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Rosetta
2020.50
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an interface for making Movers that deal with Assemblies More...
#include <AssemblyMover.hh>
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 |
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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 std::string | assembly_mover_subtag_ct_namer (std::string) |
static std::string | mover_name () |
static void | define_generic_assembly_mover_attributes (utility::tag::AttributeList &) |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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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... | |
an interface for making Movers that deal with Assemblies
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_.
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Destructor (important for properly forward-declaring smart-pointer members)
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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().
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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().
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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().
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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().
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Show the contents of the Mover.
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required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.
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required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::sewing::movers::LigandBindingAssemblyMover.
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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().
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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 |
core::Real protocols::sewing::movers::AssemblyMover::get_start_temperature | ( | ) | const |
References start_temperature_.
Referenced by AssemblyMover(), and protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly().
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get the unweighted value for a particular score term
References assembly_scorers_.
core::Size protocols::sewing::movers::AssemblyMover::get_window_width | ( | ) | const |
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void protocols::sewing::movers::AssemblyMover::output_pose | ( | data_storage::SmartAssemblyOP | assembly, |
core::pose::Pose & | pose | ||
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Referenced by generate_assembly().
void protocols::sewing::movers::AssemblyMover::parse_assembly_scorers | ( | utility::tag::TagCOP | tag, |
basic::datacache::DataMap & | datamap | ||
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Parses the AssemblyScorers subtag of AssemblyMover.
References add_scorer().
Referenced by parse_my_tag().
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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 | ||
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Parses the Requirements subtag of AssemblyMover.
References add_requirement().
Referenced by parse_my_tag().
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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().
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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_.
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Set default score function for this AssemblyMover. Called if no AssemblyScorers are specified through RosettaScripts.
References add_scorer().
Referenced by parse_my_tag().
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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_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().
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Reimplemented in protocols::sewing::movers::AppendAssemblyMover, and protocols::sewing::movers::LigandBindingAssemblyMover.
References basis_map_generator_, hashed_, segment_vector_, and window_width_.
Referenced by apply().
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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_.
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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<<().
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Referenced by AssemblyMover(), generate_assembly(), get_add_probability(), parse_my_tag(), and set_add_probability().
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Referenced by AssemblyMover(), get_basis_map_generator(), set_basis_map_generator(), set_up_assembly(), and set_up_hashing().
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Referenced by generate_assembly().
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Referenced by generate_assembly().
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Referenced by AssemblyMover(), generate_assembly(), get_delete_probability(), parse_my_tag(), and set_delete_probability().
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Referenced by AssemblyMover(), get_edge_file_name(), parse_my_tag(), set_edge_file_name(), and set_up_hashing().
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Referenced by AssemblyMover(), get_edge_map_generator(), set_edge_map_generator(), and set_up_hashing().
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Referenced by AssemblyMover(), generate_assembly(), get_end_temperature(), parse_my_tag(), and set_end_temperature().
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Referenced by AssemblyMover(), get_hashed(), parse_my_tag(), set_hashed(), set_up_assembly(), and set_up_hashing().
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Referenced by generate_assembly(), get_lowest_score(), and set_lowest_score().
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Referenced by apply(), AssemblyMover(), generate_assembly(), get_max_cycles(), parse_my_tag(), and set_max_cycles().
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Referenced by AssemblyMover(), generate_assembly(), get_max_num_segments(), parse_my_tag(), and set_max_num_segments().
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Referenced by AssemblyMover(), get_max_segment_length(), parse_my_tag(), and set_max_segment_length().
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Referenced by AssemblyMover(), generate_assembly(), get_min_cycles(), parse_my_tag(), and set_min_cycles().
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Referenced by AssemblyMover(), get_model_file_name(), parse_my_tag(), and set_model_file_name().
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Referenced by generate_assembly().
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Referenced by AssemblyMover(), generate_assembly(), and get_output_pose_count().
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Referenced by AssemblyMover(), generate_assembly(), get_output_pose_per_move(), parse_my_tag(), and set_output_pose_per_move().
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Referenced by generate_assembly().
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Referenced by AssemblyMover(), generate_assembly(), get_recover_lowest_assembly(), parse_my_tag(), and set_recover_lowest_assembly().
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Referenced by add_requirement(), assembly_meets_requirements(), AssemblyMover(), generate_assembly(), get_requirements(), and set_requirements().
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Referenced by generate_assembly().
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Referenced by AssemblyMover(), get_segment_vector(), parse_my_tag(), set_segment_vector(), set_up_assembly(), and set_up_hashing().
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Referenced by AssemblyMover(), generate_assembly(), get_start_temperature(), parse_my_tag(), and set_start_temperature().
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Referenced by AssemblyMover(), get_window_width(), parse_my_tag(), set_up_assembly(), and set_window_width().