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protocols::sewing::movers::LigandBindingAssemblyMover Class Reference

an AssemblyMover for adding to existing poses More...

#include <LigandBindingAssemblyMover.hh>

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

Public Member Functions

 LigandBindingAssemblyMover ()
 Constructors ///. More...
 LigandBindingAssemblyMover (LigandBindingAssemblyMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~LigandBindingAssemblyMover () override=default
 Destructor (important for properly forward-declaring smart-pointer members) More...
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
data_storage::SmartAssemblyOP set_up_assembly (core::pose::Pose &pose) override
void generate_assembly (data_storage::SmartAssemblyOP, core::pose::Pose &) override
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
std::string get_name () const override
 Get the name of the Mover. More...
core::Real get_min_distance (data_storage::SmartSegmentOP, data_storage::LigandResidueOP)
void add_motif_scorers_to_score_file (core::pose::Pose &pose, data_storage::SmartAssemblyOP &assembly) override
core::Real get_distance_cutoff () const
core::Size get_segment_distance_cutoff () const
core::Size get_binding_cycles () const
< requirements::AssemblyRequirementOP
get_ligand_requirements () const
< requirements::AssemblyRequirementOP
get_non_ligand_requirements () const
bool get_build_site_only () const
void set_distance_cutoff (core::Real cutoff)
void set_segment_distance_cutoff (core::Size cutoff)
void set_binding_cycles (core::Size cycles)
void set_ligand_requirements (utility::vector1< requirements::AssemblyRequirementOP > requirements)
void set_non_ligand_requirements (utility::vector1< requirements::AssemblyRequirementOP > requirements)
void set_build_site_only (bool build_only)
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
- Public Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
 AppendAssemblyMover ()
 Constructors ///. More...
 AppendAssemblyMover (AppendAssemblyMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~AppendAssemblyMover () override=default
 Destructor (important for properly forward-declaring smart-pointer members) More...
find_starting_segment (data_storage::SmartAssemblyOP assembly)
void set_partner_pdb (core::pose::PoseOP)
void set_required_resnums (std::string)
void set_required_selector (core::select::residue_selector::ResidueSelectorCOP)
void set_segments_from_dssp (bool)
bool get_extend_mode () const
void set_extend_mode (bool)
core::pose::PoseOP get_partner_pdb () const
std::string get_required_resnums () const
core::select::residue_selector::ResidueSelectorCOP get_required_selector () const
bool get_segments_from_dssp () const
void set_modifiable_terminus (char)
char get_modifiable_terminus () const
void set_start_node_vital_segments (std::string)
std::string get_start_node_vital_segments () const
void set_output_partner (bool)
bool get_output_partner () const
std::string get_pose_segment_starts_string () const
std::string get_pose_segment_ends_string () const
void set_pose_segment_starts_string (std::string const &)
void set_pose_segment_ends_string (std::string const &)
void set_pose_segment_dssp (std::string const &)
std::string get_pose_segment_dssp () const
bool get_strict_dssp_changes () const
void set_strict_dssp_changes (bool)
void set_ligands (utility::vector1< data_storage::LigandDescription >)
< data_storage::LigandDescription
get_ligands () const
< data_storage::LigandDescription > & 
get_nonconst_ligands ()
- Public Member Functions inherited from protocols::sewing::movers::AssemblyMover
 AssemblyMover ()
 Constructors ///. More...
 AssemblyMover (AssemblyMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~AssemblyMover () override=default
 Destructor (important for properly forward-declaring smart-pointer members) More...
virtual void set_up_hashing ()
 Mover Methods ///. More...
virtual core::Real score (data_storage::SmartAssemblyOP)
 return the weighted sum of all score terms for the assembly. More...
void revert_score ()
 resets scorers to their score before the move that is now being reverted More...
virtual core::Size add_scorer (scoring::AssemblyScorerOP scorer)
 add an AssemblyScorer and its weight to the ScorerMap More...
virtual core::Real get_unweighted_score_term (data_storage::SmartAssemblyOP, core::Size scorer_index)
 get the unweighted value for a particular score term More...
virtual void print_statistics (data_storage::SmartAssemblyOP) const
bool assembly_meets_requirements (data_storage::SmartAssemblyOP assembly)
void parse_requirements (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
 Parses the Requirements subtag of AssemblyMover. More...
void parse_assembly_scorers (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
 Parses the AssemblyScorers subtag of AssemblyMover. More...
virtual void set_default_assembly_scorers ()
 Set default score function for this AssemblyMover. Called if no AssemblyScorers are specified through RosettaScripts. More...
virtual void set_default_requirements ()
 Set default requirements for this AssemblyMover. Called if no requirements are specified through RosettaScripts. More...
void add_requirement (requirements::AssemblyRequirementOP requirement)
 Add requirements to the mover from the outside (not sure if we'll need this? More...
core::Size get_window_width () const
hashing::SegmentVectorCOP get_segment_vector () const
hashing::BasisMapGeneratorOP get_basis_map_generator () const
hashing::EdgeMapGeneratorOP get_edge_map_generator () const
std::string get_model_file_name () const
std::string get_edge_file_name () const
< scoring::AssemblyScorerOP
get_assembly_scorers () const
< 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 Public Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
static std::string class_name ()
 Show the contents of the Mover. More...
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &)
static void attributes_for_append_assembly_mover (utility::tag::AttributeList &attributes)
- Static Public Member Functions inherited from protocols::sewing::movers::AssemblyMover
static std::string class_name ()
 Show the contents of the Mover. More...
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &)
static std::string assembly_mover_subtag_ct_namer (std::string)
static std::string mover_name ()
static void define_generic_assembly_mover_attributes (utility::tag::AttributeList &)
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...

Private Attributes

core::Real distance_cutoff_
core::Size segment_distance_cutoff_
core::Size binding_cycles_
std::map< core::Size,
< data_storage::LigandDescription
< requirements::AssemblyRequirementOP
< requirements::AssemblyRequirementOP
bool build_site_only_ = false

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings
- Protected Member Functions inherited from protocols::sewing::movers::AppendAssemblyMover
hashing::AlignmentFGMSettingsOP alignment_settings ()
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

an AssemblyMover for adding to existing poses

Constructor & Destructor Documentation

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

Constructors ///.

Default constructor

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

Copy constructor (not needed unless you need deep copies)

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

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

Member Function Documentation

void protocols::sewing::movers::LigandBindingAssemblyMover::add_motif_scorers_to_score_file ( core::pose::Pose pose,
data_storage::SmartAssemblyOP assembly 
void protocols::sewing::movers::LigandBindingAssemblyMover::apply ( core::pose::Pose pose)
std::string protocols::sewing::movers::LigandBindingAssemblyMover::class_name ( )
protocols::moves::MoverOP protocols::sewing::movers::LigandBindingAssemblyMover::clone ( ) const

required in the context of the parser/scripting scheme

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

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

required in the context of the parser/scripting scheme

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

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

References binding_cycles_.

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

References build_site_only_.

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

References distance_cutoff_.

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

References ligand_requirements_.

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

Get the name of the Mover.

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

References class_name().

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::LigandBindingAssemblyMover::get_non_ligand_requirements ( ) const
core::Size protocols::sewing::movers::LigandBindingAssemblyMover::get_segment_distance_cutoff ( ) const
void protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
void protocols::sewing::movers::LigandBindingAssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::sewing::movers::LigandBindingAssemblyMover::set_binding_cycles ( core::Size  cycles)

References binding_cycles_.

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

References build_site_only_.

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

References distance_cutoff_.

Referenced by parse_my_tag().

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

References ligand_requirements_.

void protocols::sewing::movers::LigandBindingAssemblyMover::set_non_ligand_requirements ( utility::vector1< requirements::AssemblyRequirementOP requirements)
void protocols::sewing::movers::LigandBindingAssemblyMover::set_segment_distance_cutoff ( core::Size  cutoff)

References segment_distance_cutoff_.

Referenced by parse_my_tag().

data_storage::SmartAssemblyOP protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly ( core::pose::Pose pose)
void protocols::sewing::movers::LigandBindingAssemblyMover::show ( std::ostream &  output = std::cout) const

Show the contents of the Mover.

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

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

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

Member Data Documentation

std::map< core::Size, hashing::LigandBindingResPlacerOP > protocols::sewing::movers::LigandBindingAssemblyMover::binder_finders_
core::Size protocols::sewing::movers::LigandBindingAssemblyMover::binding_cycles_
bool protocols::sewing::movers::LigandBindingAssemblyMover::build_site_only_ = false
core::Real protocols::sewing::movers::LigandBindingAssemblyMover::distance_cutoff_
utility::vector1< data_storage::LigandDescription > protocols::sewing::movers::LigandBindingAssemblyMover::expanded_ligands_

Referenced by set_up_assembly().

utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::LigandBindingAssemblyMover::ligand_requirements_
utility::vector1< requirements::AssemblyRequirementOP > protocols::sewing::movers::LigandBindingAssemblyMover::non_ligand_requirements_
core::Size protocols::sewing::movers::LigandBindingAssemblyMover::segment_distance_cutoff_

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