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protocols::simple_moves::StructProfileMover Class Reference

#include <StructProfileMover.hh>

Inheritance diagram for protocols::simple_moves::StructProfileMover:
Inheritance graph
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Public Member Functions

 StructProfileMover ()
 
 StructProfileMover (core::Real rmsThreshold, core::Size consider_topN_frags, core::Real burialWt, bool only_loops, core::Real allowed_deviation, core::Real allowed_deviation_loops, bool eliminate_background, bool outputProfile, bool add_csts_to_pose, bool ignore_terminal_res)
 
core::Size ss_type_convert (char ss_type)
 
void read_P_AA_SS_cen6 ()
 
utility::vector1< std::string > get_closest_sequence_at_res (core::pose::Pose const &pose, core::Size res, utility::vector1< core::Real > cenList)
 
utility::vector1
< utility::vector1
< std::string > > 
get_closest_sequences (core::pose::Pose const &pose, utility::vector1< core::Real > cenList, core::select::residue_selector::ResidueSubset const &subset)
 
utility::vector1
< utility::vector1< core::Size > > 
generate_counts (utility::vector1< utility::vector1< std::string > > top_frag_sequences, core::pose::Pose const &pose)
 
utility::vector1
< utility::vector1< core::Real > > 
generate_profile_score (utility::vector1< utility::vector1< core::Size > > res_per_pos, core::pose::Pose const &pose)
 
utility::vector1
< utility::vector1< core::Real > > 
generate_profile_score_wo_background (utility::vector1< utility::vector1< core::Size > > res_per_pos, utility::vector1< core::Real > cenList, core::pose::Pose const &pose)
 
void save_MSAcst_file (utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose const &pose)
 
void add_MSAcst_to_pose (utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose &pose)
 
core::Real get_cen_deviation (std::vector< core::Real > cenListFrag, utility::vector1< core::Real > cenListModel)
 
void set_profile_save_name (std::string const &name)
 
utility::vector1< core::Realcalc_cenlist (core::pose::Pose const &pose)
 
void apply (Pose &pose) override
 Main Method. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. 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...
 
void set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 

Private Types

typedef utility::vector1
< utility::vector1
< utility::vector1
< Probability > > > 
Probability_AA_n_n
 

Private Attributes

core::Real rmsThreshold_
 
std::string aa_order_
 
core::Size consider_topN_frags_
 
core::Real burialWt_
 
bool outputProfile_
 
bool add_csts_to_pose_
 
core::Size cenType_
 
protocols::indexed_structure_store::SSHashedFragmentStoreSSHashedFragmentStore_
 
Probability_AA_n_n P_AA_SS_burial_
 
core::Real allowed_deviation_
 
core::Real allowed_deviation_loops_
 
bool only_loops_
 
bool eliminate_background_
 
bool ignore_terminal_res_
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_
 
std::string profile_save_filename_
 

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...
 

Member Typedef Documentation

typedef utility::vector1< utility::vector1< utility::vector1< Probability > > > protocols::simple_moves::StructProfileMover::Probability_AA_n_n
private

Constructor & Destructor Documentation

protocols::simple_moves::StructProfileMover::StructProfileMover ( )

References aa_order_, and read_P_AA_SS_cen6().

protocols::simple_moves::StructProfileMover::StructProfileMover ( core::Real  rmsThreshold,
core::Size  consider_topN_frags,
core::Real  burialWt,
bool  only_loops,
core::Real  allowed_deviation,
core::Real  allowed_deviation_loops,
bool  eliminate_background,
bool  outputProfile,
bool  add_csts_to_pose,
bool  ignore_terminal_res 
)

Member Function Documentation

void protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose ( utility::vector1< utility::vector1< core::Real > >  profile_score,
core::pose::Pose pose 
)
void protocols::simple_moves::StructProfileMover::apply ( Pose )
overridevirtual
vector1< Real > protocols::simple_moves::StructProfileMover::calc_cenlist ( core::pose::Pose const &  pose)
moves::MoverOP protocols::simple_moves::StructProfileMover::clone ( ) const
inlineoverridevirtual

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.

vector1< vector1< core::Size > > protocols::simple_moves::StructProfileMover::generate_counts ( utility::vector1< utility::vector1< std::string > >  top_frag_sequences,
core::pose::Pose const &  pose 
)
vector1< vector1< Real > > protocols::simple_moves::StructProfileMover::generate_profile_score ( utility::vector1< utility::vector1< core::Size > >  res_per_pos,
core::pose::Pose const &  pose 
)

References only_loops_, and core::pose::Pose::secstruct().

Referenced by apply().

vector1< vector1< Real > > protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background ( utility::vector1< utility::vector1< core::Size > >  res_per_pos,
utility::vector1< core::Real cenList,
core::pose::Pose const &  pose 
)
Real protocols::simple_moves::StructProfileMover::get_cen_deviation ( std::vector< core::Real cenListFrag,
utility::vector1< core::Real cenListModel 
)
vector1< std::string > protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res ( core::pose::Pose const &  pose,
core::Size  res,
utility::vector1< core::Real cenList 
)
vector1< vector1< std::string > > protocols::simple_moves::StructProfileMover::get_closest_sequences ( core::pose::Pose const &  pose,
utility::vector1< core::Real cenList,
core::select::residue_selector::ResidueSubset const &  subset 
)
std::string protocols::simple_moves::StructProfileMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::simple_moves::StructProfileMover::mover_name ( )
static
void protocols::simple_moves::StructProfileMover::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 add_csts_to_pose_, allowed_deviation_, allowed_deviation_loops_, burialWt_, cenType_, consider_topN_frags_, eliminate_background_, ignore_terminal_res_, only_loops_, outputProfile_, core::select::residue_selector::parse_residue_selector(), profile_save_filename_, rmsThreshold_, set_profile_save_name(), set_residue_selector(), and SSHashedFragmentStore_.

void protocols::simple_moves::StructProfileMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::StructProfileMover::read_P_AA_SS_cen6 ( )
void protocols::simple_moves::StructProfileMover::save_MSAcst_file ( utility::vector1< utility::vector1< core::Real > >  profile_score,
core::pose::Pose const &  pose 
)
void protocols::simple_moves::StructProfileMover::set_profile_save_name ( std::string const &  name)
inline
void protocols::simple_moves::StructProfileMover::set_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector)
Size protocols::simple_moves::StructProfileMover::ss_type_convert ( char  ss_type)

Member Data Documentation

std::string protocols::simple_moves::StructProfileMover::aa_order_
private
bool protocols::simple_moves::StructProfileMover::add_csts_to_pose_
private
core::Real protocols::simple_moves::StructProfileMover::allowed_deviation_
private
core::Real protocols::simple_moves::StructProfileMover::allowed_deviation_loops_
private
core::Real protocols::simple_moves::StructProfileMover::burialWt_
private
core::Size protocols::simple_moves::StructProfileMover::cenType_
private
core::Size protocols::simple_moves::StructProfileMover::consider_topN_frags_
private
bool protocols::simple_moves::StructProfileMover::eliminate_background_
private
bool protocols::simple_moves::StructProfileMover::ignore_terminal_res_
private
bool protocols::simple_moves::StructProfileMover::only_loops_
private
bool protocols::simple_moves::StructProfileMover::outputProfile_
private
Probability_AA_n_n protocols::simple_moves::StructProfileMover::P_AA_SS_burial_
private
std::string protocols::simple_moves::StructProfileMover::profile_save_filename_
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::StructProfileMover::residue_selector_
private

Referenced by apply(), and set_residue_selector().

core::Real protocols::simple_moves::StructProfileMover::rmsThreshold_
private
protocols::indexed_structure_store::SSHashedFragmentStore* protocols::simple_moves::StructProfileMover::SSHashedFragmentStore_
private

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