Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::movers::ERRASER2Protocol Class Reference

Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job. More...

#include <ERRASER2Protocol.hh>

Inheritance diagram for protocols::rna::movers::ERRASER2Protocol:
Inheritance graph

Public Member Functions

 ERRASER2Protocol ()
 Constructors ///. More...
 ERRASER2Protocol (ERRASER2Protocol const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~ERRASER2Protocol () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. 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...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void score_function (core::scoring::ScoreFunctionOP const &scorefxn_in)
core::scoring::ScoreFunctionOP score_function () const
void n_rounds (core::Size const n_rounds)
core::Size n_rounds () const
void rebuild_residue_selector (core::select::residue_selector::ResidueSelectorCOP const &residue_selector)
core::select::residue_selector::ResidueSelectorCOP rebuild_residue_selector () 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 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 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

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover configure_master_mover (Pose const &start_pose)
void resample_full_model (core::Size const resample_round, core::pose::Pose &start_pose, utility::vector1< core::Size > const &definite_residues, core::Size const nstruct)

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_ = nullptr
bool minimize_protein_ = false
core::Size n_rounds_ = 3
core::select::residue_selector::ResidueSelectorCOP rebuild_residue_selector_ = nullptr

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

Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job.

Constructor & Destructor Documentation

◆ ERRASER2Protocol() [1/2]

protocols::rna::movers::ERRASER2Protocol::ERRASER2Protocol ( )

Constructors ///.

Default constructor

◆ ERRASER2Protocol() [2/2]

protocols::rna::movers::ERRASER2Protocol::ERRASER2Protocol ( ERRASER2Protocol const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References rebuild_residue_selector_, and scorefxn_.

◆ ~ERRASER2Protocol()

protocols::rna::movers::ERRASER2Protocol::~ERRASER2Protocol ( )

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ apply()

void protocols::rna::movers::ERRASER2Protocol::apply ( core::pose::Pose start_pose)

Mover Methods ///.

Apply the mover

Perform the erraser2 protocol in a working directory

This function also does pose readin (because it could be resuming from checkpoints). In MPI contexts, this function is run on every core. (We use a work-partition job distribution framework by default, where each core is just assigned a fixed set of nstruct.) As a result, it needs to take two ints, which represent its rank and the total number of processors. Since MPI libraries use signed ints, we follow their convention rather than contorting ourselves to make them Sizes.

Apply the mover

Implements protocols::moves::Mover.

References protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate(), protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn(), protocols::rna::movers::ErraserMinimizerMover::minimize_protein(), protocols::rna::movers::ErraserMinimizerMover::scorefxn(), protocols::rna::movers::show_accuracy_report(), core::pose::Pose::size(), protocols::rna::movers::TR(), and protocols::rna::movers::ErraserMinimizerMover::work_partition().

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::ERRASER2Protocol::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ configure_master_mover()

mover::StepWiseMasterMover protocols::rna::movers::ERRASER2Protocol::configure_master_mover ( Pose const &  start_pose)

◆ fresh_instance()

protocols::moves::MoverOP protocols::rna::movers::ERRASER2Protocol::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::rna::movers::ERRASER2Protocol::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ mover_name()

std::string protocols::rna::movers::ERRASER2Protocol::mover_name ( )

◆ n_rounds() [1/2]

core::Size protocols::rna::movers::ERRASER2Protocol::n_rounds ( ) const

References n_rounds_.

◆ n_rounds() [2/2]

void protocols::rna::movers::ERRASER2Protocol::n_rounds ( core::Size const  n_rounds)

References n_rounds(), and n_rounds_.

Referenced by n_rounds().

◆ parse_my_tag()

void protocols::rna::movers::ERRASER2Protocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

◆ provide_xml_schema()

void protocols::rna::movers::ERRASER2Protocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ rebuild_residue_selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector ( ) const

◆ rebuild_residue_selector() [2/2]

void protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector ( core::select::residue_selector::ResidueSelectorCOP const &  residue_selector)

◆ resample_full_model()

void protocols::rna::movers::ERRASER2Protocol::resample_full_model ( core::Size const  resample_round,
core::pose::Pose start_pose,
utility::vector1< core::Size > const &  definite_residues,
core::Size const  nstruct 

◆ score_function() [1/2]

core::scoring::ScoreFunctionOP protocols::rna::movers::ERRASER2Protocol::score_function ( ) const

References scorefxn_.

◆ score_function() [2/2]

void protocols::rna::movers::ERRASER2Protocol::score_function ( core::scoring::ScoreFunctionOP const &  scorefxn_in)

References scorefxn_.

◆ show()

void protocols::rna::movers::ERRASER2Protocol::show ( std::ostream &  output = std::cout) const

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

◆ minimize_protein_

bool protocols::rna::movers::ERRASER2Protocol::minimize_protein_ = false

◆ n_rounds_

core::Size protocols::rna::movers::ERRASER2Protocol::n_rounds_ = 3

Referenced by n_rounds().

◆ rebuild_residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector_ = nullptr

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::movers::ERRASER2Protocol::scorefxn_ = nullptr

Referenced by ERRASER2Protocol(), and score_function().

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