Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | Friends | List of all members
protocols::loops::loop_closure::ccd::CcdLoopClosureMover Class Reference

#include <CcdLoopClosureMover.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::CcdLoopClosureMover:
Inheritance graph
Collaboration diagram for protocols::loops::loop_closure::ccd::CcdLoopClosureMover:
Collaboration graph

Public Member Functions

 CcdLoopClosureMover (Loop const &loop_def, core::kinematics::MoveMapCOP mm)
 ~CcdLoopClosureMover ()
void set_max_rama_score_increase (core::Real input_max_rama_score_increase)
void set_max_total_delta (core::Real input_max_delta_helix, core::Real input_max_delta_strand, core::Real input_max_delta_loop)
void set_tolerance (core::Real input_tolerance)
void set_ccd_cycles (core::Size input_ccd_cycles)
void set_bRama_check (bool input_bRama_check)
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
core::Real forward_deviation () const
core::Real backward_deviation () const
bool success () const
Loop get_loop () const
core::Size get_loop_start () const
core::Size get_loop_stop () const
core::Size get_loop_cut () const
core::Size get_loop_size () const
core::Real get_loop_skip_rate () const
std::string get_loop_extended () const
core::Real get_max_rama_score_increase () const
core::Real get_tolerance () const
core::Real get_max_total_delta (std::string secstr) const
core::Size get_ccd_cycles () const
std::string bRama_check () const
core::kinematics::MoveMap movemap () const
- 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 Attributes

Loop loop_
core::kinematics::MoveMapCOP movemap_
core::Real max_rama_score_increase_
core::Real max_total_delta_helix_
core::Real max_total_delta_strand_
core::Real max_total_delta_loop_
core::Real tolerance_
Size ccd_cycles_
bool bRama_check_
core::Real forward_deviation_
core::Real backward_deviation_
core::Real torsion_delta_
core::Real rama_delta_
Size actual_cycles_


std::ostream & operator<< (std::ostream &os, CcdLoopClosureMover const &mover)

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings
- 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...

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::CcdLoopClosureMover::CcdLoopClosureMover ( Loop const &  loop_def,
core::kinematics::MoveMapCOP  mm 
protocols::loops::loop_closure::ccd::CcdLoopClosureMover::~CcdLoopClosureMover ( )

Member Function Documentation

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply ( core::pose::Pose pose)
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::backward_deviation ( ) const
std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::bRama_check ( ) const
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::forward_deviation ( ) const
core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_ccd_cycles ( ) const
Loop protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop ( ) const

References loop_.

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_cut ( ) const
std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_extended ( ) const
core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_size ( ) const
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_skip_rate ( ) const
core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_start ( ) const
core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_stop ( ) const
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_max_rama_score_increase ( ) const
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_max_total_delta ( std::string  secstr) const
std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_name ( ) const

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

Implements protocols::moves::Mover.

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_tolerance ( ) const
core::kinematics::MoveMap protocols::loops::loop_closure::ccd::CcdLoopClosureMover::movemap ( ) const
void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_bRama_check ( bool  input_bRama_check)

References bRama_check_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_ccd_cycles ( core::Size  input_ccd_cycles)

References ccd_cycles_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_max_rama_score_increase ( core::Real  input_max_rama_score_increase)
void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_max_total_delta ( core::Real  input_max_delta_helix,
core::Real  input_max_delta_strand,
core::Real  input_max_delta_loop 
void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_tolerance ( core::Real  input_tolerance)

References tolerance_.

bool protocols::loops::loop_closure::ccd::CcdLoopClosureMover::success ( ) const

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
CcdLoopClosureMover const &  mover 

Member Data Documentation

Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::actual_cycles_

Referenced by apply().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::backward_deviation_

Referenced by apply(), and backward_deviation().

bool protocols::loops::loop_closure::ccd::CcdLoopClosureMover::bRama_check_

Referenced by apply(), bRama_check(), and set_bRama_check().

Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::ccd_cycles_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::forward_deviation_

Referenced by apply(), and forward_deviation().

Loop protocols::loops::loop_closure::ccd::CcdLoopClosureMover::loop_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_rama_score_increase_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_helix_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_loop_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_strand_
core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::CcdLoopClosureMover::movemap_

Referenced by apply(), and movemap().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::rama_delta_

Referenced by apply().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::tolerance_
core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::torsion_delta_

Referenced by apply().

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