#include <MergePDBMover.hh>

Inheritance diagram for protocols::pose_creation::MergePDBMover:

[legend]

Classes
struct	Overlap

Public Types
typedef core::select::residue_selector::ResidueSelectorOP	ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorCOP	ResidueSelectorCOP

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
	MergePDBMover ()
	Constructor. More...

void	determine_overlap (Pose const pose, core::Size chain_id)
	Determines the overlaps. stores the start and end position in the struct Overlap. More...

bool	check_duplicate (Pose &pose)
	fast check to maake sure the pose isn't a structural duplicate More...

void	generate_overlaps (Pose &pose, core::Size chain_id)
	Uses the overlap to generate poses. More...

core::Size	closest_non_overlap_residue (core::pose::Pose const &pose, core::Size resid, core::Size start_overlap_resid, core::Size end_overlap_resid)
	Figures out the closest residue that's not part of the overlap. More...

void	increase_range_to_ignore_ss_element (core::pose::Pose const &pose, core::Size init_start, core::Size init_end, core::Size &ss_start, core::Size &ss_end)
	Gets the entire SS element the match is on. More...

void	copy_sequence (core::Size start_overlap_resid, core::Size end_overlap_resid, core::Size start_overlap_input_pose_resid, core::Size start_overlap_xml_pose_resid, core::pose::Pose const &input_pose, core::pose::Pose const &xml_pose, core::pose::Pose &output_pose)
	Copies the sequence in the overlap region as appropriate. This sets the initial residues before the pack and minimize is called. More...

void	pack_and_minimize (Pose const pose, core::Real baseline_score)
	packs and minimizes if no clashes as determined by score0 More...

core::pose::PoseOP	get_additional_output () override
	any poses that score lower than the input files is output More...

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

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

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 &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

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 Attributes
utility::vector1< MergePDBMover::Overlap >	overlaps_

core::pose::PoseOP	xml_input_pose_

std::string	overlap_location_pose_

core::Real	overlap_max_rmsd_

core::Size	overlap_length_

core::Size	overlap_scan_range_cmdLine_

core::Size	overlap_scan_range_xml_

core::Real	design_range_

core::Real	packing_range_

core::scoring::ScoreFunctionOP	sfxn_

core::scoring::ScoreFunctionOP	asymm_score_

core::pack::task::TaskFactoryOP	task_factory_

bool	do_minimize_

std::string	chain_

std::string	symm_file_

std::string	no_design_label_

std::string	init_overlap_sequence_

core::Real	duplicate_rmsd_pose_threshold_

bool	detect_disulf_before_repack_

bool	output_only_first_

bool	output_overlap_positions_

bool	do_design_

core::Real	clash_threshold_

core::select::residue_selector::ResidueSelectorCOP	selector_cmd_

core::select::residue_selector::ResidueSelectorCOP	selector_xml_

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...

Member Typedef Documentation

◆ ResidueSelectorCOP

typedef core::select::residue_selector::ResidueSelectorCOP protocols::pose_creation::MergePDBMover::ResidueSelectorCOP

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP protocols::pose_creation::MergePDBMover::ResidueSelectorOP

Constructor & Destructor Documentation

◆ MergePDBMover()

protocols::pose_creation::MergePDBMover::MergePDBMover ( )

Constructor.

Member Function Documentation

◆ apply()

void protocols::pose_creation::MergePDBMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References asymm_score_, chain_, determine_overlap(), do_design_, generate_overlaps(), get_additional_output(), core::pose::get_chain_id_from_chain(), core::pose::has_chain(), core::pose::symmetry::is_symmetric(), overlaps_, pack_and_minimize(), sfxn_, protocols::pose_creation::TR(), and xml_input_pose_.

◆ check_duplicate()

bool protocols::pose_creation::MergePDBMover::check_duplicate ( Pose & pose )

fast check to maake sure the pose isn't a structural duplicate

References core::scoring::CA_rmsd(), duplicate_rmsd_pose_threshold_, core::conformation::Residue::is_virtual_residue(), overlaps_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by generate_overlaps().

◆ clone()

moves::MoverOP protocols::pose_creation::MergePDBMover::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.

◆ closest_non_overlap_residue()

Size protocols::pose_creation::MergePDBMover::closest_non_overlap_residue	(	core::pose::Pose const &	pose,
		core::Size	resid,
		core::Size	start_overlap_resid,
		core::Size	end_overlap_resid
	)

Figures out the closest residue that's not part of the overlap.

References core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by copy_sequence().

◆ copy_sequence()

void protocols::pose_creation::MergePDBMover::copy_sequence	(	core::Size	start_overlap_resid,
		core::Size	end_overlap_resid,
		core::Size	start_overlap_input_pose_resid,
		core::Size	start_overlap_xml_pose_resid,
		core::pose::Pose const &	input_pose,
		core::pose::Pose const &	xml_pose,
		core::pose::Pose &	output_pose
	)

Copies the sequence in the overlap region as appropriate. This sets the initial residues before the pack and minimize is called.

References protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), closest_non_overlap_residue(), increase_range_to_ignore_ss_element(), init_overlap_sequence_, overlap_location_pose_, and protocols::pose_creation::TR().

Referenced by generate_overlaps().

◆ determine_overlap()

void protocols::pose_creation::MergePDBMover::determine_overlap	(	Pose const	pose,
		core::Size	chain_id
	)

Determines the overlaps. stores the start and end position in the struct Overlap.

References core::scoring::CA_rmsd(), core::pose::chain_end_res(), core::pose::symmetry::get_nres_asymmetric_unit(), core::pose::get_resnums_for_chain_id(), core::conformation::symmetry::is_symmetric(), overlap_length_, overlap_location_pose_, overlap_max_rmsd_, overlap_scan_range_cmdLine_, overlap_scan_range_xml_, overlaps_, core::pose::pdbslice(), core::pose::res_in_chain(), core::select::residue_selector::selection_positions(), selector_cmd_, selector_xml_, protocols::pose_creation::TR(), and xml_input_pose_.

Referenced by apply().

◆ fresh_instance()

moves::MoverOP protocols::pose_creation::MergePDBMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ generate_overlaps()

void protocols::pose_creation::MergePDBMover::generate_overlaps	(	Pose &	pose,
		core::Size	chain_id
	)

Uses the overlap to generate poses.

References protocols::simple_moves::AddPDBInfoMover::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::symmetry::ExtractAsymmetricPoseMover::apply(), asymm_score_, core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::CENTROID, core::pose::chain_end_res(), check_duplicate(), clash_threshold_, protocols::symmetry::ExtractAsymmetricPoseMover::clear_sym_def(), core::pose::Pose::clone(), copy_sequence(), design_range_, core::pose::symmetry::extract_asymmetric_unit(), core::pose::get_chains(), core::pose::get_resnums_for_chain_id(), core::pose::initialize_atomid_map(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_pose(), no_design_label_, overlap_location_pose_, overlaps_, core::scoring::pair, core::pose::Pose::pdb_info(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::pose::res_in_chain(), core::pose::Pose::residue(), sfxn_, core::pose::Pose::size(), core::scoring::superimpose_pose(), symm_file_, protocols::pose_creation::TR(), and xml_input_pose_.

Referenced by apply().

◆ get_additional_output()

core::pose::PoseOP protocols::pose_creation::MergePDBMover::get_additional_output ( )

overridevirtual

any poses that score lower than the input files is output

Reimplemented from protocols::moves::Mover.

References protocols::moves::FAIL_DO_NOT_RETRY, protocols::jd2::JobDistributor::get_instance(), protocols::moves::MS_SUCCESS, output_overlap_positions_, overlaps_, and protocols::moves::Mover::set_last_move_status().

Referenced by apply().

◆ get_name()

std::string protocols::pose_creation::MergePDBMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ increase_range_to_ignore_ss_element()

void protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element	(	core::pose::Pose const &	pose,
		core::Size	init_start,
		core::Size	init_end,
		core::Size &	ss_start,
		core::Size &	ss_end
	)

Gets the entire SS element the match is on.

increases the range to ignore to include the entire secondary structure element

References protocols::simple_filters::dssp(), and core::pose::Pose::total_residue().

Referenced by copy_sequence().

◆ mover_name()

std::string protocols::pose_creation::MergePDBMover::mover_name ( )

static

Referenced by get_name(), protocols::pose_creation::MergePDBMoverCreator::keyname(), and provide_xml_schema().

◆ pack_and_minimize()

void protocols::pose_creation::MergePDBMover::pack_and_minimize	(	Pose const	pose,
		core::Real	baseline_score
	)

◆ parse_my_tag()

void protocols::pose_creation::MergePDBMover::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 chain_, clash_threshold_, design_range_, detect_disulf_before_repack_, do_design_, do_minimize_, duplicate_rmsd_pose_threshold_, core::select::residue_selector::get_residue_selector(), init_overlap_sequence_, no_design_label_, output_only_first_, output_overlap_positions_, overlap_length_, overlap_location_pose_, overlap_max_rmsd_, overlap_scan_range_cmdLine_, overlap_scan_range_xml_, packing_range_, core::pack::task::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), selector_cmd_, selector_xml_, sfxn_, symm_file_, task_factory_, protocols::pose_creation::TR(), and xml_input_pose_.