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protocols::docking::DockSetupMover Class Reference

allows docking using simulated or parallel tempering More...

#include <DockSetupMover.hh>

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

Public Member Functions

 DockSetupMover ()
 default constructor fills values with the expected defaults More...
 
protocols::moves::MoverOP clone () const override
 clone More...
 
 DockSetupMover (DockSetupMover const &rhs)
 copy ctor More...
 
DockSetupMoveroperator= (DockSetupMover const &rhs)
 assignment operator More...
 
void set_defaults ()
 Assigns default values to primitive members. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string const & partners () const
 
void set_partners (std::string const &setting)
 returns the docking partners chain identifiers More...
 
void show (std::ostream &out=std::cout) const override
 --------------------------------——— Getters ---------------------------------——— 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...
 
std::string get_name () const override
 ---------------— End initializing helpers ------------------------------— 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 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

void copy (DockSetupMover &lhs, DockSetupMover const &rhs)
 
- 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

std::string partners_
 — configurables --— More...
 
protocols::rigid::RigidBodyPerturbNoCenterMoverOP rb_mover_
 
DockJumps movable_jumps_
 
protocols::docking::RigidBodyInfoOP rigid_body_info_
 

Friends

std::ostream & operator<< (std::ostream &out, const DockSetupMover &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::DockSetupMover::DockSetupMover ( )

default constructor fills values with the expected defaults

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

copy ctor

References copy().

Member Function Documentation

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

clone

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

void protocols::docking::DockSetupMover::copy ( DockSetupMover lhs,
DockSetupMover const &  rhs 
)
protected
std::string protocols::docking::DockSetupMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::docking::DockSetupMover::mover_name ( )
static
DockSetupMover & protocols::docking::DockSetupMover::operator= ( DockSetupMover const &  rhs)

assignment operator

References copy().

void protocols::docking::DockSetupMover::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 movable_jumps_, protocols::rosetta_scripts::parse_mover(), partners(), partners_, rb_mover_, rigid_body_info_, set_partners(), and tr().

std::string const& protocols::docking::DockSetupMover::partners ( ) const
inline

References partners_.

Referenced by parse_my_tag().

void protocols::docking::DockSetupMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::DockSetupMover::set_defaults ( )

Assigns default values to primitive members.

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

References partners_.

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

returns the docking partners chain identifiers

References partners_.

Referenced by parse_my_tag().

void protocols::docking::DockSetupMover::show ( std::ostream &  out = std::cout) const
overridevirtual

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

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

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

References protocols::comparative_modeling::features::A, movable_jumps_, and partners_.

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

Friends And Related Function Documentation

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

Member Data Documentation

DockJumps protocols::docking::DockSetupMover::movable_jumps_
private

Referenced by apply(), copy(), parse_my_tag(), and show().

std::string protocols::docking::DockSetupMover::partners_
private

— configurables --—

Referenced by apply(), copy(), parse_my_tag(), partners(), set_defaults(), set_partners(), and show().

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockSetupMover::rb_mover_
private

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

protocols::docking::RigidBodyInfoOP protocols::docking::DockSetupMover::rigid_body_info_
private

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


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