsion_database_fname_.

Member Data Documentation

◆ add_sequence_constraints_only_

bool protocols::splice::Splice::add_sequence_constraints_only_

private

Referenced by add_sequence_constraints(), add_sequence_constraints_only(), generate_sequence_profile(), and Splice().

◆ allow_all_aa_

bool protocols::splice::Splice::allow_all_aa_

private

Referenced by allow_all_aa().

◆ allowed_cuts_

core::Size protocols::splice::Splice::allowed_cuts_

private

Referenced by chainbreak_check(), and parse_my_tag().

◆ bb_comp_db_

std::map< std::string, BBMatchingOP > protocols::splice::Splice::bb_comp_db_

private

Referenced by find_dbase_entry(), and parse_my_tag().

◆ ccd_

bool protocols::splice::Splice::ccd_

private

Referenced by apply(), ccd(), and generate_sequence_profile().

◆ CG_const_

bool protocols::splice::Splice::CG_const_

private

Referenced by apply(), and parse_my_tag().

◆ chain_num_

core::Size protocols::splice::Splice::chain_num_

private

Referenced by add_sequence_constraints(), apply(), chain_num(), chainbreak_check(), copy_stretch(), find_dbase_entry(), and parse_my_tag().

◆ checkpointing_file_

std::string protocols::splice::Splice::checkpointing_file_

private

Referenced by checkpointing_file(), load_from_checkpoint(), parse_my_tag(), and save_to_checkpoint().

◆ coor_const_

core::Real protocols::splice::Splice::coor_const_

private

Referenced by coor_const().

◆ current_dbase_entry_

utility::vector1< core::Size >::const_iterator protocols::splice::Splice::current_dbase_entry_

private

Referenced by find_dbase_entry(), load_from_checkpoint(), and save_to_checkpoint().

◆ current_segment_pos

core::Size protocols::splice::Splice::current_segment_pos

private

Referenced by get_current_seg().

◆ cut_secondarystruc_

bool protocols::splice::Splice::cut_secondarystruc_

private

Referenced by cut_secondarystruc().

◆ database_entry_

core::Size protocols::splice::Splice::database_entry_

private

Referenced by database_entry().

◆ database_pdb_entry_

std::string protocols::splice::Splice::database_pdb_entry_

private

Referenced by database_pdb_entry(), find_dbase_entry(), and parse_my_tag().

◆ database_segment_map_

std::map< std::string, std::string> protocols::splice::Splice::database_segment_map_

private

Referenced by parse_my_tag(), and set_fold_tree().

◆ dbase_iterate_

bool protocols::splice::Splice::dbase_iterate_

private

Referenced by dbase_iterate().

◆ dbase_subset_

utility::vector1< core::Size > protocols::splice::Splice::dbase_subset_

private

Referenced by dbase_begin(), dbase_end(), find_dbase_entry(), load_from_checkpoint(), save_to_checkpoint(), and Splice().

◆ debug_

bool protocols::splice::Splice::debug_

private

Referenced by apply(), copy_stretch(), find_dbase_entry(), parse_my_tag(), rb_adjust_template(), read_torsion_database(), and superimpose_source_on_pose().

◆ delete_hairpin_

bool protocols::splice::Splice::delete_hairpin_

private

Referenced by delete_hairpin().

◆ delete_hairpin_c_

core::Size protocols::splice::Splice::delete_hairpin_c_

private

Referenced by delete_hairpin_c().

◆ delete_hairpin_n_

core::Size protocols::splice::Splice::delete_hairpin_n_

private

Referenced by delete_hairpin_n().

◆ delta_lengths_

utility::vector1< int > protocols::splice::Splice::delta_lengths_

private

Referenced by delta_lengths(), find_dbase_entry(), parse_my_tag(), and Splice().

◆ design_

bool protocols::splice::Splice::design_

private

Referenced by design().

◆ design_shell_

core::Real protocols::splice::Splice::design_shell_

private

Referenced by design_shell(), and Splice().

◆ design_task_factory_

core::pack::task::TaskFactoryOP protocols::splice::Splice::design_task_factory_

private

Referenced by design_task_factory().

◆ dihedral_const_

core::Real protocols::splice::Splice::dihedral_const_

private

Referenced by dihedral_const().

◆ dofs_pdb_name

std::string protocols::splice::Splice::dofs_pdb_name

private

Referenced by apply(), generate_sequence_profile(), get_dofs_pdb_name(), and set_dofs_pdb_name().

◆ end_dbase_subset_

DataccacheBoolDataOP protocols::splice::Splice::end_dbase_subset_

private

Referenced by find_dbase_entry(), parse_my_tag(), and Splice().

◆ enzdes_

bool protocols::splice::Splice::enzdes_

private

Referenced by parse_my_tag().

◆ equal_length_

bool protocols::splice::Splice::equal_length_

private

Referenced by equal_length().

◆ first_pass_

bool protocols::splice::Splice::first_pass_

private

Referenced by find_dbase_entry(), and retrieve_values().

◆ from_res_

core::pose::ResidueIndexDescriptionCOP protocols::splice::Splice::from_res_

private

Referenced by from_res(), and parse_my_tag().

◆ ignore_chain_break_

bool protocols::splice::Splice::ignore_chain_break_

private

Referenced by apply(), and parse_my_tag().

◆ locked_res_

utility::pointer::shared_ptr< basic::datacache::DataMapObj < utility::vector1< core::Size > > > protocols::splice::Splice::locked_res_

private

Referenced by locked_res(), and parse_my_tag().

◆ locked_res_id_

char protocols::splice::Splice::locked_res_id_

private

Referenced by locked_res_id().

◆ loop_dbase_file_name_

std::string protocols::splice::Splice::loop_dbase_file_name_

private

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

◆ loop_pdb_source_

std::string protocols::splice::Splice::loop_pdb_source_

private

Referenced by apply(), and loop_pdb_source().

◆ min_seg_

bool protocols::splice::Splice::min_seg_

private

Referenced by apply(), and parse_my_tag().

◆ mover_name_

std::string protocols::splice::Splice::mover_name_

private

Referenced by apply(), chainbreak_check(), copy_stretch(), find_dbase_entry(), parse_my_tag(), rb_adjust_template(), and superimpose_source_on_pose().

◆ mover_tag_

utility::pointer::shared_ptr< basic::datacache::DataMapObj< std::string > > protocols::splice::Splice::mover_tag_

private

Referenced by apply(), and parse_my_tag().

◆ order_segments_

std::map< std::string, utility::vector1< std::string > > protocols::splice::Splice::order_segments_

private

Referenced by parse_my_tag(), and Splice().

◆ Pdb4LetName_

std::string protocols::splice::Splice::Pdb4LetName_

private

Referenced by add_sequence_constraints(), apply(), and generate_sequence_profile().

◆ pdb_segments_

std::map< std::string, std::string > protocols::splice::Splice::pdb_segments_

private

Referenced by apply(), find_dbase_entry(), generate_sequence_profile(), load_pdb_segments_from_pose_comments(), modify_pdb_segments_with_current_segment(), and Splice().

◆ pdb_to_H3_seq_map_

std::map< std::string, std::string > protocols::splice::Splice::pdb_to_H3_seq_map_

private

Referenced by generate_sequence_profile(), and parse_my_tag().

◆ poly_ala_

bool protocols::splice::Splice::poly_ala_

private

Referenced by poly_ala().

◆ profile_weight_away_from_interface_

core::Real protocols::splice::Splice::profile_weight_away_from_interface_

private

Referenced by profile_weight_away_from_interface(), and Splice().

◆ protein_family_

std::string protocols::splice::Splice::protein_family_

private

Referenced by apply(), find_dbase_entry(), find_non_active_site_cut_site(), generate_sequence_profile(), parse_my_tag(), protein_family(), and superimpose_source_on_pose().

◆ protein_family_to_database_

std::map< std::string, std::string> protocols::splice::Splice::protein_family_to_database_

private

Referenced by parse_my_tag(), and Splice().

◆ randomize_cut_

bool protocols::splice::Splice::randomize_cut_

private

Referenced by randomize_cut().

◆ rb_sensitive_

bool protocols::splice::Splice::rb_sensitive_

private

Referenced by rb_sensitive(), and Splice().

◆ repack_shell_

core::Real protocols::splice::Splice::repack_shell_

private

Referenced by repack_shell(), and Splice().

◆ res_move_

core::Size protocols::splice::Splice::res_move_

private

Referenced by res_move().

◆ restrict_to_repacking_chain2_

bool protocols::splice::Splice::restrict_to_repacking_chain2_

private

Referenced by restrict_to_repacking_chain2(), and Splice().

◆ rms_cutoff_

core::Real protocols::splice::Splice::rms_cutoff_

private

Referenced by rms_cutoff().

◆ rms_cutoff_loop_

core::Real protocols::splice::Splice::rms_cutoff_loop_

private

Referenced by rms_cutoff_loop().

◆ rtmin_

bool protocols::splice::Splice::rtmin_

private

Referenced by rtmin().

◆ saved_fold_tree_

core::kinematics::FoldTreeOP protocols::splice::Splice::saved_fold_tree_

private

Referenced by apply().

◆ saved_from_res_

core::Size protocols::splice::Splice::saved_from_res_

private

Referenced by retrieve_values(), and save_values().

◆ saved_to_res_

core::Size protocols::splice::Splice::saved_to_res_

private

Referenced by retrieve_values(), and save_values().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::splice::Splice::scorefxn_

private

Referenced by scorefxn().

◆ segment_names_ordered_

utility::vector1< std::string > protocols::splice::Splice::segment_names_ordered_

private

Referenced by find_dbase_entry(), generate_sequence_profile(), get_segment_names_ordered(), parse_my_tag(), set_fold_tree(), and set_segment_names_ordered().

◆ segment_type_

std::string protocols::splice::Splice::segment_type_

private

Referenced by add_sequence_constraints(), apply(), copy_stretch(), find_dbase_entry(), find_non_active_site_cut_site(), generate_sequence_profile(), modify_pdb_segments_with_current_segment(), parse_my_tag(), read_splice_segments(), and superimpose_source_on_pose().

◆ set_cut_res_

core::Size protocols::splice::Splice::set_cut_res_

private

Referenced by set_cut_res().

◆ set_fold_tree_only_

bool protocols::splice::Splice::set_fold_tree_only_

private

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

◆ skip_alignment_

bool protocols::splice::Splice::skip_alignment_

private

Referenced by skip_alignment(), and Splice().

◆ source_pdb_

std::string protocols::splice::Splice::source_pdb_

private

Referenced by apply(), generate_sequence_profile(), parse_my_tag(), and source_pdb().

◆ source_pdb_from_res_

core::Size protocols::splice::Splice::source_pdb_from_res_

private

Referenced by source_pdb_from_res().

◆ source_pdb_to_res_

core::Size protocols::splice::Splice::source_pdb_to_res_

private

Referenced by source_pdb_to_res().

◆ source_pose_

core::pose::PoseOP protocols::splice::Splice::source_pose_

private

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

◆ splice_filter_

protocols::filters::FilterOP protocols::splice::Splice::splice_filter_

private

Referenced by splice_filter().

◆ splice_segments_

std::map< std::string, SpliceSegmentOP > protocols::splice::Splice::splice_segments_

private

Referenced by find_non_active_site_cut_site(), generate_sequence_profile(), parse_my_tag(), read_splice_segments(), and Splice().

◆ start_pose_

core::pose::PoseCOP protocols::splice::Splice::start_pose_

private

Referenced by parse_my_tag().

◆ superimposed_

bool protocols::splice::Splice::superimposed_

private

Referenced by superimposed().

◆ tail_segment_

std::string protocols::splice::Splice::tail_segment_

private

Referenced by add_dihedral_constraints(), apply(), find_dbase_entry(), and parse_my_tag().

◆ tail_torsion_database_

utility::vector1< ResidueBBDofs > protocols::splice::Splice::tail_torsion_database_

private

Referenced by apply(), and read_torsion_database().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::splice::Splice::task_factory_

private

Referenced by task_factory().

◆ template_file_

std::string protocols::splice::Splice::template_file_

private

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

◆ template_pose_

core::pose::PoseCOP protocols::splice::Splice::template_pose_

private

Referenced by apply(), find_dbase_entry(), parse_my_tag(), rb_adjust_template(), and set_fold_tree().

◆ thread_original_sequence_

bool protocols::splice::Splice::thread_original_sequence_

private

Referenced by thread_original_sequence().

◆ to_res_

core::pose::ResidueIndexDescriptionCOP protocols::splice::Splice::to_res_

private

Referenced by parse_my_tag(), and to_res().

◆ tolerance_

core::Real protocols::splice::Splice::tolerance_

private

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

◆ torsion_database_

utility::vector1< ResidueBBDofs > protocols::splice::Splice::torsion_database_

private

Referenced by apply(), find_dbase_entry(), parse_my_tag(), read_torsion_database(), set_fold_tree(), Splice(), and torsion_database().

◆ torsion_database_fname_

std::string protocols::splice::Splice::torsion_database_fname_

private

Referenced by apply(), generate_sequence_profile(), parse_my_tag(), read_torsion_database(), set_fold_tree(), and torsion_database_fname().

◆ use_sequence_profiles_

bool protocols::splice::Splice::use_sequence_profiles_

private

Referenced by add_sequence_constraints(), apply(), generate_sequence_profile(), parse_my_tag(), and read_splice_segments().

◆ vl_vh_cut

core::Size protocols::splice::Splice::vl_vh_cut

private

Referenced by apply(), set_fold_tree(), and tail_fold_tree().

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

src/protocols/splice/Splice.hh
src/protocols/splice/Splice.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ DataccacheBoolDataOP

◆ dbase_const_iterator

◆ Pose

Constructor & Destructor Documentation

◆ Splice()

◆ ~Splice()

Member Function Documentation

◆ add_coordinate_constraints()

◆ add_dihedral_constraints()

◆ add_sequence_constraints()

◆ add_sequence_constraints_only() [1/2]

◆ add_sequence_constraints_only() [2/2]

◆ allow_all_aa() [1/2]

◆ allow_all_aa() [2/2]

◆ apply()

◆ ccd() [1/2]

◆ ccd() [2/2]

◆ chain_num() [1/2]

◆ chain_num() [2/2]

◆ chainbreak_check()

◆ checkpointing_file() [1/2]

◆ checkpointing_file() [2/2]

◆ clone()

◆ coor_const()

◆ copy_stretch()

◆ correct_bb_O_placements()

◆ cut_secondarystruc() [1/2]

◆ cut_secondarystruc() [2/2]

◆ database_entry() [1/2]

◆ database_entry() [2/2]

◆ database_pdb_entry() [1/2]

◆ database_pdb_entry() [2/2]

◆ dbase_begin()

◆ dbase_end()

◆ dbase_iterate() [1/2]

◆ dbase_iterate() [2/2]

◆ delete_hairpin() [1/2]

◆ delete_hairpin() [2/2]

◆ delete_hairpin_c() [1/2]

◆ delete_hairpin_c() [2/2]

◆ delete_hairpin_n() [1/2]

◆ delete_hairpin_n() [2/2]

◆ delta_lengths() [1/2]

◆ delta_lengths() [2/2]

◆ design() [1/2]

◆ design() [2/2]

◆ design_shell() [1/2]

◆ design_shell() [2/2]

◆ design_task_factory() [1/2]

◆ design_task_factory() [2/2]

◆ dihedral_const()

◆ equal_length() [1/2]

◆ equal_length() [2/2]

◆ find_dbase_entry()

◆ find_non_active_site_cut_site()

◆ fold_tree()

◆ fresh_instance()

◆ from_res() [1/2]

◆ from_res() [2/2]

◆ generate_sequence_profile()

◆ get_current_seg()

◆ get_dofs_pdb_name()

◆ get_name()

◆ get_segment_names_ordered()

◆ load_from_checkpoint()

◆ load_pdb_segments_from_pose_comments()

◆ locked_res() [1/2]

◆ locked_res() [2/2]

◆ locked_res_id() [1/2]

◆ locked_res_id() [2/2]

◆ loop_dbase_file_name() [1/2]

◆ loop_dbase_file_name() [2/2]