protocols::sewing::movers::AppendAssemblyMover Class Reference

an AssemblyMover for adding to existing poses More...

#include <AppendAssemblyMover.hh>

Inheritance diagram for protocols::sewing::movers::AppendAssemblyMover:

Public Member Functions
	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...
void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...
data_storage::SmartAssemblyOP	set_up_assembly (core::pose::Pose &) override
virtual data_storage::SmartSegmentOP	find_starting_segment (data_storage::SmartAssemblyOP assembly)
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	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)
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...
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...
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
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 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...

Protected Member Functions
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...

Private Attributes
utility::pointer::DeepCopyOP < core::pose::Pose >	partner_pdb_
std::string	required_resnums_
core::select::residue_selector::ResidueSelectorCOP	required_selector_
utility::vector1 < data_storage::LigandDescription >	ligands_
bool	segments_from_dssp_ = true
char	modifiable_terminus_ = 'B'
std::string	start_node_vital_segments_
bool	output_partner_ = true
std::string	pose_segment_starts_string_
std::string	pose_segment_ends_string_
std::string	pose_segment_dssp_
bool	strict_dssp_changes_ = false
bool	extend_mode_ = false
hashing::AlignmentFGMSettingsOP	alignment_settings_

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

Detailed Description

an AssemblyMover for adding to existing poses

Constructor & Destructor Documentation

protocols::sewing::movers::AppendAssemblyMover::AppendAssemblyMover

(

)

Constructors ///.

Default constructor

References protocols::sewing::movers::AssemblyMover::set_add_probability(), protocols::sewing::movers::AssemblyMover::set_delete_probability(), protocols::sewing::movers::AssemblyMover::set_end_temperature(), protocols::sewing::movers::AssemblyMover::set_max_cycles(), protocols::sewing::movers::AssemblyMover::set_min_cycles(), set_modifiable_terminus(), set_output_partner(), set_start_node_vital_segments(), and protocols::sewing::movers::AssemblyMover::set_start_temperature().

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

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::sewing::movers::AppendAssemblyMover::~AppendAssemblyMover ( )

overridedefault

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

Member Function Documentation

hashing::AlignmentFGMSettingsOP protocols::sewing::movers::AppendAssemblyMover::alignment_settings ( )

protected

References alignment_settings_.

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

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

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

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

References protocols::sewing::movers::AssemblyMover::add_motif_scorers_to_score_file(), alignment_settings_, protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_from_alignment(), extend_mode_, protocols::moves::FAIL_RETRY, protocols::sewing::movers::AssemblyMover::generate_assembly(), protocols::sewing::movers::AssemblyMover::get_basis_map_generator(), protocols::sewing::movers::AssemblyMover::get_max_cycles(), get_modifiable_terminus(), get_output_partner(), get_start_node_vital_segments(), protocols::sewing::movers::AssemblyMover::print_statistics(), protocols::moves::Mover::set_last_move_status(), protocols::sewing::movers::AssemblyMover::set_max_cycles(), protocols::sewing::movers::AssemblyMover::set_min_cycles(), set_up_assembly(), and protocols::TR().

void protocols::sewing::movers::AppendAssemblyMover::attributes_for_append_assembly_mover ( utility::tag::AttributeList &  attributes )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), and protocols::sewing::movers::AssemblyMover::define_generic_assembly_mover_attributes().

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

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

static

Show the contents of the Mover.

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

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

data_storage::SmartSegmentOP protocols::sewing::movers::AppendAssemblyMover::find_starting_segment ( data_storage::SmartAssemblyOP  assembly )

virtual

References alignment_settings(), protocols::sewing::movers::AssemblyMover::get_basis_map_generator(), protocols::sewing::movers::AssemblyMover::get_hashed(), and core::scoring::rg.

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

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

bool protocols::sewing::movers::AppendAssemblyMover::get_extend_mode

(

)

const

References extend_mode_.

utility::vector1< data_storage::LigandDescription > protocols::sewing::movers::AppendAssemblyMover::get_ligands

(

)

const

References ligands_.

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

char protocols::sewing::movers::AppendAssemblyMover::get_modifiable_terminus

(

)

const

References modifiable_terminus_.

Referenced by apply().

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

overridevirtual

Get the name of the Mover.

Implements protocols::moves::Mover.

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

References class_name().

utility::vector1< data_storage::LigandDescription > & protocols::sewing::movers::AppendAssemblyMover::get_nonconst_ligands

(

)

References ligands_.

bool protocols::sewing::movers::AppendAssemblyMover::get_output_partner

(

)

const

References output_partner_.

Referenced by apply().

core::pose::PoseOP protocols::sewing::movers::AppendAssemblyMover::get_partner_pdb

(

)

const

References partner_pdb_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_dssp

(

)

const

References pose_segment_dssp_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_ends_string

(

)

const

References pose_segment_ends_string_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_starts_string

(

)

const

References pose_segment_starts_string_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::get_required_resnums

(

)

const

References required_resnums_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

core::select::residue_selector::ResidueSelectorCOP protocols::sewing::movers::AppendAssemblyMover::get_required_selector

(

)

const

References required_selector_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

bool protocols::sewing::movers::AppendAssemblyMover::get_segments_from_dssp

(

)

const

References segments_from_dssp_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::get_start_node_vital_segments

(

)

const

References start_node_vital_segments_.

Referenced by apply(), and set_up_assembly().

bool protocols::sewing::movers::AppendAssemblyMover::get_strict_dssp_changes

(

)

const

References strict_dssp_changes_.

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().

void protocols::sewing::movers::AppendAssemblyMover::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 alignment_settings_, protocols::sewing::hashing::AlignmentFileGeneratorMover::alignment_settings_from_tag(), extend_mode_, protocols::sewing::movers::AssemblyMover::get_hashed(), core::select::residue_selector::get_residue_selector(), ligands_, modifiable_terminus_, output_partner_, protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligand_conformers(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag(), protocols::sewing::movers::AssemblyMover::parse_my_tag(), partner_pdb_, core::import_pose::pose_from_file(), pose_segment_dssp_, pose_segment_ends_string_, pose_segment_starts_string_, required_resnums_, required_selector_, segments_from_dssp_, start_node_vital_segments_, strict_dssp_changes_, and protocols::TR().

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

void protocols::sewing::movers::AppendAssemblyMover::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(), attributes_for_append_assembly_mover(), protocols::moves::complex_type_name_for_mover(), and protocols::sewing::movers::AppendAssemblyMoverCreator::mover_name().

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

void protocols::sewing::movers::AppendAssemblyMover::set_extend_mode

(

bool

new_mode

)

References extend_mode_.

void protocols::sewing::movers::AppendAssemblyMover::set_ligands

(

utility::vector1< data_storage::LigandDescription >

input

)

References ligands_.

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

void protocols::sewing::movers::AppendAssemblyMover::set_modifiable_terminus

(

char

modifiable_terminus

)

References modifiable_terminus_.

Referenced by AppendAssemblyMover().

void protocols::sewing::movers::AppendAssemblyMover::set_output_partner

(

bool

output_partner

)

References output_partner_.

Referenced by AppendAssemblyMover().

void protocols::sewing::movers::AppendAssemblyMover::set_partner_pdb

(

core::pose::PoseOP

partner

)

References partner_pdb_.

void protocols::sewing::movers::AppendAssemblyMover::set_pose_segment_dssp

(

std::string const &

input

)

References pose_segment_dssp_.

void protocols::sewing::movers::AppendAssemblyMover::set_pose_segment_ends_string

(

std::string const &

input

)

References pose_segment_ends_string_.

void protocols::sewing::movers::AppendAssemblyMover::set_pose_segment_starts_string

(

std::string const &

input

)

References pose_segment_starts_string_.

void protocols::sewing::movers::AppendAssemblyMover::set_required_resnums

(

std::string

required

)

References required_resnums_.

void protocols::sewing::movers::AppendAssemblyMover::set_required_selector

(

core::select::residue_selector::ResidueSelectorCOP

select

)

References required_selector_.

void protocols::sewing::movers::AppendAssemblyMover::set_segments_from_dssp

(

bool

set

)

References segments_from_dssp_.

void protocols::sewing::movers::AppendAssemblyMover::set_start_node_vital_segments

(

std::string

start_node_vital_segments

)

References start_node_vital_segments_.

Referenced by AppendAssemblyMover().

void protocols::sewing::movers::AppendAssemblyMover::set_strict_dssp_changes

(

bool

input

)

References strict_dssp_changes_.

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

overridevirtual

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

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

References protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), find_starting_segment(), protocols::sewing::movers::AssemblyMover::get_basis_map_generator(), protocols::sewing::movers::AssemblyMover::get_hashed(), protocols::sewing::movers::AssemblyMover::get_segment_vector(), get_start_node_vital_segments(), protocols::sewing::movers::AssemblyMover::get_window_width(), ligands_, partner_pdb_, pose_segment_dssp_, pose_segment_ends_string_, pose_segment_starts_string_, required_resnums_, required_selector_, segments_from_dssp_, strict_dssp_changes_, and protocols::TR().

Referenced by apply().

void protocols::sewing::movers::AppendAssemblyMover::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

hashing::AlignmentFGMSettingsOP protocols::sewing::movers::AppendAssemblyMover::alignment_settings_

private

Referenced by alignment_settings(), apply(), and parse_my_tag().

bool protocols::sewing::movers::AppendAssemblyMover::extend_mode_ = false

private

Referenced by apply(), get_extend_mode(), parse_my_tag(), and set_extend_mode().

utility::vector1< data_storage::LigandDescription > protocols::sewing::movers::AppendAssemblyMover::ligands_

private

Referenced by get_ligands(), get_nonconst_ligands(), parse_my_tag(), set_ligands(), and set_up_assembly().

char protocols::sewing::movers::AppendAssemblyMover::modifiable_terminus_ = 'B'

private

Referenced by get_modifiable_terminus(), parse_my_tag(), and set_modifiable_terminus().

bool protocols::sewing::movers::AppendAssemblyMover::output_partner_ = true

private

Referenced by get_output_partner(), parse_my_tag(), and set_output_partner().

utility::pointer::DeepCopyOP< core::pose::Pose > protocols::sewing::movers::AppendAssemblyMover::partner_pdb_

private

Referenced by get_partner_pdb(), parse_my_tag(), set_partner_pdb(), and set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_dssp_

private

Referenced by get_pose_segment_dssp(), parse_my_tag(), set_pose_segment_dssp(), and set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_ends_string_

private

Referenced by get_pose_segment_ends_string(), parse_my_tag(), set_pose_segment_ends_string(), and set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_starts_string_

private

Referenced by get_pose_segment_starts_string(), parse_my_tag(), set_pose_segment_starts_string(), and set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::required_resnums_

private

Referenced by get_required_resnums(), parse_my_tag(), set_required_resnums(), and set_up_assembly().

core::select::residue_selector::ResidueSelectorCOP protocols::sewing::movers::AppendAssemblyMover::required_selector_

private

Referenced by get_required_selector(), parse_my_tag(), set_required_selector(), and set_up_assembly().

bool protocols::sewing::movers::AppendAssemblyMover::segments_from_dssp_ = true

private

Referenced by get_segments_from_dssp(), parse_my_tag(), set_segments_from_dssp(), and set_up_assembly().

std::string protocols::sewing::movers::AppendAssemblyMover::start_node_vital_segments_

private

Referenced by get_start_node_vital_segments(), parse_my_tag(), and set_start_node_vital_segments().

bool protocols::sewing::movers::AppendAssemblyMover::strict_dssp_changes_ = false

private

Referenced by get_strict_dssp_changes(), parse_my_tag(), set_strict_dssp_changes(), and set_up_assembly().

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

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