#include <BoltzmannRotamerMover.hh>

Inheritance diagram for protocols::minimization_packing::BoltzmannRotamerMover:

Public Types
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef protocols::moves::MoverOP	MoverOP

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

Public Member Functions
	BoltzmannRotamerMover ()

	BoltzmannRotamerMover (ScoreFunctionCOP scorefxn_in, PackerTaskOP &task_in)
	constructor with PackerTask More...

	BoltzmannRotamerMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in)
	constructor with TaskFactory More...

	BoltzmannRotamerMover (BoltzmannRotamerMover const &rval)
	copy constructor More...

	~BoltzmannRotamerMover () override
	destructor More...

protocols::moves::MoverOP	clone () const override
	clone this object More...

protocols::moves::MoverOP	fresh_instance () const override
	create this type of object More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

core::Size	select_rotamer (utility::vector1< std::pair< core::Size, core::Real > > const &boltzmann_factors, core::Real const &partition_function)
	select a rotamer based on Boltzmann weighted probabilities More...

void	set_score_function (core::scoring::ScoreFunctionCOP sf)

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

void	set_resnum (core::Size resnum)

void	set_ligand_resnum (core::Size ligand_resnum)

void	set_ligand_weight (core::Real ligand_weight)

void	set_temperature (core::Real temperature)

void	set_bias_sampling (bool bias_sampling)

void	set_randomize_resnum (bool randomize_resnum)

void	set_bump_check (bool bump_check)

void	set_task (PackerTaskOP task)

void	set_scorefxn (ScoreFunctionCOP scorefxn)

core::Size	get_resnum () const

core::Size	get_ligand_resnum () const

core::Real	get_ligand_weight () const

core::Real	get_temperature () const

bool	get_bias_sampling () const

bool	get_randomize_resnum () const

bool	get_bump_check () const

PackerTaskOP	get_task () const

ScoreFunctionCOP	get_scorefxn () const

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

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 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 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...

Protected Member Functions
ScoreFunctionCOP	scorefxn () const
	read access for derived classes More...

PackerTaskCOP	task (core::pose::Pose const &pose) const
	read access for derived classes, pose needed to run TaskFactory More...

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...

Private Attributes
ScoreFunctionCOP	scorefxn_

PackerTaskOP	task_

TaskFactoryCOP	factory_

bool	show_packer_task_

core::Size	resnum_
	residue number specifying the next residue to move More...

core::Size	ligand_resnum_
	residue number specifying the ligand residue (0 if no ligand) More...

core::Real	ligand_weight_
	weight for interaction between resnum_ and ligand_resnum_ More...

core::Real	temperature_
	kT value used for Boltzmann probability calculation More...

bool	bias_sampling_
	if true, bias rotamer selection based on energy More...

bool	randomize_resnum_
	if true, choose a random residue for the next move More...

bool	bump_check_
	if true, use bump check when generating rotamers More...

Member Typedef Documentation

typedef protocols::moves::MoverOP protocols::minimization_packing::BoltzmannRotamerMover::MoverOP

typedef core::pack::task::PackerTask protocols::minimization_packing::BoltzmannRotamerMover::PackerTask

typedef core::pack::task::PackerTaskCOP protocols::minimization_packing::BoltzmannRotamerMover::PackerTaskCOP

typedef core::pack::task::PackerTaskOP protocols::minimization_packing::BoltzmannRotamerMover::PackerTaskOP

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::BoltzmannRotamerMover::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::minimization_packing::BoltzmannRotamerMover::ScoreFunctionOP

typedef core::pack::task::TaskFactoryCOP protocols::minimization_packing::BoltzmannRotamerMover::TaskFactoryCOP

Constructor & Destructor Documentation

protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover ( )

References bias_sampling_, bump_check_, ligand_resnum_, ligand_weight_, randomize_resnum_, resnum_, show_packer_task_, temperature_, and protocols::moves::Mover::type().

protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover	(	ScoreFunctionCOP	scorefxn_in,
		PackerTaskOP &	task_in
	)

constructor with PackerTask

References bias_sampling_, bump_check_, ligand_resnum_, ligand_weight_, randomize_resnum_, resnum_, task_, temperature_, and protocols::moves::Mover::type().

protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover	(	ScoreFunctionCOP	scorefxn_in,
		TaskFactoryCOP	factory_in
	)

constructor with TaskFactory

References bias_sampling_, bump_check_, ligand_resnum_, ligand_weight_, randomize_resnum_, resnum_, temperature_, and protocols::moves::Mover::type().

protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover ( BoltzmannRotamerMover const & rval )

default

copy constructor

protocols::minimization_packing::BoltzmannRotamerMover::~BoltzmannRotamerMover ( )

overridedefault

destructor

Member Function Documentation

void protocols::minimization_packing::BoltzmannRotamerMover::apply ( core::pose::Pose & )

overridevirtual

BoltzmannRotamerMover::MoverOP protocols::minimization_packing::BoltzmannRotamerMover::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

Referenced by apply().

BoltzmannRotamerMover::MoverOP protocols::minimization_packing::BoltzmannRotamerMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

bool protocols::minimization_packing::BoltzmannRotamerMover::get_bias_sampling ( ) const

References bias_sampling_.

bool protocols::minimization_packing::BoltzmannRotamerMover::get_bump_check ( ) const

References bump_check_.

core::Size protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_resnum ( ) const

References ligand_resnum_.

core::Real protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_weight ( ) const

References ligand_weight_.

std::string protocols::minimization_packing::BoltzmannRotamerMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::minimization_packing::BoltzmannRotamerMover::get_randomize_resnum ( ) const

References randomize_resnum_.

core::Size protocols::minimization_packing::BoltzmannRotamerMover::get_resnum ( ) const

References resnum_.

core::scoring::ScoreFunctionCOP protocols::minimization_packing::BoltzmannRotamerMover::get_scorefxn ( ) const

References scorefxn_.

core::pack::task::PackerTaskOP protocols::minimization_packing::BoltzmannRotamerMover::get_task ( ) const

References task_.

core::Real protocols::minimization_packing::BoltzmannRotamerMover::get_temperature ( ) const

References temperature_.

std::string protocols::minimization_packing::BoltzmannRotamerMover::mover_name ( )

static

Referenced by get_name(), protocols::minimization_packing::BoltzmannRotamerMoverCreator::keyname(), and provide_xml_schema().

void protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn_, set_task_factory(), and show_packer_task_.

void protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::minimization_packing::BoltzmannRotamerMoverCreator::provide_xml_schema().

BoltzmannRotamerMover::ScoreFunctionCOP protocols::minimization_packing::BoltzmannRotamerMover::scorefxn ( ) const

protected

read access for derived classes

References scorefxn_.

Referenced by set_scorefxn(), and show().

core::Size protocols::minimization_packing::BoltzmannRotamerMover::select_rotamer	(	utility::vector1< std::pair< core::Size, core::Real > > const &	boltzmann_factors,
		core::Real const &	partition_function
	)

select a rotamer based on Boltzmann weighted probabilities

References bias_sampling_, compare_values(), and rot().

Referenced by apply().

void protocols::minimization_packing::BoltzmannRotamerMover::set_bias_sampling ( bool bias_sampling )

References bias_sampling_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_bump_check ( bool bump_check )

References core::pack::rotamer_set::bump_check(), and bump_check_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_resnum ( core::Size ligand_resnum )

References ligand_resnum_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_weight ( core::Real ligand_weight )

References ligand_weight_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_randomize_resnum ( bool randomize_resnum )

References randomize_resnum_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_resnum ( core::Size resnum )

References resnum_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_score_function ( core::scoring::ScoreFunctionCOP sf )

References scorefxn_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_scorefxn ( ScoreFunctionCOP scorefxn )

References scorefxn(), and scorefxn_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_task ( PackerTaskOP task )

References task(), and task_.

void protocols::minimization_packing::BoltzmannRotamerMover::set_task_factory ( core::pack::task::TaskFactoryCOP tf )

References factory_.

Referenced by parse_my_tag().

void protocols::minimization_packing::BoltzmannRotamerMover::set_temperature ( core::Real temperature )

References temperature_.

void protocols::minimization_packing::BoltzmannRotamerMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References scorefxn().

Referenced by protocols::minimization_packing::operator<<().

BoltzmannRotamerMover::PackerTaskCOP protocols::minimization_packing::BoltzmannRotamerMover::task ( core::pose::Pose const & pose ) const

protected

read access for derived classes, pose needed to run TaskFactory

read access for derived classes

References factory_, and task_.

Referenced by apply(), and set_task().

Member Data Documentation

bool protocols::minimization_packing::BoltzmannRotamerMover::bias_sampling_

private

if true, bias rotamer selection based on energy

Referenced by BoltzmannRotamerMover(), get_bias_sampling(), select_rotamer(), and set_bias_sampling().

bool protocols::minimization_packing::BoltzmannRotamerMover::bump_check_

private

if true, use bump check when generating rotamers

Referenced by apply(), BoltzmannRotamerMover(), get_bump_check(), and set_bump_check().

TaskFactoryCOP protocols::minimization_packing::BoltzmannRotamerMover::factory_

private

Referenced by set_task_factory(), and task().

core::Size protocols::minimization_packing::BoltzmannRotamerMover::ligand_resnum_

private

residue number specifying the ligand residue (0 if no ligand)

Referenced by apply(), BoltzmannRotamerMover(), get_ligand_resnum(), and set_ligand_resnum().

core::Real protocols::minimization_packing::BoltzmannRotamerMover::ligand_weight_

private

weight for interaction between resnum_ and ligand_resnum_

Referenced by apply(), BoltzmannRotamerMover(), get_ligand_weight(), and set_ligand_weight().

bool protocols::minimization_packing::BoltzmannRotamerMover::randomize_resnum_

private

if true, choose a random residue for the next move

Referenced by apply(), BoltzmannRotamerMover(), get_randomize_resnum(), and set_randomize_resnum().

core::Size protocols::minimization_packing::BoltzmannRotamerMover::resnum_

private

residue number specifying the next residue to move

Referenced by apply(), BoltzmannRotamerMover(), get_resnum(), and set_resnum().

ScoreFunctionCOP protocols::minimization_packing::BoltzmannRotamerMover::scorefxn_

private

Referenced by apply(), get_scorefxn(), parse_my_tag(), scorefxn(), set_score_function(), and set_scorefxn().

bool protocols::minimization_packing::BoltzmannRotamerMover::show_packer_task_

private

Referenced by apply(), BoltzmannRotamerMover(), and parse_my_tag().

PackerTaskOP protocols::minimization_packing::BoltzmannRotamerMover::task_

private

Referenced by BoltzmannRotamerMover(), get_task(), set_task(), and task().

core::Real protocols::minimization_packing::BoltzmannRotamerMover::temperature_

private

kT value used for Boltzmann probability calculation

Referenced by apply(), BoltzmannRotamerMover(), get_temperature(), and set_temperature().

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

src/protocols/minimization_packing/BoltzmannRotamerMover.hh
src/protocols/minimization_packing/BoltzmannRotamerMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation