#include <SpliceInAntibody.hh>

Inheritance diagram for protocols::splice::SpliceInAntibody:

[legend]

Public Member Functions
	SpliceInAntibody ()

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...

	~SpliceInAntibody () override

core::Size	find_dbase_entry (core::pose::Pose const &pose) override

core::Size	database_entry () const

void	database_entry (core::Size const d)

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

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

bool	dbase_iterate () const

void	dbase_iterate (bool const d)

bool	min_seg () const

void	min_seg (bool const d)

void	database_pdb_entry (std::string const &s)

std::string	database_pdb_entry () const

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

core::scoring::ScoreFunctionOP	scorefxn () const

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

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

core::Size	set_anchor_res () override

void	find_vl_vh_cut (core::pose::Pose pose)

void	update_vl_vh_cut ()

void	find_disulfide_postions (core::pose::Pose const &pose, utility::vector1< core::Size > &cys_pos)

void	assign_from_res_to_res (core::pose::Pose const &pose) override

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

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

void	antibody_DB (std::string const &s)

std::string	antibody_DB ()

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

Public Member Functions inherited from protocols::splice::SpliceInTail
	SpliceInTail ()

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...

	~SpliceInTail () override

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

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

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

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

core::Size	set_anchor_res () override

core::Size	find_dbase_entry (core::pose::Pose const &pose) override

void	assign_from_res_to_res (core::pose::Pose const &pose) override

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

Public Member Functions inherited from protocols::splice::SpliceIn
	SpliceIn ()

	~SpliceIn () override

core::Size	database_entry () const

void	database_entry (core::Size const d)

void	load_from_checkpoint ()

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

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

bool	dbase_iterate () const

void	dbase_iterate (bool const d)

bool	min_seg () const

void	min_seg (bool const d)

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

virtual void	read_torsion_database ()

void	database_pdb_entry (std::string const &s)

std::string	database_pdb_entry () const

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

core::scoring::ScoreFunctionOP	scorefxn () const

void	rtmin (core::pose::Pose &pose, core::pack::task::TaskFactoryOP tf)

void	pack (core::pose::Pose &pose, core::pack::task::TaskFactoryOP tf)

Public Member Functions inherited from protocols::splice::SpliceOut
	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_source_from_to_res ()

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

static std::string	mover_name ()

Static Public Member Functions inherited from protocols::splice::SpliceIn
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	mover_name ()

Static Public Member Functions inherited from protocols::splice::SpliceOut
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...

Private Attributes
core::Size	vl_vh_cut_ =0

utility::vector1< core::Size >	pose_cys_pos_

utility::vector1< core::Size >	template_cys_pos_

std::string	antibody_DB_

int	tail_diff_ =0

Additional Inherited Members
Public Types inherited from protocols::splice::SpliceOut
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

Protected Member Functions inherited from protocols::splice::SpliceOut
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 inherited from protocols::splice::SpliceIn
utility::vector1< core::Size >	dbase_subset_

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

bool	dbase_iterate_

DataccacheBoolDataOP	end_dbase_subset_

std::string	checkpointing_file_

bool	min_seg_

utility::vector1< ResidueBBDofs >	torsion_database_

bool	first_pass_

core::Size	database_entry_

std::string	database_pdb_entry_

utility::vector1< ResidueBBDofs >	tail_torsion_database_

utility::vector1< int >	delta_lengths_

core::Size	allowed_cuts_

Protected Attributes inherited from protocols::splice::SpliceOut
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)

Constructor & Destructor Documentation

◆ SpliceInAntibody()

protocols::splice::SpliceInAntibody::SpliceInAntibody ( )

References protocols::splice::SpliceIn::allowed_cuts_, protocols::splice::SpliceIn::dbase_subset_, protocols::splice::SpliceManager::design_shell(), protocols::splice::SpliceIn::end_dbase_subset_, core::io::mmtf::pdb_comments, protocols::splice::SpliceManager::profile_weight_away_from_interface(), protocols::splice::SpliceOut::protein_family_to_database_, protocols::splice::SpliceManager::rb_sensitive(), protocols::splice::SpliceManager::repack_shell(), protocols::splice::SpliceManager::segment_names_ordered(), protocols::splice::SpliceOut::splicemanager, and protocols::splice::SpliceOut::tolerance_.

◆ ~SpliceInAntibody()

protocols::splice::SpliceInAntibody::~SpliceInAntibody ( )

overridedefault

Member Function Documentation

◆ adjust_n_ter_tail_length()

void protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length ( core::pose::Pose & pose )

References protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::protein_interface_design::movers::LoopLengthChange::delta(), protocols::protein_interface_design::movers::LoopLengthChange::direction(), protocols::splice::SpliceManager::dofs(), protocols::protein_interface_design::movers::LoopLengthChange::loop_end(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), pose_cys_pos_, protocols::splice::SpliceManager::segment_type(), protocols::splice::SpliceOut::splicemanager, protocols::protein_interface_design::movers::LoopLengthChange::tail(), tail_diff_, protocols::splice::TR(), and vl_vh_cut_.

Referenced by apply().

◆ adjust_template_jump()

void protocols::splice::SpliceInAntibody::adjust_template_jump ( core::pose::Pose & pose )

References protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SetAtomTree::chain(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), protocols::splice::SpliceOut::splicemanager, protocols::splice::SpliceManager::template_pose(), and protocols::splice::TR().

◆ antibody_DB() [1/2]

std::string protocols::splice::SpliceInAntibody::antibody_DB ( )

inline

References antibody_DB_.

Referenced by parse_my_tag().

◆ antibody_DB() [2/2]

void protocols::splice::SpliceInAntibody::antibody_DB ( std::string const & s )

inline

References antibody_DB_.

◆ apply()

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

overridevirtual

Main Method.

Reimplemented from protocols::splice::SpliceIn.

◆ assign_from_res_to_res()

void protocols::splice::SpliceInAntibody::assign_from_res_to_res ( core::pose::Pose const & pose )

overridevirtual

Reimplemented from protocols::splice::SpliceIn.

Referenced by apply().

◆ build_ideal_segment()

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

overridevirtual

Reimplemented from protocols::splice::SpliceIn.

References protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceManager::segment_type(), protocols::splice::SpliceOut::splicemanager, and protocols::splice::SpliceManager::tail_seg().

◆ clone()

protocols::moves::MoverOP protocols::splice::SpliceInAntibody::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::splice::SpliceIn.

◆ database_entry() [1/2]

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

inline

References protocols::splice::SpliceIn::database_entry_.

Referenced by parse_my_tag().

◆ database_entry() [2/2]

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

inline

References protocols::splice::SpliceIn::database_entry_.

◆ database_pdb_entry() [1/2]

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

inline

References protocols::splice::SpliceIn::database_pdb_entry_.

Referenced by apply(), and parse_my_tag().

◆ database_pdb_entry() [2/2]

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

inline

References protocols::splice::SpliceIn::database_pdb_entry_.

◆ dbase_begin()

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

inline

References protocols::splice::SpliceIn::dbase_subset_.

◆ dbase_end()

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

inline

References protocols::splice::SpliceIn::dbase_subset_.

◆ dbase_iterate() [1/2]

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

inline

References protocols::splice::SpliceIn::dbase_iterate_.

Referenced by apply(), and parse_my_tag().

◆ dbase_iterate() [2/2]

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

inline

References protocols::splice::SpliceIn::dbase_iterate_.

◆ find_dbase_entry()

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

overridevirtual

Reimplemented from protocols::splice::SpliceIn.

References protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::SpliceManager::segment_type(), protocols::splice::SpliceOut::splicemanager, and protocols::splice::SpliceManager::tail_seg().

Referenced by apply().

◆ find_disulfide_postions()

void protocols::splice::SpliceInAntibody::find_disulfide_postions	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > &	cys_pos
	)

References core::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by apply(), assign_from_res_to_res(), and set_fold_tree_nodes().

◆ find_vl_vh_cut()

void protocols::splice::SpliceInAntibody::find_vl_vh_cut ( core::pose::Pose pose )

References protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::TR(), and vl_vh_cut_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::splice::SpliceInAntibody::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::splice::SpliceIn.

◆ get_name()

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

overridevirtual

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

Reimplemented from protocols::splice::SpliceIn.

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

◆ min_seg() [1/2]

bool protocols::splice::SpliceInAntibody::min_seg ( ) const

inline

References protocols::splice::SpliceIn::min_seg_.

Referenced by parse_my_tag().

◆ min_seg() [2/2]

void protocols::splice::SpliceInAntibody::min_seg ( bool const d )

inline

References protocols::splice::SpliceIn::min_seg_.

◆ mover_name()

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

static

Referenced by provide_xml_schema().

◆ parse_my_tag()

void protocols::splice::SpliceInAntibody::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::splice::SpliceIn.