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

#include <ErraserMinimizerMover.hh>

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

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, bool const initialize_scorefxn=true)
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 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 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

◆ AtomID

◆ Pose

◆ ScoreFunctionOP

◆ Tag

typedef utility::tag::Tag protocols::rna::movers::ErraserMinimizerMover::Tag

Constructor & Destructor Documentation

◆ ErraserMinimizerMover()

protocols::rna::movers::ErraserMinimizerMover::ErraserMinimizerMover ( )

◆ ~ErraserMinimizerMover()

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

Member Function Documentation

◆ add_fixed_res_constraints()

void protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints ( pose::Pose pose,
core::Size const  fixed_res_num,
core::Size const  my_anchor 

◆ add_virtual_res()

int protocols::rna::movers::ErraserMinimizerMover::add_virtual_res ( Pose pose)

◆ apply()

void protocols::rna::movers::ErraserMinimizerMover::apply ( Pose )

◆ constrain_phosphate()

void protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate ( bool const  setting)

◆ edens_scorefxn()

void protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn ( core::scoring::ScoreFunctionOP const &  sfxn)

◆ get_name()

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

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

Implements protocols::moves::Mover.

References mover_name().

◆ i_want_this_atom_to_move() [1/2]

bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move ( core::chemical::ResidueType const &  residue_type,
core::Size const &  atomno 

◆ i_want_this_atom_to_move() [2/2]

bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move ( Pose const &  pose,
AtomID const &  atom_id 

◆ initialize_from_options()

void protocols::rna::movers::ErraserMinimizerMover::initialize_from_options ( utility::options::OptionCollection const &  options,
bool const  initialize_scorefxn = true 

◆ minimize_protein()

void protocols::rna::movers::ErraserMinimizerMover::minimize_protein ( bool const  setting)

◆ movemap_setup()

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 

◆ mover_name()

std::string protocols::rna::movers::ErraserMinimizerMover::mover_name ( )

◆ nproc() [1/2]

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

Returns the total MPI nproc.

References nproc_.

Referenced by nproc().

◆ nproc() [2/2]

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

Sets the total MPI nproc.

References nproc(), and nproc_.

◆ nstruct() [1/2]

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

References nstruct_.

◆ nstruct() [2/2]

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

References nstruct(), and nstruct_.

Referenced by nstruct().

◆ parse_my_tag()

void protocols::rna::movers::ErraserMinimizerMover::parse_my_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 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_.

◆ pose_preliminaries()

void protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries ( Pose pose)

◆ process_entire_pose()

void protocols::rna::movers::ErraserMinimizerMover::process_entire_pose ( Pose pose)

◆ provide_xml_schema()

void protocols::rna::movers::ErraserMinimizerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ pyrimidine_flip_trial()

void protocols::rna::movers::ErraserMinimizerMover::pyrimidine_flip_trial ( pose::Pose pose)

◆ rank() [1/2]

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

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

References rank_.

Referenced by rank().

◆ rank() [2/2]

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_.

◆ scorefxn()

void protocols::rna::movers::ErraserMinimizerMover::scorefxn ( core::scoring::ScoreFunctionOP const &  sfxn)

◆ setup_fold_tree()

void protocols::rna::movers::ErraserMinimizerMover::setup_fold_tree ( pose::Pose pose)

◆ turn_off_for_chunks()

void protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks ( core::kinematics::MoveMap mm,
Pose const &  pose,
std::set< core::Size > const &  chunk 

◆ vary_bond_geometry()

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 

◆ work_partition() [1/2]

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

References work_partition_.

◆ work_partition() [2/2]

void protocols::rna::movers::ErraserMinimizerMover::work_partition ( bool const  work_partition)

Member Data Documentation

◆ attempt_pyrimidine_flip_

bool protocols::rna::movers::ErraserMinimizerMover::attempt_pyrimidine_flip_

◆ bond_angle_list_

utility::vector1< std::pair< AtomID, std::pair< AtomID, AtomID > > > protocols::rna::movers::ErraserMinimizerMover::bond_angle_list_

◆ bonded_atom_list_

utility::vector1< std::pair< AtomID, AtomID > > protocols::rna::movers::ErraserMinimizerMover::bonded_atom_list_

◆ chunks_

utility::vector1< std::set< core::Size > > protocols::rna::movers::ErraserMinimizerMover::chunks_

◆ constrain_phosphate_

bool protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate_

◆ cutpoint_list_

utility::vector1< core::Size > protocols::rna::movers::ErraserMinimizerMover::cutpoint_list_

◆ edens_scorefxn_

ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn_

Referenced by edens_scorefxn().

◆ fixed_res_list_

std::set< core::Size > protocols::rna::movers::ErraserMinimizerMover::fixed_res_list_

◆ minimize_protein_

bool protocols::rna::movers::ErraserMinimizerMover::minimize_protein_ = true

◆ nproc_

int protocols::rna::movers::ErraserMinimizerMover::nproc_ = 1

Referenced by nproc(), and pose_preliminaries().

◆ nstruct_

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

Referenced by nstruct(), and process_entire_pose().

◆ output_pdb_name_

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

Referenced by parse_my_tag().

◆ rank_

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

Referenced by rank().

◆ ready_set_only_

bool protocols::rna::movers::ErraserMinimizerMover::ready_set_only_

◆ scorefxn_

ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::scorefxn_

◆ skip_minimize_

bool protocols::rna::movers::ErraserMinimizerMover::skip_minimize_

◆ vary_bond_geometry_

bool protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry_

◆ virtual_res_pos

core::Size protocols::rna::movers::ErraserMinimizerMover::virtual_res_pos

◆ work_partition_

bool protocols::rna::movers::ErraserMinimizerMover::work_partition_ = true

Referenced by apply(), and work_partition().

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