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Rosetta
2020.50
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#include <SegmentSequenceProfileMover.hh>
Public Member Functions | |
SegmentSequenceProfileMover ()=default | |
void | structure_store_path (std::string path) |
std::string | structure_store_path () |
core::select::residue_selector::ResidueSelectorCOP | selector () |
void | selector (core::select::residue_selector::ResidueSelectorCOP new_selector) |
SegmentSequenceProfileConfig | profile_config () |
void | profile_config (SegmentSequenceProfileConfig new_profile_config) |
std::string | output_lookup_count () |
void | output_lookup_count (std::string new_output_lookup_count) |
std::string | output_pssm_filename () |
void | output_pssm_filename (std::string new_output_pssm_filename) |
std::string | output_pssm_inline () |
void | output_pssm_inline (std::string const &new_output_pssm_inline) |
bool | apply_profile () |
void | apply_profile (bool new_apply_profile) |
std::string | scaling () |
void | scaling (std::string new_scaling) |
core::Real | weight () |
void | weight (core::Real new_weight) |
indexed_structure_store::StructureStoreOP | structure_store () |
search::StructureDatabaseOP | structure_database () |
moves::MoverOP | clone () const override |
Return a clone of the Mover object. More... | |
void | apply (Pose &pose) override |
Main Method. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
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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... | |
virtual MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. 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 void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. 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 | mover_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Static Public Attributes | |
static std::string | pssm_output_order |
Private Member Functions | |
void | init_structure_store () |
core::sequence::SequenceProfile | to_sequence_profile (SegmentSequenceProfileResult::ArrayXaa profile) |
void | write_profile (core::sequence::SequenceProfile profile, std::ostream &outstream) |
Private Attributes | |
std::string | structure_store_path_ |
core::select::residue_selector::ResidueSelectorCOP | selector_ |
SegmentSequenceProfileConfig | profile_config_ |
std::string | output_lookup_count_ = "" |
std::string | output_pssm_filename_ = "" |
std::string | output_pssm_inline_ = "" |
bool | apply_profile_ = true |
std::string | scaling_ = "prob" |
core::Real | weight_ = 1 |
StructureStoreOP | structure_store_ |
search::StructureDatabaseOP | structure_database_ |
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... | |
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default |
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::simple_moves::FavorSequenceProfile::apply(), apply_profile_, protocols::indexed_structure_store::SegmentSequenceProfile::config, protocols::jd2::current_output_name(), protocols::jd2::get_current_job(), protocols::jd2::jd2_used(), protocols::indexed_structure_store::SegmentSequenceProfileResult::log_odds, core::chemical::num_canonical_aas, core::conformation::membrane::out, output_lookup_count_, output_pssm_filename_, output_pssm_inline_, profile_config_, protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, protocols::indexed_structure_store::SegmentSequenceProfileResult::query_results, protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance, scaling_, protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), selector_, protocols::simple_moves::FavorSequenceProfile::set_profile(), protocols::simple_moves::FavorSequenceProfile::set_scaling(), protocols::simple_moves::FavorSequenceProfile::set_weight(), core::pose::setPoseExtraScore(), structure_database(), structure_store(), to_sequence_profile(), core::pose::Pose::total_residue(), protocols::indexed_structure_store::TR(), weight_, and write_profile().
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inline |
References apply_profile_.
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References apply_profile_.
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overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
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private |
References structure_database_, structure_store_, and structure_store_path().
Referenced by structure_database(), and structure_store().
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static |
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inline |
References output_lookup_count_.
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References output_lookup_count_.
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References output_pssm_filename_.
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References output_pssm_filename_.
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inline |
References output_pssm_inline_.
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inline |
References output_pssm_inline_.
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overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References apply_profile_, output_lookup_count_, output_pssm_filename_, output_pssm_inline_, core::select::residue_selector::parse_residue_selector(), profile_config_, protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance, scaling_, selector_, structure_store_path(), and weight_.
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inline |
References profile_config_.
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References profile_config_.
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static |
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References scaling_.
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References scaling_.
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References selector_.
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References selector_.
search::StructureDatabaseOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_database | ( | ) |
References init_structure_store(), and structure_database_.
Referenced by apply().
StructureStoreOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store | ( | ) |
References init_structure_store(), and structure_store_.
Referenced by apply().
void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path | ( | std::string | path | ) |
References protocols::hybridization::path, structure_database_, structure_store_, and structure_store_path_.
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path | ( | ) |
References structure_store_path_.
Referenced by init_structure_store(), and parse_my_tag().
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private |
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References weight_.
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References weight_.
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private |
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Referenced by apply(), apply_profile(), and parse_my_tag().
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Referenced by apply(), output_lookup_count(), and parse_my_tag().
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Referenced by apply(), output_pssm_filename(), and parse_my_tag().
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Referenced by apply(), output_pssm_inline(), and parse_my_tag().
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Referenced by apply(), parse_my_tag(), and profile_config().
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Referenced by to_sequence_profile().
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Referenced by apply(), parse_my_tag(), and scaling().
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Referenced by apply(), parse_my_tag(), and selector().
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Referenced by init_structure_store(), structure_database(), and structure_store_path().
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Referenced by init_structure_store(), structure_store(), and structure_store_path().
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Referenced by structure_store_path().
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Referenced by apply(), parse_my_tag(), and weight().