an AssemblyMover for adding to existing poses More...

#include <LigandBindingAssemblyMover.hh>

Inheritance diagram for protocols::sewing::movers::LigandBindingAssemblyMover:

[legend]

Public Member Functions
	LigandBindingAssemblyMover ()
	Constructors ///. More...

	LigandBindingAssemblyMover (LigandBindingAssemblyMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~LigandBindingAssemblyMover () override=default
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

data_storage::SmartAssemblyOP	set_up_assembly (core::pose::Pose &pose) override

void	generate_assembly (data_storage::SmartAssemblyOP, core::pose::Pose &) override

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

std::string	get_name () const override
	Get the name of the Mover. More...

core::Real	get_min_distance (data_storage::SmartSegmentOP, data_storage::LigandResidueOP)

void	add_motif_scorers_to_score_file (core::pose::Pose &pose, data_storage::SmartAssemblyOP &assembly) override

core::Real	get_distance_cutoff () const

core::Size	get_segment_distance_cutoff () const

core::Size	get_binding_cycles () const

utility::vector1< requirements::AssemblyRequirementOP >	get_ligand_requirements () const

utility::vector1< requirements::AssemblyRequirementOP >	get_non_ligand_requirements () const

bool	get_build_site_only () const

void	set_distance_cutoff (core::Real cutoff)

void	set_segment_distance_cutoff (core::Size cutoff)

void	set_binding_cycles (core::Size cycles)

void	set_ligand_requirements (utility::vector1< requirements::AssemblyRequirementOP > requirements)

void	set_non_ligand_requirements (utility::vector1< requirements::AssemblyRequirementOP > requirements)

void	set_build_site_only (bool build_only)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

Public Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
	AppendAssemblyMover ()
	Constructors ///. More...

	AppendAssemblyMover (AppendAssemblyMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~AppendAssemblyMover () override=default
	Destructor (important for properly forward-declaring smart-pointer members) More...

virtual data_storage::SmartSegmentOP	find_starting_segment (data_storage::SmartAssemblyOP assembly)

void	set_partner_pdb (core::pose::PoseOP)

void	set_required_resnums (std::string)

void	set_required_selector (core::select::residue_selector::ResidueSelectorCOP)

void	set_segments_from_dssp (bool)

bool	get_extend_mode () const

void	set_extend_mode (bool)

core::pose::PoseOP	get_partner_pdb () const

std::string	get_required_resnums () const

core::select::residue_selector::ResidueSelectorCOP	get_required_selector () const

bool	get_segments_from_dssp () const

void	set_modifiable_terminus (char)

char	get_modifiable_terminus () const

void	set_start_node_vital_segments (std::string)

std::string	get_start_node_vital_segments () const

void	set_output_partner (bool)

bool	get_output_partner () const

std::string	get_pose_segment_starts_string () const

std::string	get_pose_segment_ends_string () const

void	set_pose_segment_starts_string (std::string const &)

void	set_pose_segment_ends_string (std::string const &)

void	set_pose_segment_dssp (std::string const &)

std::string	get_pose_segment_dssp () const

bool	get_strict_dssp_changes () const

void	set_strict_dssp_changes (bool)

void	set_ligands (utility::vector1< data_storage::LigandDescription >)

utility::vector1< data_storage::LigandDescription >	get_ligands () const

utility::vector1< data_storage::LigandDescription > &	get_nonconst_ligands ()

Public Member Functions inherited from protocols::sewing::movers::AssemblyMover
	AssemblyMover ()
	Constructors ///. More...

	AssemblyMover (AssemblyMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~AssemblyMover () override=default
	Destructor (important for properly forward-declaring smart-pointer members) More...

virtual void	set_up_hashing ()
	Mover Methods ///. More...

virtual core::Real	score (data_storage::SmartAssemblyOP)
	return the weighted sum of all score terms for the assembly. More...

void	revert_score ()
	resets scorers to their score before the move that is now being reverted More...

virtual core::Size	add_scorer (scoring::AssemblyScorerOP scorer)
	add an AssemblyScorer and its weight to the ScorerMap More...

virtual core::Real	get_unweighted_score_term (data_storage::SmartAssemblyOP, core::Size scorer_index)
	get the unweighted value for a particular score term More...

virtual void	print_statistics (data_storage::SmartAssemblyOP) const

bool	assembly_meets_requirements (data_storage::SmartAssemblyOP assembly)

void	parse_requirements (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	Parses the Requirements subtag of AssemblyMover. More...

void	parse_assembly_scorers (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	Parses the AssemblyScorers subtag of AssemblyMover. More...

virtual void	set_default_assembly_scorers ()
	Set default score function for this AssemblyMover. Called if no AssemblyScorers are specified through RosettaScripts. More...

virtual void	set_default_requirements ()
	Set default requirements for this AssemblyMover. Called if no requirements are specified through RosettaScripts. More...

void	add_requirement (requirements::AssemblyRequirementOP requirement)
	Add requirements to the mover from the outside (not sure if we'll need this? More...

core::Size	get_window_width () const

hashing::SegmentVectorCOP	get_segment_vector () const

hashing::BasisMapGeneratorOP	get_basis_map_generator () const

hashing::EdgeMapGeneratorOP	get_edge_map_generator () const

std::string	get_model_file_name () const

std::string	get_edge_file_name () const

utility::vector1< scoring::AssemblyScorerOP >	get_assembly_scorers () const

utility::vector1< requirements::AssemblyRequirementOP >	get_requirements () const

bool	get_hashed () const

core::Real	get_start_temperature () const

core::Real	get_end_temperature () const

core::Size	get_max_num_segments () const

core::Size	get_max_segment_length () const

core::Size	get_min_cycles () const

core::Size	get_max_cycles () const

core::Real	get_add_probability () const

core::Real	get_delete_probability () const

core::Real	get_conformer_switch_probability () const

bool	get_output_pose_per_move () const

core::Size	get_output_pose_count () const

core::Real	get_lowest_score () const

void	set_window_width (core::Size width)

void	set_segment_vector (hashing::SegmentVectorCOP segvec)

void	set_basis_map_generator (hashing::BasisMapGeneratorOP bmg)

void	set_edge_map_generator (hashing::EdgeMapGeneratorOP emg)

void	set_model_file_name (std::string models)

void	set_edge_file_name (std::string edges)

void	set_assembly_scorers (utility::vector1< scoring::AssemblyScorerOP > assembly_scorers)

void	set_requirements (utility::vector1< requirements::AssemblyRequirementOP > requirements)

void	set_hashed (bool hashed)

void	set_start_temperature (core::Real temp)

void	set_end_temperature (core::Real temp)

void	set_max_num_segments (core::Size max_segs)

void	set_max_segment_length (core::Size max_seg_length)

void	set_min_cycles (core::Size min_cycles)

void	set_max_cycles (core::Size max_cycles)

void	set_add_probability (core::Real add_probability)

void	set_delete_probability (core::Real delete_probability)

void	set_conformer_switch_probability (core::Real prob)

void	set_output_pose_per_move (bool output_pose_per_move)

void	output_pose (data_storage::SmartAssemblyOP assembly, core::pose::Pose &)

void	set_lowest_score (core::Real lowest_score)

void	set_recover_lowest_assembly (bool)

bool	get_recover_lowest_assembly () const

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 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	class_name ()
	Show the contents of the Mover. More...

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

Static Public Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
static std::string	class_name ()
	Show the contents of the Mover. More...

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

static void	attributes_for_append_assembly_mover (utility::tag::AttributeList &attributes)

Static Public Member Functions inherited from protocols::sewing::movers::AssemblyMover
static std::string	class_name ()
	Show the contents of the Mover. More...

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

static std::string	assembly_mover_subtag_ct_namer (std::string)

static std::string	mover_name ()

static void	define_generic_assembly_mover_attributes (utility::tag::AttributeList &)

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

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

Private Attributes
core::Real	distance_cutoff_

core::Size	segment_distance_cutoff_

core::Size	binding_cycles_

std::map< core::Size, hashing::LigandBindingResPlacerOP >	binder_finders_

utility::vector1< data_storage::LigandDescription >	expanded_ligands_

utility::vector1< requirements::AssemblyRequirementOP >	ligand_requirements_

utility::vector1< requirements::AssemblyRequirementOP >	non_ligand_requirements_

bool	build_site_only_ = false

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

Protected Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
hashing::AlignmentFGMSettingsOP	alignment_settings ()

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

an AssemblyMover for adding to existing poses

Constructor & Destructor Documentation

◆ LigandBindingAssemblyMover() [1/2]

protocols::sewing::movers::LigandBindingAssemblyMover::LigandBindingAssemblyMover ( )

Constructors ///.

Default constructor

◆ LigandBindingAssemblyMover() [2/2]

protocols::sewing::movers::LigandBindingAssemblyMover::LigandBindingAssemblyMover ( LigandBindingAssemblyMover const & src )

default

Copy constructor (not needed unless you need deep copies)

◆ ~LigandBindingAssemblyMover()

protocols::sewing::movers::LigandBindingAssemblyMover::~LigandBindingAssemblyMover ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ add_motif_scorers_to_score_file()

void protocols::sewing::movers::LigandBindingAssemblyMover::add_motif_scorers_to_score_file	(	core::pose::Pose &	pose,
		data_storage::SmartAssemblyOP &	assembly
	)

overridevirtual

Reimplemented from protocols::sewing::movers::AssemblyMover.

References protocols::sewing::movers::AssemblyMover::add_motif_scorers_to_score_file(), binder_finders_, core::pose::setPoseExtraScore(), and core::id::to_string().

Referenced by apply().

◆ apply()

void protocols::sewing::movers::LigandBindingAssemblyMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Reimplemented from protocols::sewing::movers::AppendAssemblyMover.

References add_motif_scorers_to_score_file(), protocols::sewing::movers::AppendAssemblyMover::alignment_settings(), protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_from_alignment(), protocols::moves::FAIL_DO_NOT_RETRY, generate_assembly(), protocols::sewing::movers::AssemblyMover::get_basis_map_generator(), protocols::moves::Mover::get_last_move_status(), protocols::moves::MS_SUCCESS, protocols::sewing::movers::AssemblyMover::print_statistics(), protocols::moves::Mover::set_last_move_status(), set_up_assembly(), and protocols::TR().

◆ class_name()

std::string protocols::sewing::movers::LigandBindingAssemblyMover::class_name ( )

static

Show the contents of the Mover.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMoverCreator::class_name(), get_name(), protocols::sewing::movers::LigandBindingAssemblyMoverCreator::keyname(), protocols::sewing::movers::LigandBindingAssemblyMoverCreator::mover_name(), and provide_xml_schema().

◆ clone()

protocols::moves::MoverOP protocols::sewing::movers::LigandBindingAssemblyMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::sewing::movers::AppendAssemblyMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::sewing::movers::LigandBindingAssemblyMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::sewing::movers::AppendAssemblyMover.

◆ generate_assembly()

void protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly	(	data_storage::SmartAssemblyOP	assembly,
		core::pose::Pose &	pose
	)

overridevirtual

Reimplemented from protocols::sewing::movers::AssemblyMover.

References binder_finders_, binding_cycles_, build_site_only_, core::kinematics::distance(), distance_cutoff_, protocols::moves::FAIL_DO_NOT_RETRY, protocols::sewing::movers::AssemblyMover::generate_assembly(), protocols::sewing::movers::AssemblyMover::get_add_probability(), protocols::sewing::movers::AssemblyMover::get_delete_probability(), protocols::sewing::movers::AppendAssemblyMover::get_ligands(), get_min_distance(), protocols::sewing::movers::AssemblyMover::get_start_temperature(), ligand_requirements_, non_ligand_requirements_, protocols::sewing::movers::AssemblyMover::print_statistics(), core::scoring::rg, protocols::sewing::movers::AssemblyMover::score(), segment_distance_cutoff_, protocols::moves::Mover::set_last_move_status(), and protocols::TR().

Referenced by apply().

◆ get_binding_cycles()

core::Size protocols::sewing::movers::LigandBindingAssemblyMover::get_binding_cycles ( ) const

References binding_cycles_.

◆ get_build_site_only()

bool protocols::sewing::movers::LigandBindingAssemblyMover::get_build_site_only ( ) const

References build_site_only_.

◆ get_distance_cutoff()

core::Real protocols::sewing::movers::LigandBindingAssemblyMover::get_distance_cutoff ( ) const

References distance_cutoff_.

◆ get_ligand_requirements()

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::LigandBindingAssemblyMover::get_ligand_requirements ( ) const

References ligand_requirements_.

◆ get_min_distance()

core::Real protocols::sewing::movers::LigandBindingAssemblyMover::get_min_distance	(	data_storage::SmartSegmentOP	seg,
		data_storage::LigandResidueOP	ligand
	)

References core::pose::center_of_mass(), core::kinematics::distance(), and protocols::sewing::data_storage::ligand.

Referenced by generate_assembly().

◆ get_name()

std::string protocols::sewing::movers::LigandBindingAssemblyMover::get_name ( ) const

overridevirtual

Get the name of the Mover.

Reimplemented from protocols::sewing::movers::AppendAssemblyMover.

References class_name().

◆ get_non_ligand_requirements()

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::LigandBindingAssemblyMover::get_non_ligand_requirements ( ) const

References non_ligand_requirements_.

◆ get_segment_distance_cutoff()

core::Size protocols::sewing::movers::LigandBindingAssemblyMover::get_segment_distance_cutoff ( ) const

References segment_distance_cutoff_.

◆ parse_my_tag()

void protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::sewing::movers::AppendAssemblyMover.

References binding_cycles_, build_site_only_, protocols::sewing::movers::AppendAssemblyMover::get_ligands(), protocols::sewing::movers::AssemblyMover::get_requirements(), ligand_requirements_, non_ligand_requirements_, protocols::sewing::hashing::LigandBindingResPlacer::parse_ideal_contacts(), protocols::sewing::hashing::LigandBindingResPlacer::parse_ligand_files(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), set_distance_cutoff(), protocols::sewing::movers::AppendAssemblyMover::set_ligands(), set_segment_distance_cutoff(), and protocols::TR().

◆ provide_xml_schema()

void protocols::sewing::movers::LigandBindingAssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::sewing::hashing::AlignmentFileGeneratorMover::append_ligands_subelement(), protocols::sewing::movers::AssemblyMover::assembly_mover_subtag_ct_namer(), protocols::sewing::movers::AppendAssemblyMover::attributes_for_append_assembly_mover(), class_name(), and protocols::moves::complex_type_name_for_mover().

Referenced by protocols::sewing::movers::LigandBindingAssemblyMoverCreator::provide_xml_schema().

◆ set_binding_cycles()

void protocols::sewing::movers::LigandBindingAssemblyMover::set_binding_cycles ( core::Size cycles )

References binding_cycles_.

◆ set_build_site_only()

void protocols::sewing::movers::LigandBindingAssemblyMover::set_build_site_only ( bool build_only )

References build_site_only_.

◆ set_distance_cutoff()

void protocols::sewing::movers::LigandBindingAssemblyMover::set_distance_cutoff ( core::Real cutoff )

References distance_cutoff_.

Referenced by parse_my_tag().

◆ set_ligand_requirements()

void protocols::sewing::movers::LigandBindingAssemblyMover::set_ligand_requirements ( utility::vector1< requirements::AssemblyRequirementOP > requirements )

References ligand_requirements_.

◆ set_non_ligand_requirements()

void protocols::sewing::movers::LigandBindingAssemblyMover::set_non_ligand_requirements ( utility::vector1< requirements::AssemblyRequirementOP > requirements )

References non_ligand_requirements_.