protocols::mean_field::GenMeanFieldMover Class Reference

#include <GenMeanFieldMover.hh>

Inheritance diagram for protocols::mean_field::GenMeanFieldMover:

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 Strings &	info ()
	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 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_
utility::vector1 < core::pack::task::PackerTaskOP >	tasks_
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

typedef protocols::moves::Mover protocols::mean_field::GenMeanFieldMover::parent

private

Constructor & Destructor Documentation

protocols::mean_field::GenMeanFieldMover::GenMeanFieldMover

(

)

default ctor

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

overridedefault

Member Function Documentation

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

overridevirtual

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

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.

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

inlinestatic

Referenced by provide_xml_schema().

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

inlinestatic

Referenced by provide_xml_schema().

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

inlinestatic

Referenced by provide_xml_schema().

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

inlinestatic

Referenced by provide_xml_schema().

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

inlinestatic

Referenced by provide_xml_schema().

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

inlinestatic

Referenced by provide_xml_schema().

protocols::moves::MoverOP protocols::mean_field::GenMeanFieldMover::fresh_instance ( ) const

overridevirtual

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

overridevirtual

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

inline

References init_option_.

Referenced by calc_mean_field(), and parse_my_tag().

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

inline

References init_option_.

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

inline

References lambda_memory_.

Referenced by calc_mean_field(), and parse_my_tag().

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

inline

References lambda_memory_.

std::string protocols::mean_field::GenMeanFieldMover::mover_name ( )

static

Referenced by get_name(), protocols::mean_field::GenMeanFieldMoverCreator::keyname(), and provide_xml_schema().

void protocols::mean_field::GenMeanFieldMover::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 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

Remarks

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 )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), default_value_for_init_option(), default_value_for_lambda_memory(), default_value_for_temperature(), default_value_for_threshold(), default_value_for_tolerance(), default_value_for_unbound(), mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::mean_field::GenMeanFieldMoverCreator::provide_xml_schema().

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

reports distances between predicted AAMatrix and am

only runs if Design is set for the MeanField and if there is a "gold standard" AAMatrix to compare to

References aa_matrix_, protocols::mean_field::AAMatrix::ave_abs_diff(), protocols::mean_field::AAMatrix::cosine_distance(), protocols::mean_field::AAMatrix::empty(), protocols::mean_field::AAMatrix::frob_distance(), task_, and protocols::mean_field::TR().

Referenced by report_aa_matrix().

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

inline

References scorefxn_.

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

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

inline

References scorefxn(), and scorefxn_.

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

inline

References task_factory_.

Referenced by parse_my_tag(), prepare_task_poses(), and task_factory().

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

inline

References task_factory(), and task_factory_.

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

inline

References temperature_.

Referenced by calc_mean_field(), and parse_my_tag().

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

inline

References temperature_.

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

inline

References threshold_.

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

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

inline

References threshold(), and threshold_.

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

inline

References tolerance_.

Referenced by calc_mean_field(), and parse_my_tag().

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

inline

References tolerance_.

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

inline

References type_.

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

inline

References type_.

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

inline

References unbound_.

Referenced by parse_my_tag(), and prepare_task_poses().

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

inline

References unbound_.

Member Data Documentation

protocols::mean_field::AAMatrix protocols::mean_field::GenMeanFieldMover::aa_matrix_

private

Referenced by read_aa_matrix(), report_aa_matrix(), and report_dist().

core::Size protocols::mean_field::GenMeanFieldMover::init_option_

private

Referenced by init_option().

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

private

Referenced by lambda_memory().

protocols::mean_field::MeanFieldOP protocols::mean_field::GenMeanFieldMover::mean_field_

private

Referenced by calc_mean_field(), report_aa_matrix(), and report_rot_prob().

utility::vector1< std::string > protocols::mean_field::GenMeanFieldMover::pdb_list_

private

Referenced by prepare_task_poses(), and read_input_pdbs().

core::pose::PoseOPs protocols::mean_field::GenMeanFieldMover::poses_

private

Referenced by calc_mean_field(), prepare_task_poses(), and report_aa_matrix().

protocols::mean_field::AAMatrix protocols::mean_field::GenMeanFieldMover::pred_aa_matrix_

private

Referenced by calc_mean_field(), and report_aa_matrix().

core::scoring::ScoreFunctionOP protocols::mean_field::GenMeanFieldMover::scorefxn_

private

Referenced by scorefxn().

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

private

Referenced by apply(), calc_mean_field(), prepare_task_poses(), report_aa_matrix(), and report_dist().

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

private

Referenced by task_factory().

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

private

Referenced by calc_mean_field(), and prepare_task_poses().

core::Real protocols::mean_field::GenMeanFieldMover::temperature_

private

Referenced by temperature().

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

private

Referenced by threshold().

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

private

Referenced by tolerance().

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

private

Referenced by type().

bool protocols::mean_field::GenMeanFieldMover::unbound_

private

Referenced by unbound().

---

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

• src/protocols/mean_field/GenMeanFieldMover.hh
• src/protocols/mean_field/GenMeanFieldMover.cc