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protocols::rna::movers::ErraserMinimizerMover Class Reference

#include <ErraserMinimizerMover.hh>

Inheritance diagram for protocols::rna::movers::ErraserMinimizerMover:
Inheritance graph
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Public Member Functions

 ErraserMinimizerMover ()
 
 ~ErraserMinimizerMover () override=default
 
void pyrimidine_flip_trial (Pose &pose)
 
void setup_fold_tree (Pose &pose)
 
void minimize_protein (bool const setting)
 
void initialize_from_options (utility::options::OptionCollection const &options)
 
core::kinematics::MoveMap movemap_setup (Pose &pose, std::set< core::Size > &cut_upper, std::set< core::Size > &cut_lower, ObjexxFCL::FArray1D< bool > &allow_insert)
 
void apply (Pose &pose) override
 Main Method. More...
 
void process_entire_pose (Pose &pose)
 
void pose_preliminaries (Pose &pose)
 Some pose setup functions that can be separated from apply. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
bool i_want_this_atom_to_move (core::chemical::ResidueType const &residue_type, core::Size const &atomno)
 
bool i_want_this_atom_to_move (Pose const &pose, AtomID const &atom_id)
 
int add_virtual_res (Pose &pose)
 
void vary_bond_geometry (core::kinematics::MoveMap &mm, Pose &pose, ObjexxFCL::FArray1D< bool > &allow_insert, std::set< core::Size > const &chunk)
 
void turn_off_for_chunks (core::kinematics::MoveMap &mm, Pose const &pose, std::set< core::Size > const &chunk)
 
void add_fixed_res_constraints (Pose &pose, core::Size const fixed_res_num, core::Size const my_anchor)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void scorefxn (core::scoring::ScoreFunctionOP const &sfxn)
 
void edens_scorefxn (core::scoring::ScoreFunctionOP const &sfxn)
 
void nstruct (core::Size const nstruct)
 
core::Size nstruct ()
 
void constrain_phosphate (bool const setting)
 
void rank (int const rank)
 Sets the MPI rank of the proc this Mover is running on. More...
 
int rank () const
 Returns the MPI rank of the proc this Mover is running on. More...
 
void nproc (int const nproc)
 Sets the total MPI nproc. More...
 
int nproc () const
 Returns the total MPI nproc. More...
 
void work_partition (bool const work_partition)
 
int work_partition () const
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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 core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef utility::tag::Tag Tag
 
typedef core::id::AtomID AtomID
 

Private Attributes

utility::vector1< std::pair
< AtomID, AtomID > > 
bonded_atom_list_
 
utility::vector1< std::pair
< AtomID, std::pair< AtomID,
AtomID > > > 
bond_angle_list_
 
bool vary_bond_geometry_
 
bool constrain_phosphate_
 
bool ready_set_only_
 
bool skip_minimize_
 
bool attempt_pyrimidine_flip_
 
bool minimize_protein_ = true
 
std::set< core::Sizefixed_res_list_
 
utility::vector1< core::Sizecutpoint_list_
 
std::string output_pdb_name_
 
core::Size nstruct_ = 1
 
int rank_ = 0
 
int nproc_ = 1
 
bool work_partition_ = true
 
ScoreFunctionOP scorefxn_
 
ScoreFunctionOP edens_scorefxn_
 
utility::vector1< std::set
< core::Size > > 
chunks_
 
core::Size virtual_res_pos
 

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::tag::Tag protocols::rna::movers::ErraserMinimizerMover::Tag
private

Constructor & Destructor Documentation

protocols::rna::movers::ErraserMinimizerMover::ErraserMinimizerMover ( )
protocols::rna::movers::ErraserMinimizerMover::~ErraserMinimizerMover ( )
overridedefault

Member Function Documentation

void protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints ( pose::Pose pose,
core::Size const  fixed_res_num,
core::Size const  my_anchor 
)
int protocols::rna::movers::ErraserMinimizerMover::add_virtual_res ( Pose pose)
void protocols::rna::movers::ErraserMinimizerMover::apply ( Pose )
overridevirtual
void protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate ( bool const  setting)
inline
void protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn ( core::scoring::ScoreFunctionOP const &  sfxn)
inline
std::string protocols::rna::movers::ErraserMinimizerMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move ( core::chemical::ResidueType const &  residue_type,
core::Size const &  atomno 
)
bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move ( Pose const &  pose,
AtomID const &  atom_id 
)
inline
void protocols::rna::movers::ErraserMinimizerMover::initialize_from_options ( utility::options::OptionCollection const &  options)
void protocols::rna::movers::ErraserMinimizerMover::minimize_protein ( bool const  setting)
inline
kinematics::MoveMap protocols::rna::movers::ErraserMinimizerMover::movemap_setup ( Pose pose,
std::set< core::Size > &  cut_upper,
std::set< core::Size > &  cut_lower,
ObjexxFCL::FArray1D< bool > &  allow_insert 
)
std::string protocols::rna::movers::ErraserMinimizerMover::mover_name ( )
static
void protocols::rna::movers::ErraserMinimizerMover::nproc ( int const  nproc)

Sets the total MPI nproc.

References nproc(), and nproc_.

int protocols::rna::movers::ErraserMinimizerMover::nproc ( ) const

Returns the total MPI nproc.

References nproc_.

Referenced by nproc().

void protocols::rna::movers::ErraserMinimizerMover::nstruct ( core::Size const  nstruct)
inline

References nstruct(), and nstruct_.

Referenced by nstruct().

core::Size protocols::rna::movers::ErraserMinimizerMover::nstruct ( )
inline

References nstruct_.

void protocols::rna::movers::ErraserMinimizerMover::parse_my_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 attempt_pyrimidine_flip_, constrain_phosphate_, core::scoring::ScoreFunctionFactory::create_score_function(), cutpoint_list_, fixed_res_list_, output_pdb_name_, ready_set_only_, scorefxn_, skip_minimize_, protocols::rna::movers::string_to_size_vector(), protocols::rna::movers::TR(), and vary_bond_geometry_.

void protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries ( Pose pose)
void protocols::rna::movers::ErraserMinimizerMover::process_entire_pose ( Pose pose)
void protocols::rna::movers::ErraserMinimizerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rna::movers::ErraserMinimizerMover::pyrimidine_flip_trial ( pose::Pose pose)
void protocols::rna::movers::ErraserMinimizerMover::rank ( int const  rank)

Sets the MPI rank of the proc this Mover is running on.

References rank(), and rank_.

int protocols::rna::movers::ErraserMinimizerMover::rank ( ) const

Returns the MPI rank of the proc this Mover is running on.

References rank_.

Referenced by rank().

void protocols::rna::movers::ErraserMinimizerMover::scorefxn ( core::scoring::ScoreFunctionOP const &  sfxn)
inline
void protocols::rna::movers::ErraserMinimizerMover::setup_fold_tree ( pose::Pose pose)
void protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks ( core::kinematics::MoveMap mm,
Pose const &  pose,
std::set< core::Size > const &  chunk 
)
void protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry ( core::kinematics::MoveMap mm,
pose::Pose pose,
ObjexxFCL::FArray1D< bool > &  allow_insert,
std::set< core::Size > const &  chunk 
)
void protocols::rna::movers::ErraserMinimizerMover::work_partition ( bool const  work_partition)
inline
int protocols::rna::movers::ErraserMinimizerMover::work_partition ( ) const
inline

References work_partition_.

Member Data Documentation

bool protocols::rna::movers::ErraserMinimizerMover::attempt_pyrimidine_flip_
private
utility::vector1< std::pair< AtomID, std::pair< AtomID, AtomID > > > protocols::rna::movers::ErraserMinimizerMover::bond_angle_list_
private
utility::vector1< std::pair< AtomID, AtomID > > protocols::rna::movers::ErraserMinimizerMover::bonded_atom_list_
private
utility::vector1< std::set< core::Size > > protocols::rna::movers::ErraserMinimizerMover::chunks_
private
bool protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate_
private
utility::vector1< core::Size > protocols::rna::movers::ErraserMinimizerMover::cutpoint_list_
private
ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn_
private

Referenced by edens_scorefxn().

std::set< core::Size > protocols::rna::movers::ErraserMinimizerMover::fixed_res_list_
private
bool protocols::rna::movers::ErraserMinimizerMover::minimize_protein_ = true
private
int protocols::rna::movers::ErraserMinimizerMover::nproc_ = 1
private

Referenced by nproc(), and pose_preliminaries().

core::Size protocols::rna::movers::ErraserMinimizerMover::nstruct_ = 1
private

Referenced by nstruct(), and process_entire_pose().

std::string protocols::rna::movers::ErraserMinimizerMover::output_pdb_name_
private

Referenced by parse_my_tag().

int protocols::rna::movers::ErraserMinimizerMover::rank_ = 0
private

Referenced by rank().

bool protocols::rna::movers::ErraserMinimizerMover::ready_set_only_
private
ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::scorefxn_
private
bool protocols::rna::movers::ErraserMinimizerMover::skip_minimize_
private
bool protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry_
private
core::Size protocols::rna::movers::ErraserMinimizerMover::virtual_res_pos
private
bool protocols::rna::movers::ErraserMinimizerMover::work_partition_ = true
private

Referenced by apply(), and work_partition().


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