protocols::sewing::movers::AssemblyMover Class Reference

an interface for making Movers that deal with Assemblies More...

#include <AssemblyMover.hh>

Inheritance diagram for protocols::sewing::movers::AssemblyMover:

Public Member Functions
	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...
void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...
virtual void	set_up_hashing ()
	Mover Methods ///. More...
virtual void	generate_assembly (data_storage::SmartAssemblyOP, core::pose::Pose &)
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...
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...
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	add_motif_scorers_to_score_file (core::pose::Pose &pose, data_storage::SmartAssemblyOP &assembly)
virtual void	print_statistics (data_storage::SmartAssemblyOP) const
virtual data_storage::SmartAssemblyOP	set_up_assembly (core::pose::Pose &pose)
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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...
virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...
virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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 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
hashing::EdgeMapGeneratorOP	edge_map_generator_
hashing::BasisMapGeneratorOP	basis_map_generator_
std::string	model_file_name_
std::string	edge_file_name_
utility::vector1 < scoring::AssemblyScorerOP >	assembly_scorers_
utility::vector1 < requirements::AssemblyRequirementOP >	requirements_
core::Size	max_num_segments_
core::Size	max_segment_length_
core::Size	min_cycles_
core::Size	max_cycles_
core::Real	current_add_probability_
core::Real	add_probability_
core::Real	delete_probability_
core::Real	conformer_switch_probability_
core::Real	random_action_
core::Real	score_
core::Real	old_score_
core::Real	lowest_score_
core::Real	start_temperature_
core::Real	end_temperature_
bool	output_pose_per_move_
core::Size	output_pose_count_
bool	hashed_
hashing::SegmentVectorCOP	segment_vector_
utility::vector1 < data_storage::BasisPair >	lowest_scoring_assembly_
data_storage::SmartAssemblyOP	best_assembly_
core::Size	window_width_
bool	recover_lowest_assembly_

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::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 interface for making Movers that deal with Assemblies

Constructor & Destructor Documentation

protocols::sewing::movers::AssemblyMover::AssemblyMover

(

)

Constructors ///.

Default constructor

References add_probability_, conformer_switch_probability_, delete_probability_, end_temperature_, max_cycles_, min_cycles_, output_pose_count_, output_pose_per_move_, and start_temperature_.

protocols::sewing::movers::AssemblyMover::AssemblyMover

(

AssemblyMover const &

src

)

Copy constructor (not needed unless you need deep copies)

References add_probability_, assembly_scorers_, basis_map_generator_, conformer_switch_probability_, delete_probability_, edge_file_name_, edge_map_generator_, end_temperature_, get_add_probability(), get_assembly_scorers(), get_basis_map_generator(), get_conformer_switch_probability(), get_delete_probability(), get_edge_file_name(), get_edge_map_generator(), get_end_temperature(), get_hashed(), get_max_cycles(), get_max_num_segments(), get_max_segment_length(), get_min_cycles(), get_model_file_name(), get_output_pose_count(), get_output_pose_per_move(), get_recover_lowest_assembly(), get_requirements(), get_segment_vector(), get_start_temperature(), get_window_width(), hashed_, max_cycles_, max_num_segments_, max_segment_length_, min_cycles_, model_file_name_, output_pose_count_, output_pose_per_move_, recover_lowest_assembly_, requirements_, segment_vector_, start_temperature_, and window_width_.

protocols::sewing::movers::AssemblyMover::~AssemblyMover ( )

overridedefault

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

Member Function Documentation

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

virtual

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

References assembly_scorers_, score(), core::pose::setPoseExtraScore(), core::id::to_string(), and core::pose::Pose::total_residue().

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::add_motif_scorers_to_score_file(), protocols::sewing::movers::AppendAssemblyMover::apply(), and apply().

void protocols::sewing::movers::AssemblyMover::add_requirement

(

requirements::AssemblyRequirementOP

requirement

)

Add requirements to the mover from the outside (not sure if we'll need this?

References requirements_.

Referenced by parse_requirements(), and set_default_requirements().

core::Size protocols::sewing::movers::AssemblyMover::add_scorer ( scoring::AssemblyScorerOP  scorer )

virtual

add an AssemblyScorer and its weight to the ScorerMap

We give add_scorer the scorer and not the name to accommodate possible future cases in which the scorer has additional options that we may want to set and incase there are multiple copies. Returns the index of the added scorer.

References assembly_scorers_.

Referenced by parse_assembly_scorers(), and set_default_assembly_scorers().

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

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

References add_motif_scorers_to_score_file(), protocols::moves::FAIL_RETRY, generate_assembly(), max_cycles_, print_statistics(), protocols::moves::Mover::set_last_move_status(), set_up_assembly(), and protocols::TR().

bool protocols::sewing::movers::AssemblyMover::assembly_meets_requirements

(

data_storage::SmartAssemblyOP

assembly

)

References requirements_.

Referenced by generate_assembly().

std::string protocols::sewing::movers::AssemblyMover::assembly_mover_subtag_ct_namer ( std::string  tag_name )

static

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::append_ligands_subelement(), protocols::sewing::requirements::AssemblyRequirementFactory::define_assembly_requirement_subtag(), protocols::sewing::scoring::AssemblyScorerFactory::define_assembly_scorer_subtag(), protocols::sewing::movers::AppendAssemblyMover::provide_xml_schema(), protocols::sewing::movers::LigandBindingAssemblyMover::provide_xml_schema(), and provide_xml_schema().

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

static

Show the contents of the Mover.

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

void protocols::sewing::movers::AssemblyMover::define_generic_assembly_mover_attributes ( utility::tag::AttributeList &  attributes )

static

Referenced by protocols::sewing::movers::AppendAssemblyMover::attributes_for_append_assembly_mover(), and provide_xml_schema().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

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

virtual

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

References add_probability_, assembly_meets_requirements(), best_assembly_, conformer_switch_probability_, current_add_probability_, delete_probability_, end_temperature_, lowest_score_, protocols::mean_field::max(), max_cycles_, max_num_segments_, protocols::mean_field::min(), min_cycles_, old_score_, output_pose(), output_pose_count_, output_pose_per_move_, print_statistics(), random_action_, recover_lowest_assembly_, requirements_, revert_score(), core::scoring::rg, score(), score_, start_temperature_, and protocols::TR().

Referenced by protocols::sewing::movers::AppendAssemblyMover::apply(), apply(), and protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::get_add_probability

(

)

const

References add_probability_.

Referenced by AssemblyMover(), and protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly().

utility::vector1< scoring::AssemblyScorerOP > protocols::sewing::movers::AssemblyMover::get_assembly_scorers

(

)

const

References assembly_scorers_.

Referenced by AssemblyMover().

hashing::BasisMapGeneratorOP protocols::sewing::movers::AssemblyMover::get_basis_map_generator

(

)

const

References basis_map_generator_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::apply(), protocols::sewing::movers::LigandBindingAssemblyMover::apply(), AssemblyMover(), protocols::sewing::movers::AppendAssemblyMover::find_starting_segment(), protocols::sewing::movers::AppendAssemblyMover::set_up_assembly(), and protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

core::Real protocols::sewing::movers::AssemblyMover::get_conformer_switch_probability

(

)

const

References conformer_switch_probability_.

Referenced by AssemblyMover().

core::Real protocols::sewing::movers::AssemblyMover::get_delete_probability

(

)

const

References delete_probability_.

Referenced by AssemblyMover(), and protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly().

std::string protocols::sewing::movers::AssemblyMover::get_edge_file_name

(

)

const

References edge_file_name_.

Referenced by AssemblyMover().

hashing::EdgeMapGeneratorOP protocols::sewing::movers::AssemblyMover::get_edge_map_generator

(

)

const

References edge_map_generator_.

Referenced by AssemblyMover().

core::Real protocols::sewing::movers::AssemblyMover::get_end_temperature

(

)

const

References end_temperature_.

Referenced by AssemblyMover().

bool protocols::sewing::movers::AssemblyMover::get_hashed

(

)

const

References hashed_.

Referenced by AssemblyMover(), protocols::sewing::movers::AppendAssemblyMover::find_starting_segment(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::set_up_assembly(), and protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

core::Real protocols::sewing::movers::AssemblyMover::get_lowest_score

(

)

const

References lowest_score_.

core::Size protocols::sewing::movers::AssemblyMover::get_max_cycles

(

)

const

References max_cycles_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::apply(), and AssemblyMover().

core::Size protocols::sewing::movers::AssemblyMover::get_max_num_segments

(

)

const

References max_num_segments_.

Referenced by AssemblyMover().

core::Size protocols::sewing::movers::AssemblyMover::get_max_segment_length

(

)

const

References max_segment_length_.

Referenced by AssemblyMover().

core::Size protocols::sewing::movers::AssemblyMover::get_min_cycles

(

)

const

References min_cycles_.

Referenced by AssemblyMover().

std::string protocols::sewing::movers::AssemblyMover::get_model_file_name

(

)

const

References model_file_name_.

Referenced by AssemblyMover().

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

overridevirtual

Get the name of the Mover.

Implements protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

core::Size protocols::sewing::movers::AssemblyMover::get_output_pose_count

(

)

const

References output_pose_count_.

Referenced by AssemblyMover().

bool protocols::sewing::movers::AssemblyMover::get_output_pose_per_move

(

)

const

References output_pose_per_move_.

Referenced by AssemblyMover().

bool protocols::sewing::movers::AssemblyMover::get_recover_lowest_assembly

(

)

const

References recover_lowest_assembly_.

Referenced by AssemblyMover().

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::AssemblyMover::get_requirements

(

)

const

References requirements_.

Referenced by AssemblyMover(), and protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag().

hashing::SegmentVectorCOP protocols::sewing::movers::AssemblyMover::get_segment_vector

(

)

const

References segment_vector_.

Referenced by AssemblyMover(), protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly(), and protocols::sewing::movers::AppendAssemblyMover::set_up_assembly().

core::Real protocols::sewing::movers::AssemblyMover::get_start_temperature

(

)

const

References start_temperature_.

Referenced by AssemblyMover(), and protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::get_unweighted_score_term ( data_storage::SmartAssemblyOP  assembly, core::Size  scorer_index  )

virtual

get the unweighted value for a particular score term

References assembly_scorers_.

core::Size protocols::sewing::movers::AssemblyMover::get_window_width

(

)

const

References window_width_.

Referenced by AssemblyMover(), protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly(), and protocols::sewing::movers::AppendAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AssemblyMover::mover_name ( )

static

Referenced by protocols::sewing::movers::AssemblyMoverCreator::class_name(), protocols::sewing::movers::AssemblyMoverCreator::keyname(), and provide_xml_schema().

void protocols::sewing::movers::AssemblyMover::output_pose	(	data_storage::SmartAssemblyOP	assembly,
		core::pose::Pose &	pose
	)

Referenced by generate_assembly().

void protocols::sewing::movers::AssemblyMover::parse_assembly_scorers	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

Parses the AssemblyScorers subtag of AssemblyMover.

References add_scorer().

Referenced by parse_my_tag().

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

overridevirtual

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

References add_probability_, conformer_switch_probability_, delete_probability_, edge_file_name_, end_temperature_, hashed_, max_cycles_, max_num_segments_, max_segment_length_, min_cycles_, model_file_name_, output_pose_per_move_, parse_assembly_scorers(), parse_requirements(), protocols::sewing::hashing::ModelFileReader::read_model_file(), recover_lowest_assembly_, segment_vector_, set_default_assembly_scorers(), set_default_requirements(), set_up_hashing(), start_temperature_, protocols::TR(), and window_width_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::parse_my_tag().

void protocols::sewing::movers::AssemblyMover::parse_requirements	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

Parses the Requirements subtag of AssemblyMover.

References add_requirement().

Referenced by parse_my_tag().

void protocols::sewing::movers::AssemblyMover::print_statistics ( data_storage::SmartAssemblyOP  assembly ) const

virtual

References protocols::TR().

Referenced by protocols::sewing::movers::AppendAssemblyMover::apply(), protocols::sewing::movers::LigandBindingAssemblyMover::apply(), apply(), protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly(), and generate_assembly().

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

static

References assembly_mover_subtag_ct_namer(), protocols::moves::complex_type_name_for_mover(), define_generic_assembly_mover_attributes(), and mover_name().

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

void protocols::sewing::movers::AssemblyMover::revert_score

(

)

resets scorers to their score before the move that is now being reverted

References assembly_scorers_.

Referenced by generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::score ( data_storage::SmartAssemblyOP  assembly )

virtual

return the weighted sum of all score terms for the assembly.

References assembly_scorers_, and core::scoring::total_score.

Referenced by add_motif_scorers_to_score_file(), protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly(), and generate_assembly().

void protocols::sewing::movers::AssemblyMover::set_add_probability

(

core::Real

add_probability

)

References add_probability_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover().

void protocols::sewing::movers::AssemblyMover::set_assembly_scorers

(

utility::vector1< scoring::AssemblyScorerOP >

assembly_scorers

)

References assembly_scorers_.

void protocols::sewing::movers::AssemblyMover::set_basis_map_generator

(

hashing::BasisMapGeneratorOP

bmg

)

References basis_map_generator_.

void protocols::sewing::movers::AssemblyMover::set_conformer_switch_probability

(

core::Real

prob

)

References conformer_switch_probability_.

void protocols::sewing::movers::AssemblyMover::set_default_assembly_scorers ( )

virtual

Set default score function for this AssemblyMover. Called if no AssemblyScorers are specified through RosettaScripts.

References add_scorer().

Referenced by parse_my_tag().

void protocols::sewing::movers::AssemblyMover::set_default_requirements ( )

virtual

Set default requirements for this AssemblyMover. Called if no requirements are specified through RosettaScripts.

References add_requirement(), and protocols::TR().

Referenced by parse_my_tag().

void protocols::sewing::movers::AssemblyMover::set_delete_probability

(

core::Real

delete_probability

)

References delete_probability_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover().

void protocols::sewing::movers::AssemblyMover::set_edge_file_name

(

std::string

edges

)

References edge_file_name_.

void protocols::sewing::movers::AssemblyMover::set_edge_map_generator

(

hashing::EdgeMapGeneratorOP

emg

)

References edge_map_generator_.

void protocols::sewing::movers::AssemblyMover::set_end_temperature

(

core::Real

temp

)

References end_temperature_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover().

void protocols::sewing::movers::AssemblyMover::set_hashed

(

bool

hashed

)

References hashed_.

void protocols::sewing::movers::AssemblyMover::set_lowest_score

(

core::Real

lowest_score

)

References lowest_score_.

void protocols::sewing::movers::AssemblyMover::set_max_cycles

(

core::Size

max_cycles

)

References max_cycles_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover(), and protocols::sewing::movers::AppendAssemblyMover::apply().

void protocols::sewing::movers::AssemblyMover::set_max_num_segments

(

core::Size

max_segs

)

References max_num_segments_.

void protocols::sewing::movers::AssemblyMover::set_max_segment_length

(

core::Size

max_seg_length

)

References max_segment_length_.

void protocols::sewing::movers::AssemblyMover::set_min_cycles

(

core::Size

min_cycles

)

References min_cycles_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover(), and protocols::sewing::movers::AppendAssemblyMover::apply().

void protocols::sewing::movers::AssemblyMover::set_model_file_name

(

std::string

models

)

References model_file_name_.

void protocols::sewing::movers::AssemblyMover::set_output_pose_per_move

(

bool

output_pose_per_move

)

References output_pose_per_move_.

void protocols::sewing::movers::AssemblyMover::set_recover_lowest_assembly

(

bool

new_setting

)

References recover_lowest_assembly_.

void protocols::sewing::movers::AssemblyMover::set_requirements

(

utility::vector1< requirements::AssemblyRequirementOP >

requirements

)

References requirements_.

void protocols::sewing::movers::AssemblyMover::set_segment_vector

(

hashing::SegmentVectorCOP

segvec

)

References segment_vector_.

void protocols::sewing::movers::AssemblyMover::set_start_temperature

(

core::Real

temp

)

References start_temperature_.

Referenced by protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover().

data_storage::SmartAssemblyOP protocols::sewing::movers::AssemblyMover::set_up_assembly ( core::pose::Pose &  pose )

virtual

Reimplemented in protocols::sewing::movers::AppendAssemblyMover, and protocols::sewing::movers::LigandBindingAssemblyMover.

References basis_map_generator_, hashed_, segment_vector_, and window_width_.

Referenced by apply().

void protocols::sewing::movers::AssemblyMover::set_up_hashing ( )

virtual

Mover Methods ///.

References basis_map_generator_, edge_file_name_, edge_map_generator_, hashed_, and segment_vector_.

Referenced by parse_my_tag().

void protocols::sewing::movers::AssemblyMover::set_window_width

(

core::Size

width

)

References window_width_.

void protocols::sewing::movers::AssemblyMover::show ( std::ostream &  output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.

References protocols::moves::Mover::show().

Referenced by protocols::sewing::movers::operator<<().

Member Data Documentation

core::Real protocols::sewing::movers::AssemblyMover::add_probability_

private

Referenced by AssemblyMover(), generate_assembly(), get_add_probability(), parse_my_tag(), and set_add_probability().

utility::vector1< scoring::AssemblyScorerOP > protocols::sewing::movers::AssemblyMover::assembly_scorers_

private

Referenced by add_motif_scorers_to_score_file(), add_scorer(), AssemblyMover(), get_assembly_scorers(), get_unweighted_score_term(), revert_score(), score(), and set_assembly_scorers().

hashing::BasisMapGeneratorOP protocols::sewing::movers::AssemblyMover::basis_map_generator_

private

Referenced by AssemblyMover(), get_basis_map_generator(), set_basis_map_generator(), set_up_assembly(), and set_up_hashing().

data_storage::SmartAssemblyOP protocols::sewing::movers::AssemblyMover::best_assembly_

private

Referenced by generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::conformer_switch_probability_

private

Referenced by AssemblyMover(), generate_assembly(), get_conformer_switch_probability(), parse_my_tag(), and set_conformer_switch_probability().

core::Real protocols::sewing::movers::AssemblyMover::current_add_probability_

private

Referenced by generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::delete_probability_

private

Referenced by AssemblyMover(), generate_assembly(), get_delete_probability(), parse_my_tag(), and set_delete_probability().

std::string protocols::sewing::movers::AssemblyMover::edge_file_name_

private

Referenced by AssemblyMover(), get_edge_file_name(), parse_my_tag(), set_edge_file_name(), and set_up_hashing().

hashing::EdgeMapGeneratorOP protocols::sewing::movers::AssemblyMover::edge_map_generator_

private

Referenced by AssemblyMover(), get_edge_map_generator(), set_edge_map_generator(), and set_up_hashing().

core::Real protocols::sewing::movers::AssemblyMover::end_temperature_

private

Referenced by AssemblyMover(), generate_assembly(), get_end_temperature(), parse_my_tag(), and set_end_temperature().

bool protocols::sewing::movers::AssemblyMover::hashed_

private

Referenced by AssemblyMover(), get_hashed(), parse_my_tag(), set_hashed(), set_up_assembly(), and set_up_hashing().

core::Real protocols::sewing::movers::AssemblyMover::lowest_score_

private

Referenced by generate_assembly(), get_lowest_score(), and set_lowest_score().

utility::vector1< data_storage::BasisPair > protocols::sewing::movers::AssemblyMover::lowest_scoring_assembly_

private

core::Size protocols::sewing::movers::AssemblyMover::max_cycles_

private

Referenced by apply(), AssemblyMover(), generate_assembly(), get_max_cycles(), parse_my_tag(), and set_max_cycles().

core::Size protocols::sewing::movers::AssemblyMover::max_num_segments_

private

Referenced by AssemblyMover(), generate_assembly(), get_max_num_segments(), parse_my_tag(), and set_max_num_segments().

core::Size protocols::sewing::movers::AssemblyMover::max_segment_length_

private

Referenced by AssemblyMover(), get_max_segment_length(), parse_my_tag(), and set_max_segment_length().

core::Size protocols::sewing::movers::AssemblyMover::min_cycles_

private

Referenced by AssemblyMover(), generate_assembly(), get_min_cycles(), parse_my_tag(), and set_min_cycles().

std::string protocols::sewing::movers::AssemblyMover::model_file_name_

private

Referenced by AssemblyMover(), get_model_file_name(), parse_my_tag(), and set_model_file_name().

core::Real protocols::sewing::movers::AssemblyMover::old_score_

private

Referenced by generate_assembly().

core::Size protocols::sewing::movers::AssemblyMover::output_pose_count_

private

Referenced by AssemblyMover(), generate_assembly(), and get_output_pose_count().

bool protocols::sewing::movers::AssemblyMover::output_pose_per_move_

private

Referenced by AssemblyMover(), generate_assembly(), get_output_pose_per_move(), parse_my_tag(), and set_output_pose_per_move().

core::Real protocols::sewing::movers::AssemblyMover::random_action_

private

Referenced by generate_assembly().

bool protocols::sewing::movers::AssemblyMover::recover_lowest_assembly_

private

Referenced by AssemblyMover(), generate_assembly(), get_recover_lowest_assembly(), parse_my_tag(), and set_recover_lowest_assembly().

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::AssemblyMover::requirements_

private

Referenced by add_requirement(), assembly_meets_requirements(), AssemblyMover(), generate_assembly(), get_requirements(), and set_requirements().

core::Real protocols::sewing::movers::AssemblyMover::score_

private

Referenced by generate_assembly().

hashing::SegmentVectorCOP protocols::sewing::movers::AssemblyMover::segment_vector_

private

Referenced by AssemblyMover(), get_segment_vector(), parse_my_tag(), set_segment_vector(), set_up_assembly(), and set_up_hashing().

core::Real protocols::sewing::movers::AssemblyMover::start_temperature_

private

Referenced by AssemblyMover(), generate_assembly(), get_start_temperature(), parse_my_tag(), and set_start_temperature().

core::Size protocols::sewing::movers::AssemblyMover::window_width_

private

Referenced by AssemblyMover(), get_window_width(), parse_my_tag(), set_up_assembly(), and set_window_width().

---

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

• src/protocols/sewing/movers/AssemblyMover.hh
• src/protocols/sewing/movers/AssemblyMover.cc