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protocols::mean_field::GenMeanFieldMover Class Reference

#include <GenMeanFieldMover.hh>

Inheritance diagram for protocols::mean_field::GenMeanFieldMover:
Inheritance graph

Public Member Functions

 GenMeanFieldMover ()
 default ctor More...
 ~GenMeanFieldMover () override
void apply (core::pose::Pose &pose) override
 performs main work of Mover More...
void report_aa_matrix () const
 reports the specificity profile (AAMatrix) and backbone boltzmann probs, as appropriate More...
void report_rot_prob () const
 reports rotamer probabilities (RotMatrix) More...
void report_dist (AAMatrix const &am) const
 reports distances between predicted AAMatrix and am More...
void read_aa_matrix ()
 reads in a AAMatrix (generally the experimental gold standard with which to compare the predicted) More...
void read_input_pdbs ()
 reads in the input pdbs More...
void prepare_task_poses (core::pose::Pose const &pose)
 prepares the task and unbinds the poses if necessary More...
void calc_mean_field ()
 instantiates the appropriate MF class and calls processing methods More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) 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...
core::pack::task::TaskFactoryOP task_factory () const
void task_factory (core::pack::task::TaskFactoryOP task_factory)
core::scoring::ScoreFunctionOP scorefxn () const
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
core::Real lambda_memory () const
void lambda_memory (core::Real const lm)
core::Real tolerance () const
void tolerance (core::Real const tol)
core::Real temperature () const
void temperature (core::Real const temp)
core::Real threshold () const
void threshold (core::Real const threshold)
core::Size init_option () const
void init_option (core::Size const iopt)
bool unbound () const
void unbound (bool const ub)
std::string type () const
void type (std::string const &s)
- 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 core::Real default_value_for_lambda_memory ()
static core::Real default_value_for_tolerance ()
static core::Real default_value_for_temperature ()
static core::Size default_value_for_init_option ()
static core::Real default_value_for_threshold ()
static bool default_value_for_unbound ()
- 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 protocols::moves::Mover parent

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
core::scoring::ScoreFunctionOP scorefxn_
core::Real lambda_memory_
core::Real tolerance_
core::Real temperature_
core::Size init_option_
core::Real threshold_
bool unbound_
std::string type_
core::pack::task::PackerTaskOP task_
< core::pack::task::PackerTaskOP
core::pose::PoseOPs poses_
utility::vector1< std::string > pdb_list_
protocols::mean_field::MeanFieldOP mean_field_
protocols::mean_field::AAMatrix aa_matrix_
protocols::mean_field::AAMatrix pred_aa_matrix_

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

Constructor & Destructor Documentation

protocols::mean_field::GenMeanFieldMover::GenMeanFieldMover ( )

default ctor

protocols::mean_field::GenMeanFieldMover::~GenMeanFieldMover ( )

Member Function Documentation

void protocols::mean_field::GenMeanFieldMover::apply ( core::pose::Pose pose)

performs main work of Mover

calls other methods to:

  1. read input AAMatrix and pdbs
  2. prepare task and poses
  3. call the mean-field algorithm
  4. report probabilities of rotamers, specificity profile (AAMatrix), BB Boltzmann probabilities, and distances

Implements protocols::moves::Mover.

References calc_mean_field(), prepare_task_poses(), read_aa_matrix(), read_input_pdbs(), report_aa_matrix(), report_rot_prob(), and task_.

void protocols::mean_field::GenMeanFieldMover::calc_mean_field ( )

instantiates the appropriate MF class and calls processing methods

uses MeanFieldFactory to create a MeanField class, calls MeanField::process

since AAMatrix is used in DesignMeanField and FlexBBDesignMeanField but not in MeanField or FlexBBMeanField

must perform a cast of the mean_field_ to retrieve the predicted AAMatrix

References protocols::mean_field::MeanFieldFactory::create_mean_field(), init_option(), lambda_memory(), mean_field_, poses_, pred_aa_matrix_, scorefxn(), task_, tasks_, temperature(), threshold(), and tolerance().

Referenced by apply().

protocols::moves::MoverOP protocols::mean_field::GenMeanFieldMover::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.

static core::Size protocols::mean_field::GenMeanFieldMover::default_value_for_init_option ( )

Referenced by provide_xml_schema().

static core::Real protocols::mean_field::GenMeanFieldMover::default_value_for_lambda_memory ( )

Referenced by provide_xml_schema().

static core::Real protocols::mean_field::GenMeanFieldMover::default_value_for_temperature ( )

Referenced by provide_xml_schema().

static core::Real protocols::mean_field::GenMeanFieldMover::default_value_for_threshold ( )

Referenced by provide_xml_schema().

static core::Real protocols::mean_field::GenMeanFieldMover::default_value_for_tolerance ( )

Referenced by provide_xml_schema().

static bool protocols::mean_field::GenMeanFieldMover::default_value_for_unbound ( )

Referenced by provide_xml_schema().

protocols::moves::MoverOP protocols::mean_field::GenMeanFieldMover::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.

std::string protocols::mean_field::GenMeanFieldMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::mean_field::GenMeanFieldMover::init_option ( ) const

References init_option_.

Referenced by calc_mean_field(), and parse_my_tag().

void protocols::mean_field::GenMeanFieldMover::init_option ( core::Size const  iopt)

References init_option_.

core::Real protocols::mean_field::GenMeanFieldMover::lambda_memory ( ) const

References lambda_memory_.

Referenced by calc_mean_field(), and parse_my_tag().

void protocols::mean_field::GenMeanFieldMover::lambda_memory ( core::Real const  lm)

References lambda_memory_.

std::string protocols::mean_field::GenMeanFieldMover::mover_name ( )
void protocols::mean_field::GenMeanFieldMover::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 init_option(), lambda_memory(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn(), task_factory(), temperature(), threshold(), tolerance(), protocols::mean_field::TR(), and unbound().

void protocols::mean_field::GenMeanFieldMover::prepare_task_poses ( core::pose::Pose const &  pose)

prepares the task and unbinds the poses if necessary

initalize poses_ from list of pdbs

creates a task from the task_factory

unbinds the poses by the last jump if unbound is set to true

Error if no residues are set as packable by the task_

References protocols::pack_daemon::error_message, pdb_list_, core::import_pose::poseOPs_from_files(), poses_, task_, task_factory(), tasks_, protocols::toolbox::rigid_body::translate(), and unbound().

Referenced by apply().

void protocols::mean_field::GenMeanFieldMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::mean_field::GenMeanFieldMover::read_aa_matrix ( )

reads in a AAMatrix (generally the experimental gold standard with which to compare the predicted)

reads the AAMatrix from aa_matrix

Error if file cannot be opened

References aa_matrix_, protocols::mean_field::AAMatrix::build_aa_matrix(), protocols::abinitio::filename(), protocols::mean_field::AAMatrix::show(), and protocols::mean_field::TR().

Referenced by apply().

void protocols::mean_field::GenMeanFieldMover::read_input_pdbs ( )

reads in the input pdbs

read input pdbs into pdb_list_ from bb_list or s if bb_list is empty

Error if bb_list specified but there are no elements in the list

References protocols::pack_daemon::error_message, protocols::abinitio::filename(), and pdb_list_.

Referenced by apply().

void protocols::mean_field::GenMeanFieldMover::report_aa_matrix ( ) const

reports the specificity profile (AAMatrix) and backbone boltzmann probs, as appropriate

reports AAMatrix to output stream and to file (if dump_transfac is set)

if gold standard AAMatrix has been set, outputs distances between AAMatrix and gold standard

if FlexBB, reports bb_boltz_probs, AAMatrixs and list of pdbs to output/files

References protocols::mean_field::FlexBBDesignMeanField::aa_matrices(), aa_matrix_, protocols::mean_field::AAMatrix::dump_transfac(), protocols::mean_field::AAMatrix::empty(), protocols::abinitio::filename(), protocols::mean_field::jagged_array< T, A >::max_size_col(), mean_field_, poses_, pred_aa_matrix_, report_dist(), protocols::mean_field::AAMatrix::show(), task_, core::id::to_string(), and protocols::mean_field::TR().

Referenced by apply().

void protocols::mean_field::GenMeanFieldMover::report_dist ( AAMatrix const &  am) const
void protocols::mean_field::GenMeanFieldMover::report_rot_prob ( ) const

reports rotamer probabilities (RotMatrix)

References mean_field_, and protocols::mean_field::TR().

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::mean_field::GenMeanFieldMover::scorefxn ( ) const

References scorefxn_.

Referenced by calc_mean_field(), parse_my_tag(), and scorefxn().

void protocols::mean_field::GenMeanFieldMover::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn(), and scorefxn_.

core::pack::task::TaskFactoryOP protocols::mean_field::GenMeanFieldMover::task_factory ( ) const
void protocols::mean_field::GenMeanFieldMover::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::Real protocols::mean_field::GenMeanFieldMover::temperature ( ) const

References temperature_.

Referenced by calc_mean_field(), and parse_my_tag().

void protocols::mean_field::GenMeanFieldMover::temperature ( core::Real const  temp)

References temperature_.

core::Real protocols::mean_field::GenMeanFieldMover::threshold ( ) const

References threshold_.

Referenced by calc_mean_field(), parse_my_tag(), and threshold().

void protocols::mean_field::GenMeanFieldMover::threshold ( core::Real const  threshold)

References threshold(), and threshold_.

core::Real protocols::mean_field::GenMeanFieldMover::tolerance ( ) const

References tolerance_.

Referenced by calc_mean_field(), and parse_my_tag().

void protocols::mean_field::GenMeanFieldMover::tolerance ( core::Real const  tol)

References tolerance_.

std::string protocols::mean_field::GenMeanFieldMover::type ( ) const

References type_.

void protocols::mean_field::GenMeanFieldMover::type ( std::string const &  s)

References type_.

bool protocols::mean_field::GenMeanFieldMover::unbound ( ) const

References unbound_.

Referenced by parse_my_tag(), and prepare_task_poses().

void protocols::mean_field::GenMeanFieldMover::unbound ( bool const  ub)

References unbound_.

Member Data Documentation

protocols::mean_field::AAMatrix protocols::mean_field::GenMeanFieldMover::aa_matrix_
core::Size protocols::mean_field::GenMeanFieldMover::init_option_

Referenced by init_option().

core::Real protocols::mean_field::GenMeanFieldMover::lambda_memory_

Referenced by lambda_memory().

protocols::mean_field::MeanFieldOP protocols::mean_field::GenMeanFieldMover::mean_field_
utility::vector1< std::string > protocols::mean_field::GenMeanFieldMover::pdb_list_
core::pose::PoseOPs protocols::mean_field::GenMeanFieldMover::poses_
protocols::mean_field::AAMatrix protocols::mean_field::GenMeanFieldMover::pred_aa_matrix_
core::scoring::ScoreFunctionOP protocols::mean_field::GenMeanFieldMover::scorefxn_

Referenced by scorefxn().

core::pack::task::PackerTaskOP protocols::mean_field::GenMeanFieldMover::task_
core::pack::task::TaskFactoryOP protocols::mean_field::GenMeanFieldMover::task_factory_

Referenced by task_factory().

utility::vector1< core::pack::task::PackerTaskOP > protocols::mean_field::GenMeanFieldMover::tasks_
core::Real protocols::mean_field::GenMeanFieldMover::temperature_

Referenced by temperature().

core::Real protocols::mean_field::GenMeanFieldMover::threshold_

Referenced by threshold().

core::Real protocols::mean_field::GenMeanFieldMover::tolerance_

Referenced by tolerance().

std::string protocols::mean_field::GenMeanFieldMover::type_

Referenced by type().

bool protocols::mean_field::GenMeanFieldMover::unbound_

Referenced by unbound().

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