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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
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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 ( )
overridedefault

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 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::append_residue ( core::pose::Pose pose,
core::Size const  offset 
)
private
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)
overridevirtual

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 
)
private
bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( core::pose::Pose const &  pose)
private
protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::AddMover::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.

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

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
private
std::string protocols::stepwise::monte_carlo::mover::AddMover::get_name ( ) const
overridevirtual

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 ( )
static
void protocols::stepwise::monte_carlo::mover::AddMover::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 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 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue ( core::pose::Pose pose,
core::Size const  offset 
)
private

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)
static
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_monte_carlo_internal ( core::pose::Pose pose) const
private
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_swa ( core::pose::Pose pose,
core::Size const  res_to_add 
) const
private
void protocols::stepwise::monte_carlo::mover::AddMover::set_designing_with_noncanonicals ( bool const  setting)
inline
void protocols::stepwise::monte_carlo::mover::AddMover::set_internal_cycles ( core::Size const  setting)
inline

References internal_cycles_.

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

References kT_.

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

References minimize_single_res_.

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

References presample_by_swa_.

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

References sample_pH_.

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

References sample_range_large_.

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

References sample_range_small_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_start_added_residue_in_aform ( core::Size const  setting)
inline
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)
private
void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions ( core::pose::Pose pose)
private

Member Data Documentation

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

Referenced by apply(), and parse_my_tag().

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

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