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protocols::comparative_modeling::MultiThreadingMover Class Reference

#include <MultiThreadingMover.hh>

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Public Types

typedef
core::sequence::SequenceAlignment 
Alignment
 
typedef utility::vector1
< Alignment
Alignments
 
typedef utility::vector1
< core::pose::Pose
Poses
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 MultiThreadingMover (Alignments const &aligns, Poses const &template_poses)
 align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model. More...
 
virtual ~MultiThreadingMover ()
 
void build_loops (bool setting)
 Returns the SequenceAlignments used in threading. More...
 
void randomize_loop_coords (bool setting)
 
void repack_query (bool setting)
 
bool build_loops () const
 
bool repack_query () const
 
bool randomize_loop_coords ()
 
void min_loop_size (core::Size const new_size)
 
Size min_loop_size () const
 
utility::vector1
< core::fragment::FragSetOP
frag_libs () const
 
void frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
 
virtual void apply (core::pose::Pose &query_pose)
 Threads the given Pose onto the template_pose with the SequenceAlignment provided. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void check_internals () const
 

Private Attributes

Poses template_poses_
 
Alignments alignments_
 
bool build_query_loops_
 
bool repack_query_
 
bool randomize_loop_coords_
 
core::Size min_loop_size_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_
 

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::comparative_modeling::MultiThreadingMover::MultiThreadingMover ( Alignments const &  aligns,
Poses const &  template_poses 
)

align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.

virtual protocols::comparative_modeling::MultiThreadingMover::~MultiThreadingMover ( )
inlinevirtual

Member Function Documentation

void protocols::comparative_modeling::MultiThreadingMover::apply ( core::pose::Pose query_pose)
virtual
void protocols::comparative_modeling::MultiThreadingMover::build_loops ( bool  setting)

Returns the SequenceAlignments used in threading.

Manipulate the SequenceAlignments associated with this object.

References build_query_loops_.

bool protocols::comparative_modeling::MultiThreadingMover::build_loops ( ) const

References build_query_loops_.

void protocols::comparative_modeling::MultiThreadingMover::check_internals ( ) const
private

References alignments_, and template_poses_.

Referenced by apply().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::MultiThreadingMover::frag_libs ( ) const

References frag_libs_.

void protocols::comparative_modeling::MultiThreadingMover::frag_libs ( utility::vector1< core::fragment::FragSetOP new_libs)

References frag_libs_.

std::string protocols::comparative_modeling::MultiThreadingMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::comparative_modeling::MultiThreadingMover::min_loop_size ( core::Size const  new_size)

References min_loop_size_.

core::Size protocols::comparative_modeling::MultiThreadingMover::min_loop_size ( ) const

References min_loop_size_.

void protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords ( bool  setting)
bool protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords ( )
void protocols::comparative_modeling::MultiThreadingMover::repack_query ( bool  setting)

References repack_query_.

bool protocols::comparative_modeling::MultiThreadingMover::repack_query ( ) const

References repack_query_.

Member Data Documentation

Alignments protocols::comparative_modeling::MultiThreadingMover::alignments_
private

Referenced by apply(), and check_internals().

bool protocols::comparative_modeling::MultiThreadingMover::build_query_loops_
private

Referenced by build_loops().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::MultiThreadingMover::frag_libs_
private

Referenced by frag_libs().

core::Size protocols::comparative_modeling::MultiThreadingMover::min_loop_size_
private

Referenced by min_loop_size().

bool protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords_
private

Referenced by randomize_loop_coords().

bool protocols::comparative_modeling::MultiThreadingMover::repack_query_
private

Referenced by repack_query().

Poses protocols::comparative_modeling::MultiThreadingMover::template_poses_
private

Referenced by apply(), and check_internals().


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