Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::antibody::RefineOneCDRLoopCentroid Class Reference

#include <RefineOneCDRLoopCentroid.hh>

Public Member Functions

 RefineOneCDRLoopCentroid (AntibodyInfoCOP antibody_info, CDRNameEnum const &loop_name)
 constructor with arguments More...
 RefineOneCDRLoopCentroid (AntibodyInfoCOP antibody_info, CDRNameEnum const &loop_name, core::scoring::ScoreFunctionCOP scorefxn)
 RefineOneCDRLoopCentroid (loops::Loop const &a_cdr_loop)
 constructor with arguments More...
 RefineOneCDRLoopCentroid (loops::Loop const &a_cdr_loop, core::scoring::ScoreFunctionCOP scorefxn)
 ~RefineOneCDRLoopCentroid ()
 default destructor More...
virtual void apply (pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void set_benchmark (bool const &setting)
void set_snugfit (bool const &setting)
void set_refine_input_loop (bool const &setting)
void set_score_function (core::scoring::ScoreFunctionCOP scorefxn)
- 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
void set_type (std::string const &setting)
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
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Member Functions

void set_default ()
void finalize_setup (core::pose::Pose const &pose)
void loop_centroid_relax (pose::Pose &pose, Size const loop_begin, Size const loop_end)
 actually relaxes the region specified More...

Private Attributes

loops::Loop the_cdr_loop_
bool benchmark_
bool snug_fit_
bool refine_input_loop_
scoring::ScoreFunctionOP lowres_scorefxn_

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::stringStrings
- 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 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::antibody::RefineOneCDRLoopCentroid::RefineOneCDRLoopCentroid ( AntibodyInfoCOP  antibody_info,
CDRNameEnum const &  loop_name 

constructor with arguments

References set_default(), and the_cdr_loop_.

protocols::antibody::RefineOneCDRLoopCentroid::RefineOneCDRLoopCentroid ( AntibodyInfoCOP  antibody_info,
CDRNameEnum const &  loop_name,
core::scoring::ScoreFunctionCOP  scorefxn 
protocols::antibody::RefineOneCDRLoopCentroid::RefineOneCDRLoopCentroid ( loops::Loop const &  a_cdr_loop)

constructor with arguments

References set_default(), and the_cdr_loop_.

protocols::antibody::RefineOneCDRLoopCentroid::RefineOneCDRLoopCentroid ( loops::Loop const &  a_cdr_loop,
core::scoring::ScoreFunctionCOP  scorefxn 
protocols::antibody::RefineOneCDRLoopCentroid::~RefineOneCDRLoopCentroid ( )

default destructor

Member Function Documentation

void protocols::antibody::RefineOneCDRLoopCentroid::apply ( pose::Pose pose)
void protocols::antibody::RefineOneCDRLoopCentroid::finalize_setup ( core::pose::Pose const &  pose)
std::string protocols::antibody::RefineOneCDRLoopCentroid::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody::RefineOneCDRLoopCentroid::loop_centroid_relax ( pose::Pose pose_in,
Size const  loop_begin,
Size const  loop_end 

actually relaxes the region specified


Detailed: This is all done in low resolution. Intention was to give
camelid CDR H1 a larger perturbation.
[in]pose,loopbegin position, loop end position
Aroop 05/07/2010
Last Modified: 05/07/2010

References protocols::moves::MoverContainer::add_mover(), core::pose::add_variant_type_to_pose_residue(), protocols::moves::SequenceMover::apply(), benchmark_, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_upper_terminus(), lowres_scorefxn_, numeric::max(), mc, min_tolerance, min_type, outer_cycles, refine_input_loop_, core::pose::Pose::residue(), protocols::antibody::simple_one_loop_fold_tree(), snug_fit_, temperature, and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::antibody::RefineOneCDRLoopCentroid::set_benchmark ( bool const &  setting)
void protocols::antibody::RefineOneCDRLoopCentroid::set_default ( )
void protocols::antibody::RefineOneCDRLoopCentroid::set_refine_input_loop ( bool const &  setting)
void protocols::antibody::RefineOneCDRLoopCentroid::set_score_function ( core::scoring::ScoreFunctionCOP  scorefxn)

References lowres_scorefxn_.

void protocols::antibody::RefineOneCDRLoopCentroid::set_snugfit ( bool const &  setting)

Member Data Documentation

bool protocols::antibody::RefineOneCDRLoopCentroid::benchmark_

Referenced by loop_centroid_relax(), and set_default().

scoring::ScoreFunctionOP protocols::antibody::RefineOneCDRLoopCentroid::lowres_scorefxn_
bool protocols::antibody::RefineOneCDRLoopCentroid::refine_input_loop_

Referenced by loop_centroid_relax(), and set_default().

bool protocols::antibody::RefineOneCDRLoopCentroid::snug_fit_

Referenced by loop_centroid_relax(), and set_default().

loops::Loop protocols::antibody::RefineOneCDRLoopCentroid::the_cdr_loop_

Referenced by apply(), and RefineOneCDRLoopCentroid().

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