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protocols::stepwise::monte_carlo::mover::AddMover Class Reference

#include <AddMover.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::mover::AddMover:
Inheritance graph

Public Member Functions

 AddMover (core::scoring::ScoreFunctionCOP scorefxn=nullptr)
 ~AddMover () override
void apply (core::pose::Pose &pose, core::Size const res_to_add_in_full_model_numbering, core::Size const res_to_build_off_in_full_model_numbering)
void apply (core::pose::Pose &pose, StepWiseMove const &swa_move)
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_kT (core::Real const &setting)
void set_sample_range_small (core::Real const setting)
void set_sample_range_large (core::Real const setting)
void set_internal_cycles (core::Size const setting)
void set_sample_pH (bool const setting)
void set_presample_added_residue (core::Size const setting)
void set_presample_by_swa (core::Size const setting)
void set_designing_with_noncanonicals (bool const setting)
void set_start_added_residue_in_aform (core::Size const setting)
void set_minimize_single_res (core::Size const setting)
void set_stepwise_modeler (protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler)
- 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 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 Member Functions

void sample_by_swa (core::pose::Pose &pose, core::Size const res_to_add) const
void sample_by_monte_carlo_internal (core::pose::Pose &pose) const
void do_append (core::pose::Pose &pose)
void do_prepend (core::pose::Pose &pose)
void append_other_pose (core::pose::Pose &pose, core::Size const offset, core::Size const other_pose_idx)
void prepend_other_pose (core::pose::Pose &pose, core::Size const offset, core::Size const other_pose_idx)
void append_residue (core::pose::Pose &pose, core::Size const offset)
void prepend_residue (core::pose::Pose &pose, core::Size const offset)
bool check_same_chain (core::pose::Pose const &pose, core::Size const res_to_add_in_full_model_numbering, core::Size const res_to_build_off_in_full_model_numbering)
bool check_same_chain (core::pose::Pose const &pose)
void setup_initial_torsions (core::pose::Pose &pose)
core::Size get_add_res (StepWiseMove const &swa_move, core::pose::Pose const &pose) const
void setup_initial_jump (core::pose::Pose &pose)
core::conformation::ResidueOP create_residue_to_add (core::pose::Pose const &pose)
 : figure out the res type of the residue to add and create it More...

Private Attributes

core::chemical::ResidueTypeSetCAP rsd_set_
core::scoring::ScoreFunctionCOP scorefxn_
bool presample_added_residue_ = true
bool presample_by_swa_ = false
bool minimize_single_res_ = false
bool start_added_residue_in_aform_ = false
bool designing_with_noncanonicals_ = false
core::Size internal_cycles_ = 50
bool sample_pH_ = false
rna::RNA_TorsionMoverOP rna_torsion_mover_
core::Real sample_range_small_ = 5.0
core::Real sample_range_large_ = 40.0
core::Real kT_ = 0.5
protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler_
core::Size suite_num_ = 0
core::Size nucleoside_num_ = 0
core::Size res_to_add_in_full_model_numbering_ = 0
core::Size res_to_build_off_in_full_model_numbering_ = 0
StepWiseMove swa_move_
std::string move_str_

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::stepwise::monte_carlo::mover::AddMover::AddMover ( core::scoring::ScoreFunctionCOP  scorefxn = nullptr)
protocols::stepwise::monte_carlo::mover::AddMover::~AddMover ( )

Member Function Documentation

void protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose ( core::pose::Pose pose,
core::Size const  offset,
core::Size const  other_pose_idx 
void protocols::stepwise::monte_carlo::mover::AddMover::append_residue ( core::pose::Pose pose,
core::Size const  offset 
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose,
core::Size const  res_to_add_in_full_model_numbering,
core::Size const  res_to_build_off_in_full_model_numbering 
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose,
StepWiseMove const &  swa_move 
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose_to_visualize)

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References apply(), core::pose::full_model_info::const_full_model_info(), and move_str_.

bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( core::pose::Pose const &  pose,
core::Size const  res_to_add_in_full_model_numbering,
core::Size const  res_to_build_off_in_full_model_numbering 
bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( core::pose::Pose const &  pose)
protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::AddMover::clone ( ) const

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.

core::conformation::ResidueOP protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add ( core::pose::Pose const &  pose)
void protocols::stepwise::monte_carlo::mover::AddMover::do_append ( core::pose::Pose pose)
void protocols::stepwise::monte_carlo::mover::AddMover::do_prepend ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::AddMover::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Size protocols::stepwise::monte_carlo::mover::AddMover::get_add_res ( StepWiseMove const &  swa_move,
core::pose::Pose const &  pose 
) const
std::string protocols::stepwise::monte_carlo::mover::AddMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::stepwise::monte_carlo::mover::AddMover::mover_name ( )
void protocols::stepwise::monte_carlo::mover::AddMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 

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 internal_cycles_, kT_, minimize_single_res_, move_str_, core::scoring::parse_score_function(), presample_added_residue_, presample_by_swa_, sample_range_large_, sample_range_small_, scorefxn_, and start_added_residue_in_aform_.

void protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose ( core::pose::Pose pose,
core::Size const  offset,
core::Size const  other_pose_idx 
void protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue ( core::pose::Pose pose,
core::Size const  offset 

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueType::atom_name(), protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, core::chemical::C_METHYLAMIDATION, create_residue_to_add(), core::chemical::rna::default_jump_atom(), core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::insert_residue_by_atoms(), core::pose::Pose::insert_residue_by_jump(), protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::FoldTree::jump_nr(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, nucleoside_num_, core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::remove_variant_type_from_pose_residue(), core::pose::full_model_info::reorder_full_model_info_after_prepend(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::slide_jump(), suite_num_, swa_move_, core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::ResidueType::upper_connect_atom(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by do_prepend().

void protocols::stepwise::monte_carlo::mover::AddMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_monte_carlo_internal ( core::pose::Pose pose) const
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_swa ( core::pose::Pose pose,
core::Size const  res_to_add 
) const
void protocols::stepwise::monte_carlo::mover::AddMover::set_designing_with_noncanonicals ( bool const  setting)
void protocols::stepwise::monte_carlo::mover::AddMover::set_internal_cycles ( core::Size const  setting)

References internal_cycles_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_kT ( core::Real const &  setting)

References kT_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_minimize_single_res ( core::Size const  setting)

References minimize_single_res_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_added_residue ( core::Size const  setting)
void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_by_swa ( core::Size const  setting)

References presample_by_swa_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_pH ( bool const  setting)

References sample_pH_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_large ( core::Real const  setting)

References sample_range_large_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_small ( core::Real const  setting)

References sample_range_small_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_start_added_residue_in_aform ( core::Size const  setting)
void protocols::stepwise::monte_carlo::mover::AddMover::set_stepwise_modeler ( protocols::stepwise::modeler::StepWiseModelerOP  stepwise_modeler)

References stepwise_modeler_.

void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump ( core::pose::Pose pose)
void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions ( core::pose::Pose pose)

Member Data Documentation

bool protocols::stepwise::monte_carlo::mover::AddMover::designing_with_noncanonicals_ = false
core::Size protocols::stepwise::monte_carlo::mover::AddMover::internal_cycles_ = 50
core::Real protocols::stepwise::monte_carlo::mover::AddMover::kT_ = 0.5
bool protocols::stepwise::monte_carlo::mover::AddMover::minimize_single_res_ = false
std::string protocols::stepwise::monte_carlo::mover::AddMover::move_str_

Referenced by apply(), and parse_my_tag().

core::Size protocols::stepwise::monte_carlo::mover::AddMover::nucleoside_num_ = 0
bool protocols::stepwise::monte_carlo::mover::AddMover::presample_added_residue_ = true
bool protocols::stepwise::monte_carlo::mover::AddMover::presample_by_swa_ = false
core::Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_add_in_full_model_numbering_ = 0
core::Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_build_off_in_full_model_numbering_ = 0
rna::RNA_TorsionMoverOP protocols::stepwise::monte_carlo::mover::AddMover::rna_torsion_mover_
core::chemical::ResidueTypeSetCAP protocols::stepwise::monte_carlo::mover::AddMover::rsd_set_
bool protocols::stepwise::monte_carlo::mover::AddMover::sample_pH_ = false
core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_large_ = 40.0
core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_small_ = 5.0
core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::mover::AddMover::scorefxn_
bool protocols::stepwise::monte_carlo::mover::AddMover::start_added_residue_in_aform_ = false
protocols::stepwise::modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::AddMover::stepwise_modeler_
core::Size protocols::stepwise::monte_carlo::mover::AddMover::suite_num_ = 0
StepWiseMove protocols::stepwise::monte_carlo::mover::AddMover::swa_move_

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