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protocols::docking::TemperedDocking Class Reference

allows docking using simulated or parallel tempering More...

#include <TemperedDocking.hh>

Inheritance diagram for protocols::docking::TemperedDocking:
Inheritance graph
[legend]

Public Member Functions

 TemperedDocking ()
 default constructor fills values with the expected defaults More...
 
protocols::moves::MoverOP clone () const override
 clone More...
 
 TemperedDocking (TemperedDocking const &rhs)
 copy ctor More...
 
TemperedDockingoperator= (TemperedDocking const &rhs)
 assignment operator More...
 
void set_defaults ()
 Assigns default values to primitive members. More...
 
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. More...
 
void set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_low)
 Sets the score function that will be used in the low-resolution phase. More...
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high)
 Sets the score function that will be used in the high-resolution phase. The same score function will be used for evaluating moves, packing and discriminating. More...
 
void set_highres_scorefxn (core::scoring::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP docking_scorefxn_pack)
 Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing. More...
 
void set_highres_scorefxn (core::scoring::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP docking_scorefxn_pack, core::scoring::ScoreFunctionCOP docking_scorefxn_output)
 Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating. More...
 
void set_sc_min (bool sc_min)
 
void apply (core::pose::Pose &pose) override
 main docking protocol More...
 
protocols::moves::MoverCOP to_centroid () const
 --------------------------------------— Getters ---------------------------------------— More...
 
std::string partners () const
 
std::string get_name () const override
 returns the docking partners chain identifiers More...
 
DockJumpsmovable_jumps ()
 
DockJumps const & movable_jumps () const
 returns ref to the jumps vector for docking More...
 
void set_autofoldtree (bool setting)
 @ return const ref to the jumps vector for docking More...
 
void set_partners (std::string const &setting)
 
void set_movable_jumps (DockJumps const &setting)
 
void set_use_constraints (bool setting)
 
void add_jump (core::SSize const jump_number)
 
void show (std::ostream &out=std::cout) const override
 ----------------------—— diagnostic output ------------------------------------—— More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 void register_options ()
 Associates relevant options with the TemperedDocking class. More...
 
- 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

void init_from_options ()
 Assigns user specified values to primitive members using command line options. More...
 
void finalize_setup (core::pose::Pose &pose)
 Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...
 
void init (DockJumps const movable_jumps, core::scoring::ScoreFunctionCOP docking_score_low, core::scoring::ScoreFunctionCOP docking_score_high)
 Sets up the instance of TemperedDocking and initializes all members based on values passed in at construction or via the command line. More...
 
void copy (TemperedDocking &lhs, TemperedDocking const &rhs)
 
void setup_objects ()
 
- 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

bool autofoldtree_
 information about the mode More...
 
bool flags_and_objects_are_in_sync_
 
bool first_apply_with_current_setup_
 
bool sc_min_
 
core::Size n_cycles_
 how many cycles of monte-carlo per trajectory in the sampler ? More...
 
core::kinematics::FoldTree fold_tree_
 
std::string partners_
 
std::string previous_sequence_
 
DockJumps movable_jumps_
 jumps that rigid_body transformations can occur over More...
 
core::scoring::ScoreFunctionCOP docking_scorefxn_low_
 
core::scoring::ScoreFunctionCOP docking_scorefxn_high_
 
core::scoring::ScoreFunctionCOP docking_scorefxn_pack_
 
core::scoring::ScoreFunctionCOP docking_scorefxn_output_
 
protocols::moves::MoverOP docking_constraint_
 
protocols::rigid::RigidBodyPerturbNoCenterMoverOP rb_mover_
 
protocols::canonical_sampling::TemperatureControllerOP tempering_
 
protocols::canonical_sampling::MetropolisHastingsMoverOP sampler_
 
std::string recover_sidechains_filename_
 
protocols::moves::MoverOP to_centroid_
 
bool use_csts_
 
core::Real rigid_rot_mag_
 
core::Real rigid_trans_mag_
 

Static Private Attributes

static bool options_registered_
 

Friends

std::ostream & operator<< (std::ostream &out, const TemperedDocking &dp)
 

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
 

Detailed Description

allows docking using simulated or parallel tempering

Constructor & Destructor Documentation

protocols::docking::TemperedDocking::TemperedDocking ( )

default constructor fills values with the expected defaults

References init().

protocols::docking::TemperedDocking::TemperedDocking ( TemperedDocking const &  rhs)

copy ctor

References copy().

Member Function Documentation

void protocols::docking::TemperedDocking::add_jump ( core::SSize const  jump_number)
inline

References movable_jumps_.

void protocols::docking::TemperedDocking::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::docking::TemperedDocking::clone ( ) const
overridevirtual

clone

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

void protocols::docking::TemperedDocking::copy ( TemperedDocking lhs,
TemperedDocking const &  rhs 
)
protected
void protocols::docking::TemperedDocking::finalize_setup ( core::pose::Pose pose)
protected

Performs the portion of setup of non-primitive members that requires a pose - called on apply.

setup steps when new pose comes in (this is not repeated for every reply, ... only when new sequence.. )

References autofoldtree_, core::pose::Pose::fold_tree(), fold_tree_, movable_jumps_, core::pose::Pose::num_jump(), partners_, rb_mover_, protocols::docking::setup_foldtree(), and tr().

Referenced by apply().

std::string protocols::docking::TemperedDocking::get_name ( ) const
inlineoverridevirtual

returns the docking partners chain identifiers

Implements protocols::moves::Mover.

void protocols::docking::TemperedDocking::init ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionCOP  docking_score_low,
core::scoring::ScoreFunctionCOP  docking_score_high 
)
protected

Sets up the instance of TemperedDocking and initializes all members based on values passed in at construction or via the command line.

References docking_scorefxn_high_, docking_scorefxn_low_, init_from_options(), movable_jumps(), movable_jumps_, set_defaults(), and setup_objects().

Referenced by TemperedDocking().

void protocols::docking::TemperedDocking::init_from_options ( )
protected
DockJumps& protocols::docking::TemperedDocking::movable_jumps ( )
inline

References movable_jumps_.

Referenced by init().

DockJumps const& protocols::docking::TemperedDocking::movable_jumps ( ) const
inline

returns ref to the jumps vector for docking

References movable_jumps_.

TemperedDocking & protocols::docking::TemperedDocking::operator= ( TemperedDocking const &  rhs)

assignment operator

References copy().

void protocols::docking::TemperedDocking::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 clone(), partners(), set_highres_scorefxn(), set_lowres_scorefxn(), and set_partners().

std::string protocols::docking::TemperedDocking::partners ( ) const
inline

References partners_.

Referenced by parse_my_tag().

void protocols::docking::TemperedDocking::register_options ( )
static
void protocols::docking::TemperedDocking::set_autofoldtree ( bool  setting)
inline

@ return const ref to the jumps vector for docking

References autofoldtree_.

void protocols::docking::TemperedDocking::set_defaults ( )

Assigns default values to primitive members.

---------------— initializing helpers ------------------------------—

References autofoldtree_, n_cycles_, partners_, and sc_min_.

Referenced by init().

void protocols::docking::TemperedDocking::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_high)

Sets the score function that will be used in the high-resolution phase. The same score function will be used for evaluating moves, packing and discriminating.

Referenced by parse_my_tag(), and set_highres_scorefxn().

void protocols::docking::TemperedDocking::set_highres_scorefxn ( core::scoring::ScoreFunctionCOP  docking_scorefxn_high,
core::scoring::ScoreFunctionCOP  docking_scorefxn_pack 
)

Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing.

References set_highres_scorefxn().

void protocols::docking::TemperedDocking::set_highres_scorefxn ( core::scoring::ScoreFunctionCOP  docking_scorefxn_high,
core::scoring::ScoreFunctionCOP  docking_scorefxn_pack,
core::scoring::ScoreFunctionCOP  docking_scorefxn_output 
)

Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::TemperedDocking::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_low)

Sets the score function that will be used in the low-resolution phase.

References docking_scorefxn_low_.

Referenced by parse_my_tag().

void protocols::docking::TemperedDocking::set_movable_jumps ( DockJumps const &  setting)
inline

References movable_jumps_.

Referenced by init_from_options().

void protocols::docking::TemperedDocking::set_partners ( std::string const &  setting)
inline

References partners_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::TemperedDocking::set_sc_min ( bool  sc_min)
void protocols::docking::TemperedDocking::set_use_constraints ( bool  setting)
void protocols::docking::TemperedDocking::setup_objects ( )
protected
void protocols::docking::TemperedDocking::show ( std::ostream &  out = std::cout) const
overridevirtual

----------------------—— diagnostic output ------------------------------------——

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

Referenced by apply().

void protocols::docking::TemperedDocking::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

References docking_constraint_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, and use_csts_.

Referenced by apply(), and setup_objects().

protocols::moves::MoverCOP protocols::docking::TemperedDocking::to_centroid ( ) const

--------------------------------------— Getters ---------------------------------------—

References to_centroid_.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const TemperedDocking dp 
)
friend

Member Data Documentation

bool protocols::docking::TemperedDocking::autofoldtree_
private

information about the mode

Referenced by copy(), finalize_setup(), set_autofoldtree(), and set_defaults().

protocols::moves::MoverOP protocols::docking::TemperedDocking::docking_constraint_
private
core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_high_
private
core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_low_
private
core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_output_
private
core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_pack_
private
bool protocols::docking::TemperedDocking::first_apply_with_current_setup_
private
bool protocols::docking::TemperedDocking::flags_and_objects_are_in_sync_
private
core::kinematics::FoldTree protocols::docking::TemperedDocking::fold_tree_
private
DockJumps protocols::docking::TemperedDocking::movable_jumps_
private

jumps that rigid_body transformations can occur over

Referenced by add_jump(), copy(), finalize_setup(), init(), movable_jumps(), protocols::docking::operator<<(), and set_movable_jumps().

core::Size protocols::docking::TemperedDocking::n_cycles_
private

how many cycles of monte-carlo per trajectory in the sampler ?

Referenced by init_from_options(), set_defaults(), and setup_objects().

bool protocols::docking::TemperedDocking::options_registered_
staticprivate

Referenced by register_options().

std::string protocols::docking::TemperedDocking::partners_
private
std::string protocols::docking::TemperedDocking::previous_sequence_
private

Referenced by apply(), copy(), and setup_objects().

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::TemperedDocking::rb_mover_
private

Referenced by finalize_setup(), and setup_objects().

std::string protocols::docking::TemperedDocking::recover_sidechains_filename_
private
core::Real protocols::docking::TemperedDocking::rigid_rot_mag_
private

Referenced by init_from_options(), and setup_objects().

core::Real protocols::docking::TemperedDocking::rigid_trans_mag_
private

Referenced by init_from_options(), and setup_objects().

protocols::canonical_sampling::MetropolisHastingsMoverOP protocols::docking::TemperedDocking::sampler_
private

Referenced by apply(), and setup_objects().

bool protocols::docking::TemperedDocking::sc_min_
private
protocols::canonical_sampling::TemperatureControllerOP protocols::docking::TemperedDocking::tempering_
private

Referenced by init_from_options(), and setup_objects().

protocols::moves::MoverOP protocols::docking::TemperedDocking::to_centroid_
private
bool protocols::docking::TemperedDocking::use_csts_
private

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