Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::sewing::movers::AppendAssemblyMover Class Reference

an AssemblyMover for adding to existing poses More...

#include <AppendAssemblyMover.hh>

Inheritance diagram for protocols::sewing::movers::AppendAssemblyMover:
Inheritance graph
[legend]

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 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 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 ( )
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
void protocols::sewing::movers::AppendAssemblyMover::apply ( core::pose::Pose pose)
overridevirtual
void protocols::sewing::movers::AppendAssemblyMover::attributes_for_append_assembly_mover ( utility::tag::AttributeList &  attributes)
static
std::string protocols::sewing::movers::AppendAssemblyMover::class_name ( )
static
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
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
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
std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_dssp ( ) const
std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_ends_string ( ) const
std::string protocols::sewing::movers::AppendAssemblyMover::get_pose_segment_starts_string ( ) const
std::string protocols::sewing::movers::AppendAssemblyMover::get_required_resnums ( ) const
core::select::residue_selector::ResidueSelectorCOP protocols::sewing::movers::AppendAssemblyMover::get_required_selector ( ) const
bool protocols::sewing::movers::AppendAssemblyMover::get_segments_from_dssp ( ) const
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
void protocols::sewing::movers::AppendAssemblyMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::sewing::movers::AppendAssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
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)
void protocols::sewing::movers::AppendAssemblyMover::set_pose_segment_starts_string ( std::string const &  input)
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)
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
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
bool protocols::sewing::movers::AppendAssemblyMover::extend_mode_ = false
private
utility::vector1< data_storage::LigandDescription > protocols::sewing::movers::AppendAssemblyMover::ligands_
private
char protocols::sewing::movers::AppendAssemblyMover::modifiable_terminus_ = 'B'
private
bool protocols::sewing::movers::AppendAssemblyMover::output_partner_ = true
private
utility::pointer::DeepCopyOP< core::pose::Pose > protocols::sewing::movers::AppendAssemblyMover::partner_pdb_
private
std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_dssp_
private
std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_ends_string_
private
std::string protocols::sewing::movers::AppendAssemblyMover::pose_segment_starts_string_
private
std::string protocols::sewing::movers::AppendAssemblyMover::required_resnums_
private
core::select::residue_selector::ResidueSelectorCOP protocols::sewing::movers::AppendAssemblyMover::required_selector_
private
bool protocols::sewing::movers::AppendAssemblyMover::segments_from_dssp_ = true
private
std::string protocols::sewing::movers::AppendAssemblyMover::start_node_vital_segments_
private
bool protocols::sewing::movers::AppendAssemblyMover::strict_dssp_changes_ = false
private

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