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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:
Inheritance graph
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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 Stringsinfo ()
 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 ( )
protocols::sewing::movers::AssemblyMover::AssemblyMover ( AssemblyMover const &  src)
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
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
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
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
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
core::Real protocols::sewing::movers::AssemblyMover::get_add_probability ( ) const
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
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
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
core::Real protocols::sewing::movers::AssemblyMover::get_lowest_score ( ) const

References lowest_score_.

core::Size protocols::sewing::movers::AssemblyMover::get_max_cycles ( ) const
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
hashing::SegmentVectorCOP protocols::sewing::movers::AssemblyMover::get_segment_vector ( ) const
core::Real protocols::sewing::movers::AssemblyMover::get_start_temperature ( ) const
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
std::string protocols::sewing::movers::AssemblyMover::mover_name ( )
static
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
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
void protocols::sewing::movers::AssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
void protocols::sewing::movers::AssemblyMover::set_add_probability ( core::Real  add_probability)
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)
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)
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)
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)
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)
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)
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)
data_storage::SmartAssemblyOP protocols::sewing::movers::AssemblyMover::set_up_assembly ( core::pose::Pose pose)
virtual
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
utility::vector1< scoring::AssemblyScorerOP > protocols::sewing::movers::AssemblyMover::assembly_scorers_
private
hashing::BasisMapGeneratorOP protocols::sewing::movers::AssemblyMover::basis_map_generator_
private
data_storage::SmartAssemblyOP protocols::sewing::movers::AssemblyMover::best_assembly_
private

Referenced by generate_assembly().

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

Referenced by generate_assembly().

core::Real protocols::sewing::movers::AssemblyMover::delete_probability_
private
std::string protocols::sewing::movers::AssemblyMover::edge_file_name_
private
hashing::EdgeMapGeneratorOP protocols::sewing::movers::AssemblyMover::edge_map_generator_
private
core::Real protocols::sewing::movers::AssemblyMover::end_temperature_
private
bool protocols::sewing::movers::AssemblyMover::hashed_
private
core::Real protocols::sewing::movers::AssemblyMover::lowest_score_
private
utility::vector1< data_storage::BasisPair > protocols::sewing::movers::AssemblyMover::lowest_scoring_assembly_
private
core::Size protocols::sewing::movers::AssemblyMover::max_cycles_
private
core::Size protocols::sewing::movers::AssemblyMover::max_num_segments_
private
core::Size protocols::sewing::movers::AssemblyMover::max_segment_length_
private
core::Size protocols::sewing::movers::AssemblyMover::min_cycles_
private
std::string protocols::sewing::movers::AssemblyMover::model_file_name_
private
core::Real protocols::sewing::movers::AssemblyMover::old_score_
private

Referenced by generate_assembly().

core::Size protocols::sewing::movers::AssemblyMover::output_pose_count_
private
bool protocols::sewing::movers::AssemblyMover::output_pose_per_move_
private
core::Real protocols::sewing::movers::AssemblyMover::random_action_
private

Referenced by generate_assembly().

bool protocols::sewing::movers::AssemblyMover::recover_lowest_assembly_
private
utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::AssemblyMover::requirements_
private
core::Real protocols::sewing::movers::AssemblyMover::score_
private

Referenced by generate_assembly().

hashing::SegmentVectorCOP protocols::sewing::movers::AssemblyMover::segment_vector_
private
core::Real protocols::sewing::movers::AssemblyMover::start_temperature_
private
core::Size protocols::sewing::movers::AssemblyMover::window_width_
private

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