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protocols::minimization_packing::BoltzmannRotamerMover Class Reference

#include <BoltzmannRotamerMover.hh>

Inheritance diagram for protocols::minimization_packing::BoltzmannRotamerMover:
Inheritance graph
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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 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 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

Constructor & Destructor Documentation

protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover ( )
protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover ( ScoreFunctionCOP  scorefxn_in,
PackerTaskOP task_in 
)
protocols::minimization_packing::BoltzmannRotamerMover::BoltzmannRotamerMover ( ScoreFunctionCOP  scorefxn_in,
TaskFactoryCOP  factory_in 
)
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
void protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
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
bool protocols::minimization_packing::BoltzmannRotamerMover::show_packer_task_
private
PackerTaskOP protocols::minimization_packing::BoltzmannRotamerMover::task_
private
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: