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protocols::indexed_structure_store::movers::SegmentSequenceProfileMover Class Reference

#include <SegmentSequenceProfileMover.hh>

Inheritance diagram for protocols::indexed_structure_store::movers::SegmentSequenceProfileMover:
Inheritance graph
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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...
 
- 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...
 
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 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 mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

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

- 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...
 

Constructor & Destructor Documentation

protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::SegmentSequenceProfileMover ( )
default

Member Function Documentation

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply ( Pose )
overridevirtual
bool protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile ( )
inline

References apply_profile_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile ( bool  new_apply_profile)
inline

References apply_profile_.

moves::MoverOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::clone ( ) const
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.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::init_structure_store ( )
private
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::mover_name ( )
static
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count ( )
inline

References output_lookup_count_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count ( std::string  new_output_lookup_count)
inline

References output_lookup_count_.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename ( )
inline

References output_pssm_filename_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename ( std::string  new_output_pssm_filename)
inline

References output_pssm_filename_.

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline ( )
inline

References output_pssm_inline_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline ( std::string const &  new_output_pssm_inline)
inline

References output_pssm_inline_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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_.

SegmentSequenceProfileConfig protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config ( )
inline

References profile_config_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config ( SegmentSequenceProfileConfig  new_profile_config)
inline

References profile_config_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling ( )
inline

References scaling_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling ( std::string  new_scaling)
inline

References scaling_.

core::select::residue_selector::ResidueSelectorCOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector ( )
inline

References selector_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector ( core::select::residue_selector::ResidueSelectorCOP  new_selector)
inline

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)
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path ( )
core::sequence::SequenceProfile protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile ( SegmentSequenceProfileResult::ArrayXaa  profile)
private
core::Real protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight ( )
inline

References weight_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight ( core::Real  new_weight)
inline

References weight_.

void protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::write_profile ( core::sequence::SequenceProfile  profile,
std::ostream &  outstream 
)
private

Member Data Documentation

bool protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply_profile_ = true
private

Referenced by apply(), apply_profile(), and parse_my_tag().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_lookup_count_ = ""
private
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_filename_ = ""
private
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::output_pssm_inline_ = ""
private
SegmentSequenceProfileConfig protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::profile_config_
private

Referenced by apply(), parse_my_tag(), and profile_config().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::pssm_output_order
static
Initial value:
= {
'A','R','N','D','C','Q','E','G','H','I','L','K','M','F','P','S','T','W','Y','V'}

Referenced by to_sequence_profile().

std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::scaling_ = "prob"
private

Referenced by apply(), parse_my_tag(), and scaling().

core::select::residue_selector::ResidueSelectorCOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::selector_
private

Referenced by apply(), parse_my_tag(), and selector().

search::StructureDatabaseOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_database_
private
StructureStoreOP protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_
private
std::string protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path_
private

Referenced by structure_store_path().

core::Real protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::weight_ = 1
private

Referenced by apply(), parse_my_tag(), and weight().


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