Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::rna::movers::RNAThreadAndMinimizeMover Class Reference

Thread a new sequence over a given RNA scaffold and do a little optimization. More...

#include <RNAThreadAndMinimizeMover.hh>

Inheritance diagram for protocols::rna::movers::RNAThreadAndMinimizeMover:
Inheritance graph

Public Member Functions

 RNAThreadAndMinimizeMover (std::string const &seq, std::string const &template_sequence_from_alignment, bool long_strategy=false, std::string const &input_sequence_type="", std::string const &mutation_list="", std::string const &insertion_list="")
 RNAThreadAndMinimizeMover ()
 ~RNAThreadAndMinimizeMover () override
void accomodate_length_change (Pose &pose, core::Size const insertion_begin, core::Size const seqpos)
void process_insertions (core::pose::Pose &pose)
void process_deletions (core::pose::Pose &pose)
void set_up_target_sequence (core::pose::Pose &pose)
void obtain_rtypes_for_target_sequence ()
void long_mutate_strategy (core::pose::Pose &pose)
void mutate_all_at_once (core::pose::Pose &pose)
core::kinematics::MoveMapOP mm_from_residues (core::pose::Pose const &pose, utility::vector1< core::Size > const &changed_pos, bool add_nearby=false)
void setup_alignment_map (std::map< core::Size, core::Size > &mapping, std::string const &sequence_from_alignment)
void apply (core::pose::Pose &pose) override
 Main Method. More...
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. 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 &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) 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::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 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 class_name ()
- 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

std::string seq_
std::string template_sequence_from_alignment_
bool long_strategy_
std::string input_sequence_type_
core::scoring::ScoreFunctionOP scorefxn_
std::string target_sequence_
utility::vector1< core::Sizeworking_res_
core::chemical::ResidueTypeCOPs rtypes_
std::string mutation_list_
std::string insertion_list_

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...

Detailed Description

Thread a new sequence over a given RNA scaffold and do a little optimization.

Constructor & Destructor Documentation

◆ RNAThreadAndMinimizeMover() [1/2]

protocols::rna::movers::RNAThreadAndMinimizeMover::RNAThreadAndMinimizeMover ( std::string const &  seq,
std::string const &  template_sequence_from_alignment,
bool  long_strategy = false,
std::string const &  input_sequence_type = "",
std::string const &  mutation_list = "",
std::string const &  insertion_list = "" 

◆ RNAThreadAndMinimizeMover() [2/2]

protocols::rna::movers::RNAThreadAndMinimizeMover::RNAThreadAndMinimizeMover ( )

◆ ~RNAThreadAndMinimizeMover()

protocols::rna::movers::RNAThreadAndMinimizeMover::~RNAThreadAndMinimizeMover ( )

Member Function Documentation

◆ accomodate_length_change()

void protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change ( Pose pose,
core::Size const  insertion_begin,
core::Size const  seqpos 

◆ apply()

void protocols::rna::movers::RNAThreadAndMinimizeMover::apply ( core::pose::Pose )

◆ class_name()

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::class_name ( )

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::RNAThreadAndMinimizeMover::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::rna::movers::RNAThreadAndMinimizeMover::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References class_name().

◆ long_mutate_strategy()

void protocols::rna::movers::RNAThreadAndMinimizeMover::long_mutate_strategy ( core::pose::Pose pose)

◆ mm_from_residues()

core::kinematics::MoveMapOP protocols::rna::movers::RNAThreadAndMinimizeMover::mm_from_residues ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  changed_pos,
bool  add_nearby = false 

◆ mutate_all_at_once()

void protocols::rna::movers::RNAThreadAndMinimizeMover::mutate_all_at_once ( core::pose::Pose pose)

◆ obtain_rtypes_for_target_sequence()

void protocols::rna::movers::RNAThreadAndMinimizeMover::obtain_rtypes_for_target_sequence ( )

◆ parse_my_tag()

void protocols::rna::movers::RNAThreadAndMinimizeMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

◆ process_deletions()

void protocols::rna::movers::RNAThreadAndMinimizeMover::process_deletions ( core::pose::Pose pose)

◆ process_insertions()

void protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions ( core::pose::Pose pose)

◆ set_up_target_sequence()

void protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence ( core::pose::Pose pose)

◆ setup_alignment_map()

void protocols::rna::movers::RNAThreadAndMinimizeMover::setup_alignment_map ( std::map< core::Size, core::Size > &  mapping,
std::string const &  sequence_from_alignment 

◆ show()

void protocols::rna::movers::RNAThreadAndMinimizeMover::show ( std::ostream &  output = std::cout) const

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

◆ input_sequence_type_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::input_sequence_type_

◆ insertion_list_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::insertion_list_

◆ long_strategy_

bool protocols::rna::movers::RNAThreadAndMinimizeMover::long_strategy_

Referenced by apply().

◆ mutation_list_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::mutation_list_

◆ rtypes_

core::chemical::ResidueTypeCOPs protocols::rna::movers::RNAThreadAndMinimizeMover::rtypes_

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::movers::RNAThreadAndMinimizeMover::scorefxn_

◆ seq_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::seq_

Referenced by apply(), and set_up_target_sequence().

◆ target_sequence_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::target_sequence_

◆ template_sequence_from_alignment_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::template_sequence_from_alignment_

◆ working_res_

utility::vector1< core::Size > protocols::rna::movers::RNAThreadAndMinimizeMover::working_res_

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