#include <SpliceOut.hh>

Inheritance diagram for protocols::splice::SpliceOut:

[legend]

Public Types
typedef core::pose::Pose	Pose

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

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
	SpliceOut ()

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

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

	~SpliceOut () override

std::string	source_pdb () const

void	source_pdb (std::string const &s)

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	cut_secondarystruc (bool const r)

bool	cut_secondarystruc () const

bool	thread_original_sequence () const

void	thread_original_sequence (bool const s)

std::string	dbase_file_name () const

void	dbase_file_name (std::string const &f)
	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...

protocols::filters::FilterOP	splice_filter () const

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

void	ccd_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

void	min_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

void	tail_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

int	SpliceOutFilter (core::pose::Pose *pose)

int	SpliceOutRMSDFilter (core::pose::Pose *pose)

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

virtual void	superimpose_source_on_pose (core::pose::Pose const &pose, core::pose::Pose &source_pose)
	add dihedral constraint to grafted loop according to source pdb dihedral angles More...

bool	rb_sensitive () const

void	rb_sensitive (bool const r)

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

void	check_source_segment ()

void	copy_dofs_from_source ()

virtual void	place_cut_site_in_segment (core::pose::Pose const &pose)
	choose cutsite randomly within loop residues on the loop (no 2ary structure) More...

void	superimposed (bool const b)

bool	superimposed ()

void	source_from_res (core::Size const c)

core::Size	source_from_res ()

void	source_to_res (core::Size const c)

core::Size	source_to_res ()

void	handle_mover_tag (TagCOP const tag, basic::datacache::DataMap &data)

virtual void	set_fold_tree_nodes (core::pose::Pose const &pose)

virtual void	set_source_from_to_res ()

virtual core::Size	set_anchor_res ()

virtual void	build_ideal_segment (core::pose::Pose &pose)

virtual void	set_loop_length_change (protocols::protein_interface_design::movers::LoopLengthChange &llc)

virtual void	write_database_to_file (core::pose::Pose const &pose)

void	parse_SpliceOut_tags (TagCOP const tag, basic::datacache::DataMap &data)

virtual void	abstract_parse_tag (TagCOP const tag)

void	randomize_cut (bool const b)

bool	randomize_cut ()

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

virtual std::string	name_for_filter ()

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

static std::string	mover_name ()

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
void	save_values ()

void	retrieve_values ()

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	check_pose_pssm_match (core::pose::PoseOP pose, utility::vector1< core::sequence::SequenceProfileOP > profile_vector)

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...

Protected Attributes
protocols::moves::MoverOP	submover_

core::Real	design_shell_ = 6.0

core::Real	repack_shell_ = 8.0

core::scoring::ScoreFunctionOP	scorefxn_

core::pose::PoseOP	source_pose_

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

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

bool	ignore_chain_break_ = false

core::Real	tolerance_ = 0.23

std::vector< std::string >	mover_type_ = {"MinMover","LoopMover_Refine_CCD","TailSegmentMover"}

utility::vector1< std::array< int, 3 > >	fold_tree_nodes_

bool	write_to_database_ = true

SpliceManager	splicemanager

void(SpliceOut::*	call_mover )(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

void(SpliceOut::*	call_mover_tail_ )(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

Private Attributes
core::Size	saved_from_res_ = 0

core::Size	saved_to_res_ = 0

std::string	source_pdb_ = ""

core::Real	rms_cutoff_ = 999999

core::Real	rms_cutoff_loop_

bool	randomize_cut_ = false
	true: place cut in a randomly chosen loop residue, if available. false: place cut at loop's end More...

bool	cut_secondarystruc_ = false

core::pack::task::TaskFactoryOP	task_factory_
	true: allows placing the cut within secondary structures More...

core::kinematics::FoldTreeOP	saved_fold_tree_

bool	thread_original_sequence_ = false

std::string	dbase_file_name_ = ""

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

protocols::filters::FilterOP	splice_filter_

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

bool	rb_sensitive_ = false

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

bool	CG_const_ = false

bool	delete_hairpin_ = false

core::Size	delete_hairpin_n_ = 0

core::Size	delete_hairpin_c_ = 0

core::Size	source_from_res_ = 0

core::Size	source_to_res_ = 0

bool	superimposed_ = false

Member Typedef Documentation

◆ dbase_const_iterator

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

◆ Pose

typedef core::pose::Pose protocols::splice::SpliceOut::Pose

Constructor & Destructor Documentation

◆ SpliceOut()

protocols::splice::SpliceOut::SpliceOut ( )

References protocols::splice::SpliceManager::adjust_stem_positions_by_template_, call_mover, core::io::mmtf::pdb_comments, protocols::splice::SpliceManager::profile_weight_away_from_interface(), protocols::splice::SpliceManager::rb_sensitive(), splicemanager, and protocols::splice::SpliceManager::template_file().

◆ ~SpliceOut()

protocols::splice::SpliceOut::~SpliceOut ( )

overridedefault

Member Function Documentation

◆ abstract_parse_tag()

void protocols::splice::SpliceOut::abstract_parse_tag ( TagCOP const tag )

virtual

Reimplemented in protocols::splice::SpliceOutTail.

References protocols::splice::SpliceManager::allowed_cuts(), cut_secondarystruc(), protocols::splice::SpliceManager::cut_site(), core::pose::parse_resnum(), randomize_cut(), splicemanager, protocols::splice::SpliceManager::template_from_res(), protocols::splice::SpliceManager::template_pose(), protocols::splice::SpliceManager::template_to_res(), and tolerance_.

Referenced by parse_my_tag(), and protocols::splice::SpliceOutAntibody::parse_my_tag().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceOutAntibody.

Referenced by protocols::splice::SpliceOutAntibody::apply(), and SpliceOutFilter().

◆ build_ideal_segment()

void protocols::splice::SpliceOut::build_ideal_segment ( core::pose::Pose & pose )

virtual

Reimplemented in protocols::splice::SpliceOutTail, protocols::splice::SpliceOutAntibody, protocols::splice::SpliceInTail, protocols::splice::SpliceInAntibody, and protocols::splice::SpliceIn.

References core::chemical::aa_from_oneletter_code(), core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), protocols::splice::SpliceManager::cut_site(), protocols::splice::SpliceManager::debug(), core::pose::Pose::delete_residue_range_slow(), core::pose::Pose::dump_pdb(), protocols::splice::SpliceManager::mover_name(), core::chemical::name_from_aa(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), splicemanager, and protocols::splice::TR().

Referenced by apply(), and protocols::splice::SpliceOutAntibody::build_ideal_segment().

◆ ccd_mover()

void protocols::splice::SpliceOut::ccd_mover	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	mm
	)

References protocols::splice::SpliceManager::cut_site(), protocols::splice::SpliceManager::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), protocols::splice::SpliceManager::mover_name(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), scorefxn(), splicemanager, submover_, protocols::splice::SpliceManager::task_factory(), protocols::splice::TR(), and protocols::splice::TR_ccd().

Referenced by handle_mover_tag(), and protocols::splice::SpliceOutAntibody::handle_tail_mover_tag().

◆ check_pose_pssm_match()

void protocols::splice::SpliceOut::check_pose_pssm_match	(	core::pose::PoseOP	pose,
		utility::vector1< core::sequence::SequenceProfileOP >	profile_vector
	)

protected

References protocols::splice::SpliceManager::source_pdb_name(), splicemanager, and protocols::splice::TR_pssm().

◆ check_source_segment()

void protocols::splice::SpliceOut::check_source_segment ( )

References protocols::simple_moves::CutChainMover::bond_length(), protocols::simple_moves::CutChainMover::chain_cut(), ignore_chain_break_, source_from_res(), source_pdb_, source_pose_, source_to_res(), and protocols::splice::TR().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::splice::SpliceOut::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.

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

◆ copy_dofs_from_source()

void protocols::splice::SpliceOut::copy_dofs_from_source ( )

References protocols::splice::SpliceManager::dofs(), protocols::splice::BBDofs::omega(), protocols::splice::BBDofs::phi(), protocols::splice::BBDofs::psi(), protocols::splice::BBDofs::resid(), protocols::splice::BBDofs::resn(), source_from_res(), source_pose_, source_to_res(), and splicemanager.

Referenced by apply().

◆ cut_secondarystruc() [1/2]

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

inline

References cut_secondarystruc_.

Referenced by abstract_parse_tag(), and place_cut_site_in_segment().

◆ cut_secondarystruc() [2/2]

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

inline

References cut_secondarystruc_.

◆ dbase_file_name() [1/2]

std::string protocols::splice::SpliceOut::dbase_file_name ( ) const

References dbase_file_name_.

◆ dbase_file_name() [2/2]

void protocols::splice::SpliceOut::dbase_file_name ( std::string const & f )

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 dbase_file_name_.

◆ delete_hairpin() [1/2]

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

inline

References delete_hairpin_.

Referenced by parse_SpliceOut_tags(), remove_hairpin(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ delete_hairpin() [2/2]

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

inline

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

◆ delete_hairpin_c() [1/2]

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

inline

References delete_hairpin_c_.

Referenced by parse_SpliceOut_tags(), remove_hairpin(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ delete_hairpin_c() [2/2]

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

inline

References delete_hairpin_c_.

◆ delete_hairpin_n() [1/2]

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

inline

References delete_hairpin_n_.

Referenced by parse_SpliceOut_tags(), remove_hairpin(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ delete_hairpin_n() [2/2]

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

inline

References delete_hairpin_n_.

◆ find_non_active_site_cut_site()

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

protected

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(), protocols::splice::parse_pdb_code(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::splice::SpliceManager::segment_type(), protocols::splice::SpliceManager::splice_segments(), splicemanager, core::pose::Pose::total_residue(), protocols::splice::TR(), and protocols::splice::TR_pssm().

◆ fresh_instance()

protocols::moves::MoverOP protocols::splice::SpliceOut::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.

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

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

◆ handle_mover_tag()

void protocols::splice::SpliceOut::handle_mover_tag	(	TagCOP const	tag,
		basic::datacache::DataMap &	data
	)

References call_mover, ccd_mover(), min_mover(), mover_name(), mover_type_, protocols::rosetta_scripts::parse_mover_or_null(), submover_, tail_mover(), and protocols::splice::TR().

Referenced by parse_SpliceOut_tags().

◆ load_pdb_segments_from_pose_comments()

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

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 core::pose::get_all_comments(), protocols::splice::SpliceManager::pdb_segments(), splicemanager, protocols::splice::TR(), and protocols::hybridization::val.

◆ min_mover()

void protocols::splice::SpliceOut::min_mover	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	mm
	)

References protocols::splice::SpliceManager::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), protocols::splice::SpliceManager::mover_name(), splicemanager, submover_, and protocols::splice::TR_min().

Referenced by handle_mover_tag(), protocols::splice::SpliceOutAntibody::handle_tail_mover_tag(), protocols::splice::SpliceIn::minimize_segment(), and minimize_segment().

◆ minimize_segment()

void protocols::splice::SpliceOut::minimize_segment ( core::pose::Pose & pose )

References protocols::splice::SpliceManager::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), min_mover(), protocols::splice::SpliceManager::mm(), protocols::splice::SpliceManager::mover_name(), core::pose::Pose::remove_constraints(), scorefxn(), splicemanager, and protocols::splice::TR().

Referenced by apply().

◆ mover_name()

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

static

Referenced by handle_mover_tag(), and provide_xml_schema().

◆ name_for_filter()

std::string protocols::splice::SpliceOut::name_for_filter ( )

virtual

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

Referenced by protocols::splice::SpliceOutAntibody::name_for_filter(), and SpliceOutFilter().

◆ parse_my_tag()

void protocols::splice::SpliceOut::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.

Reimplemented in protocols::splice::SpliceOutAntibody.

References abstract_parse_tag(), core::pose::parse_resnum(), core::scoring::parse_score_function(), protocols::splice::SpliceManager::parse_segments(), parse_SpliceOut_tags(), protocols::splice::SpliceManager::parse_tags(), scorefxn(), source_from_res(), source_pose_, source_to_res(), splicemanager, and superimposed().

◆ parse_SpliceOut_tags()

void protocols::splice::SpliceOut::parse_SpliceOut_tags	(	TagCOP const	tag,
		basic::datacache::DataMap &	data
	)

References CG_const_, delete_hairpin(), delete_hairpin_c(), delete_hairpin_n(), handle_mover_tag(), ignore_chain_break_, protocols::rosetta_scripts::parse_filter(), core::import_pose::pose_from_file(), rms_cutoff(), rms_cutoff_loop(), source_pdb(), source_pdb_, source_pose_, splice_filter(), superimposed(), and protocols::splice::TR().

Referenced by parse_my_tag(), and protocols::splice::SpliceOutAntibody::parse_my_tag().

◆ place_cut_site_in_segment()

void protocols::splice::SpliceOut::place_cut_site_in_segment ( core::pose::Pose const & pose )

virtual

choose cutsite randomly within loop residues on the loop (no 2ary structure)

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

References core::pose::Pose::conformation(), cut_secondarystruc(), protocols::splice::SpliceManager::cut_site(), protocols::simple_filters::dssp(), protocols::mean_field::min(), core::conformation::Residue::name1(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), core::conformation::Conformation::residue(), core::scoring::rg, source_from_res(), source_pose_, source_to_res(), splicemanager, and protocols::splice::TR().

Referenced by apply(), and protocols::splice::SpliceOutAntibody::place_cut_site_in_segment().

◆ provide_xml_schema()

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

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), protocols::splice::SpliceOut_complex_type_name_for_subsubtag(), protocols::splice::SpliceOut_complex_type_name_for_subtag(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

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

◆ randomize_cut() [1/2]

bool protocols::splice::SpliceOut::randomize_cut ( )

inline

References randomize_cut_.

Referenced by abstract_parse_tag().

◆ randomize_cut() [2/2]

void protocols::splice::SpliceOut::randomize_cut ( bool const b )

inline

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

◆ rb_sensitive() [1/2]

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

inline

References rb_sensitive_.

◆ rb_sensitive() [2/2]

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

inline

References rb_sensitive_.

◆ remove_hairpin()

void protocols::splice::SpliceOut::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.

◆ retrieve_values()

void protocols::splice::SpliceOut::retrieve_values ( )

protected

References protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), saved_from_res_, saved_to_res_, and splicemanager.

Referenced by SpliceOutFilter(), and SpliceOutRMSDFilter().

◆ rms_cutoff() [1/2]

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

inline

References rms_cutoff_.

Referenced by parse_SpliceOut_tags(), and SpliceOutRMSDFilter().

◆ rms_cutoff() [2/2]

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

inline

References rms_cutoff_.

◆ rms_cutoff_loop() [1/2]

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

inline

References rms_cutoff_loop_.

Referenced by parse_SpliceOut_tags(), and SpliceOutRMSDFilter().

◆ rms_cutoff_loop() [2/2]

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

inline

References rms_cutoff_loop_.

◆ save_values()

void protocols::splice::SpliceOut::save_values ( )

protected

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 protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), saved_from_res_, saved_to_res_, and splicemanager.

◆ scorefxn() [1/2]

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

References scorefxn_.

Referenced by apply(), ccd_mover(), minimize_segment(), parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), and tail_mover().

◆ scorefxn() [2/2]

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

References scorefxn_.

◆ set_anchor_res()

core::Size protocols::splice::SpliceOut::set_anchor_res ( )

virtual

Reimplemented in protocols::splice::SpliceOutTail, protocols::splice::SpliceOutAntibody, protocols::splice::SpliceInTail, protocols::splice::SpliceInAntibody, and protocols::splice::SpliceIn.

References protocols::splice::SpliceManager::pose_from_res(), and splicemanager.

Referenced by apply(), and protocols::splice::SpliceOutAntibody::set_anchor_res().

◆ set_fold_tree_nodes()

void protocols::splice::SpliceOut::set_fold_tree_nodes ( core::pose::Pose const & pose )

virtual

Reimplemented in protocols::splice::SpliceOutTail, protocols::splice::SpliceOutAntibody, protocols::splice::SpliceInTail, protocols::splice::SpliceInAntibody, and protocols::splice::SpliceIn.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::splice::SpliceManager::cut_site(), fold_tree_nodes_, core::conformation::Conformation::num_chains(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), core::pose::residue_center_of_mass(), and splicemanager.

Referenced by apply(), and protocols::splice::SpliceOutAntibody::set_fold_tree_nodes().

◆ set_loop_length_change()

void protocols::splice::SpliceOut::set_loop_length_change ( protocols::protein_interface_design::movers::LoopLengthChange & llc )

virtual

Reimplemented in protocols::splice::SpliceOutTail, protocols::splice::SpliceOutAntibody, protocols::splice::SpliceInTail, protocols::splice::SpliceInAntibody, and protocols::splice::SpliceIn.

References protocols::splice::SpliceManager::cut_site(), protocols::protein_interface_design::movers::LoopLengthChange::delta(), protocols::protein_interface_design::movers::LoopLengthChange::loop_end(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::residue_diff(), and splicemanager.

Referenced by apply(), and protocols::splice::SpliceOutAntibody::set_loop_length_change().

◆ set_source_from_to_res()

void protocols::splice::SpliceOut::set_source_from_to_res ( )

virtual

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

References protocols::rosetta_scripts::find_nearest_res(), source_from_res(), source_pose_, source_to_res(), splicemanager, protocols::splice::SpliceManager::template_from_res(), protocols::splice::SpliceManager::template_pose(), protocols::splice::SpliceManager::template_to_res(), and protocols::splice::TR().

Referenced by apply(), and protocols::splice::SpliceOutAntibody::set_source_from_to_res().

◆ source_from_res() [1/2]

core::Size protocols::splice::SpliceOut::source_from_res ( )

inline

References source_from_res_.

Referenced by protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), apply(), protocols::splice::SpliceOutAntibody::apply(), check_source_segment(), copy_dofs_from_source(), parse_my_tag(), place_cut_site_in_segment(), set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), SpliceOutRMSDFilter(), superimpose_source_on_pose(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

◆ source_from_res() [2/2]

void protocols::splice::SpliceOut::source_from_res ( core::Size const c )

inline

References source_from_res_.

◆ source_pdb() [1/2]

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

inline

References source_pdb_.

Referenced by protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), and parse_SpliceOut_tags().

◆ source_pdb() [2/2]

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

inline

References source_pdb_.

◆ source_to_res() [1/2]

core::Size protocols::splice::SpliceOut::source_to_res ( )

inline

References source_to_res_.

Referenced by apply(), protocols::splice::SpliceOutAntibody::apply(), check_source_segment(), copy_dofs_from_source(), parse_my_tag(), place_cut_site_in_segment(), set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), and superimpose_source_on_pose().

◆ source_to_res() [2/2]

void protocols::splice::SpliceOut::source_to_res ( core::Size const c )

inline

References source_to_res_.

◆ splice_filter() [1/2]

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

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 splice_filter_.

Referenced by parse_SpliceOut_tags(), and SpliceOutFilter().

◆ splice_filter() [2/2]

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

References splice_filter_.

◆ SpliceOutFilter()

int protocols::splice::SpliceOut::SpliceOutFilter ( core::pose::Pose * pose )

References core::pose::add_comment(), protocols::protein_interface_design::movers::AddChainBreak::apply(), apply(), protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), protocols::splice::SpliceManager::cut_site(), protocols::moves::FAIL_RETRY, protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), core::pose::Pose::fold_tree(), name_for_filter(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), retrieve_values(), protocols::moves::Mover::set_last_move_status(), splice_filter(), splicemanager, core::id::to_string(), and protocols::splice::TR().

Referenced by apply().

◆ SpliceOutRMSDFilter()

int protocols::splice::SpliceOut::SpliceOutRMSDFilter ( core::pose::Pose * pose )

References protocols::splice::calculate_rmsd(), protocols::splice::SpliceManager::dofs(), protocols::moves::FAIL_RETRY, protocols::splice::SpliceManager::pose_from_res(), retrieve_values(), rms_cutoff(), rms_cutoff_loop(), protocols::moves::Mover::set_last_move_status(), source_from_res(), source_pose_, and splicemanager.

Referenced by apply().

◆ superimpose_source_on_pose()

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

virtual

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

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

References protocols::toolbox::apply_superposition_transform(), protocols::splice::coords(), protocols::splice::SpliceManager::debug(), core::pose::Pose::dump_pdb(), source_from_res(), source_to_res(), splicemanager, superimposed(), protocols::seeded_abinitio::superposition_transform(), protocols::splice::SpliceManager::template_from_res(), protocols::splice::SpliceManager::template_to_res(), and protocols::splice::TR().

Referenced by apply(), and protocols::splice::SpliceOutAntibody::superimpose_source_on_pose().

◆ superimposed() [1/2]

bool protocols::splice::SpliceOut::superimposed ( )

inline

References superimposed_.

Referenced by protocols::splice::SpliceOutAntibody::apply(), parse_my_tag(), parse_SpliceOut_tags(), superimpose_source_on_pose(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

◆ superimposed() [2/2]

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

inline

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

◆ tail_mover()

void protocols::splice::SpliceOut::tail_mover	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	mm
	)

References protocols::splice::SpliceManager::debug(), core::pose::Pose::dump_pdb(), protocols::splice::SpliceManager::mover_name(), scorefxn(), protocols::moves::Mover::show(), splicemanager, submover_, protocols::splice::SpliceManager::task_factory(), and protocols::splice::TR_tail().

Referenced by handle_mover_tag(), and protocols::splice::SpliceOutAntibody::handle_tail_mover_tag().

◆ thread_original_sequence() [1/2]

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

inline

References thread_original_sequence_.

◆ thread_original_sequence() [2/2]

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

inline

References thread_original_sequence_.

◆ write_database_to_file()

void protocols::splice::SpliceOut::write_database_to_file ( core::pose::Pose const & pose )

virtual

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

References protocols::splice::SpliceManager::cut_site(), protocols::splice::SpliceManager::dbase_file_name(), core::conformation::Residue::name3(), core::pose::Pose::omega(), core::pose::Pose::phi(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), core::pose::Pose::psi(), core::pose::Pose::residue(), protocols::splice::SpliceManager::source_pdb_name(), splicemanager, protocols::splice::SpliceManager::template_from_res(), protocols::splice::SpliceManager::template_to_res(), protocols::splice::TR(), and write_to_database_.

Referenced by apply(), protocols::splice::SpliceOutAntibody::apply(), and protocols::splice::SpliceOutAntibody::write_database_to_file().

Member Data Documentation

◆ call_mover

void(SpliceOut::* protocols::splice::SpliceOut::call_mover) (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

protected

Referenced by apply(), protocols::splice::SpliceOutAntibody::apply(), handle_mover_tag(), SpliceOut(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ call_mover_tail_

void(SpliceOut::* protocols::splice::SpliceOut::call_mover_tail_) (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

protected

Referenced by protocols::splice::SpliceOutAntibody::apply(), and protocols::splice::SpliceOutAntibody::handle_tail_mover_tag().

◆ CG_const_

bool protocols::splice::SpliceOut::CG_const_ = false

private

Referenced by apply(), and parse_SpliceOut_tags().

◆ cut_secondarystruc_

bool protocols::splice::SpliceOut::cut_secondarystruc_ = false

private

Referenced by cut_secondarystruc().

◆ database_segment_map_

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

private

◆ dbase_file_name_

std::string protocols::splice::SpliceOut::dbase_file_name_ = ""

private

Referenced by dbase_file_name().

◆ delete_hairpin_

bool protocols::splice::SpliceOut::delete_hairpin_ = false

private

Referenced by delete_hairpin().

◆ delete_hairpin_c_

core::Size protocols::splice::SpliceOut::delete_hairpin_c_ = 0

private

Referenced by delete_hairpin_c().

◆ delete_hairpin_n_

core::Size protocols::splice::SpliceOut::delete_hairpin_n_ = 0

private

Referenced by delete_hairpin_n().

◆ design_shell_

core::Real protocols::splice::SpliceOut::design_shell_ = 6.0

protected

Referenced by protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ fold_tree_nodes_

utility::vector1<std::array<int, 3> > protocols::splice::SpliceOut::fold_tree_nodes_

protected

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), apply(), set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), and protocols::splice::SpliceOutTail::set_fold_tree_nodes().

◆ ignore_chain_break_

bool protocols::splice::SpliceOut::ignore_chain_break_ = false

protected

Referenced by check_source_segment(), parse_SpliceOut_tags(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ mover_tag_

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

private

◆ mover_type_

std::vector< std::string> protocols::splice::SpliceOut::mover_type_ = {"MinMover","LoopMover_Refine_CCD","TailSegmentMover"}

protected

Referenced by handle_mover_tag(), protocols::splice::SpliceOutAntibody::handle_tail_mover_tag(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ order_segments_

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

private

◆ pdb_to_H3_seq_map_

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

protected

Referenced by protocols::splice::SpliceOutAntibody::parse_my_tag().

◆ protein_family_to_database_

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

protected

Referenced by protocols::splice::SpliceInAntibody::SpliceInAntibody(), and protocols::splice::SpliceOutAntibody::SpliceOutAntibody().

◆ randomize_cut_

bool protocols::splice::SpliceOut::randomize_cut_ = false

private

true: place cut in a randomly chosen loop residue, if available. false: place cut at loop's end

Referenced by randomize_cut().

◆ rb_sensitive_

bool protocols::splice::SpliceOut::rb_sensitive_ = false

private

Referenced by rb_sensitive().

◆ repack_shell_

core::Real protocols::splice::SpliceOut::repack_shell_ = 8.0

protected

Referenced by protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

◆ rms_cutoff_

core::Real protocols::splice::SpliceOut::rms_cutoff_ = 999999

private

Referenced by rms_cutoff().

◆ rms_cutoff_loop_

core::Real protocols::splice::SpliceOut::rms_cutoff_loop_

private

Referenced by rms_cutoff_loop().

◆ saved_fold_tree_

core::kinematics::FoldTreeOP protocols::splice::SpliceOut::saved_fold_tree_

private

Referenced by apply().

◆ saved_from_res_

core::Size protocols::splice::SpliceOut::saved_from_res_ = 0

private

Referenced by retrieve_values(), and save_values().

◆ saved_to_res_

core::Size protocols::splice::SpliceOut::saved_to_res_ = 0

private

Referenced by retrieve_values(), and save_values().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::splice::SpliceOut::scorefxn_

protected

Referenced by protocols::splice::SpliceIn::scorefxn(), protocols::splice::SpliceInAntibody::scorefxn(), and scorefxn().

◆ source_from_res_

core::Size protocols::splice::SpliceOut::source_from_res_ = 0

private

Referenced by source_from_res().

◆ source_pdb_

std::string protocols::splice::SpliceOut::source_pdb_ = ""

private

Referenced by apply(), check_source_segment(), parse_SpliceOut_tags(), and source_pdb().

◆ source_pose_

core::pose::PoseOP protocols::splice::SpliceOut::source_pose_

protected

Referenced by protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), apply(), protocols::splice::SpliceOutAntibody::apply(), check_source_segment(), copy_dofs_from_source(), parse_my_tag(), parse_SpliceOut_tags(), place_cut_site_in_segment(), set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), and SpliceOutRMSDFilter().

◆ source_to_res_

core::Size protocols::splice::SpliceOut::source_to_res_ = 0

private

Referenced by source_to_res().

◆ splice_filter_

protocols::filters::FilterOP protocols::splice::SpliceOut::splice_filter_

private

Referenced by splice_filter().

◆ splicemanager

SpliceManager protocols::splice::SpliceOut::splicemanager

protected

◆ submover_

protocols::moves::MoverOP protocols::splice::SpliceOut::submover_

protected

Referenced by apply(), protocols::splice::SpliceOutAntibody::apply(), ccd_mover(), handle_mover_tag(), min_mover(), and tail_mover().

◆ superimposed_

bool protocols::splice::SpliceOut::superimposed_ = false

private

Referenced by superimposed().

◆ task_factory_

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

private

true: allows placing the cut within secondary structures

◆ thread_original_sequence_

bool protocols::splice::SpliceOut::thread_original_sequence_ = false

private

Referenced by thread_original_sequence().

◆ tolerance_

core::Real protocols::splice::SpliceOut::tolerance_ = 0.23

protected

◆ write_to_database_

bool protocols::splice::SpliceOut::write_to_database_ = true

protected

Referenced by protocols::splice::SpliceOutAntibody::apply(), write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

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

src/protocols/splice/SpliceOut.hh
src/protocols/splice/SpliceOut.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Member Typedef Documentation

◆ dbase_const_iterator

◆ Pose

Constructor & Destructor Documentation

◆ SpliceOut()

◆ ~SpliceOut()

Member Function Documentation

◆ abstract_parse_tag()

◆ apply()

◆ build_ideal_segment()

◆ ccd_mover()

◆ check_pose_pssm_match()

◆ check_source_segment()

◆ clone()

◆ copy_dofs_from_source()

◆ cut_secondarystruc() [1/2]

◆ cut_secondarystruc() [2/2]

◆ dbase_file_name() [1/2]

◆ dbase_file_name() [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]

◆ find_non_active_site_cut_site()

◆ fresh_instance()

◆ get_name()

◆ handle_mover_tag()

◆ load_pdb_segments_from_pose_comments()

◆ min_mover()

◆ minimize_segment()

◆ mover_name()

◆ name_for_filter()

◆ parse_my_tag()

◆ parse_SpliceOut_tags()

◆ place_cut_site_in_segment()

◆ provide_xml_schema()

◆ randomize_cut() [1/2]

◆ randomize_cut() [2/2]

◆ rb_sensitive() [1/2]

◆ rb_sensitive() [2/2]

◆ remove_hairpin()

◆ retrieve_values()

◆ rms_cutoff() [1/2]

◆ rms_cutoff() [2/2]

◆ rms_cutoff_loop() [1/2]

◆ rms_cutoff_loop() [2/2]

◆ save_values()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

◆ set_anchor_res()

◆ set_fold_tree_nodes()

◆ set_loop_length_change()

◆ set_source_from_to_res()

◆ source_from_res() [1/2]

◆ source_from_res() [2/2]

◆ source_pdb() [1/2]

◆ source_pdb() [2/2]

◆ source_to_res() [1/2]

◆ source_to_res() [2/2]

◆ splice_filter() [1/2]

◆ splice_filter() [2/2]

◆ SpliceOutFilter()

◆ SpliceOutRMSDFilter()

◆ superimpose_source_on_pose()

◆ superimposed() [1/2]

◆ superimposed() [2/2]

◆ tail_mover()

◆ thread_original_sequence() [1/2]

◆ thread_original_sequence() [2/2]

◆ write_database_to_file()

Member Data Documentation

◆ call_mover