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protocols::antibody2::CDRsMinPackMin Class Reference

#include <CDRsMinPackMin.hh>

Inheritance diagram for protocols::antibody2::CDRsMinPackMin:
Inheritance graph
Collaboration diagram for protocols::antibody2::CDRsMinPackMin:
Collaboration graph

Public Member Functions

 CDRsMinPackMin (AntibodyInfoOP antibody_info)
 CDRsMinPackMin (AntibodyInfoOP antibody_info, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf, core::kinematics::MoveMapOP movemap)
 ~CDRsMinPackMin ()
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
void set_move_map (core::kinematics::MoveMapCOP movemap)
void set_sc_min (bool scmin)
void set_rt_min (bool rtmin)
void set_turnoff_minimization (bool setting)
void show (std::ostream &out=std::cout)
- 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 finalize_setup (core::pose::Pose &pose)
void init ()

Private Attributes

bool sc_min_
bool rt_min_
bool turnoff_minimization_
core::Real cen_cst_
 refine H3 only More...
core::Real high_cst_
bool benchmark_
core::Size update_rounds_
bool user_defined_
AntibodyInfoOP ab_info_
core::scoring::ScoreFunctionOP loop_scorefxn_highres_
protocols::moves::SequenceMoverOP cdr_sequence_move_
core::kinematics::MoveMapOP allcdr_map_
core::pack::task::TaskFactoryOP tf_
std::string min_type_
core::Real Temperature_
core::Real min_tolerance_


std::ostream & operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)

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::antibody2::CDRsMinPackMin::CDRsMinPackMin ( AntibodyInfoOP  antibody_info)

References ab_info_, init(), and user_defined_.

protocols::antibody2::CDRsMinPackMin::CDRsMinPackMin ( AntibodyInfoOP  antibody_info,
core::scoring::ScoreFunctionOP  scorefxn,
core::pack::task::TaskFactoryOP  tf,
core::kinematics::MoveMapOP  movemap 
protocols::antibody2::CDRsMinPackMin::~CDRsMinPackMin ( )

Member Function Documentation

void protocols::antibody2::CDRsMinPackMin::apply ( core::pose::Pose pose)
void protocols::antibody2::CDRsMinPackMin::finalize_setup ( core::pose::Pose pose)
std::string protocols::antibody2::CDRsMinPackMin::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody2::CDRsMinPackMin::init ( void  )
void protocols::antibody2::CDRsMinPackMin::set_move_map ( core::kinematics::MoveMapCOP  movemap)

References allcdr_map_.

void protocols::antibody2::CDRsMinPackMin::set_rt_min ( bool  rtmin)
void protocols::antibody2::CDRsMinPackMin::set_sc_min ( bool  scmin)
void protocols::antibody2::CDRsMinPackMin::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

void protocols::antibody2::CDRsMinPackMin::set_turnoff_minimization ( bool  setting)
void protocols::antibody2::CDRsMinPackMin::show ( std::ostream &  out = std::cout)

Show the complete setup of the antibody modeler protocol

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const CDRsMinPackMin ab_m_2 

Member Data Documentation

AntibodyInfoOP protocols::antibody2::CDRsMinPackMin::ab_info_

Referenced by CDRsMinPackMin(), and finalize_setup().

core::kinematics::MoveMapOP protocols::antibody2::CDRsMinPackMin::allcdr_map_
bool protocols::antibody2::CDRsMinPackMin::benchmark_

Referenced by init().

protocols::moves::SequenceMoverOP protocols::antibody2::CDRsMinPackMin::cdr_sequence_move_

Referenced by apply(), and finalize_setup().

core::Real protocols::antibody2::CDRsMinPackMin::cen_cst_

refine H3 only

core::Real protocols::antibody2::CDRsMinPackMin::high_cst_
core::scoring::ScoreFunctionOP protocols::antibody2::CDRsMinPackMin::loop_scorefxn_highres_
core::Real protocols::antibody2::CDRsMinPackMin::min_tolerance_

Referenced by finalize_setup(), and init().

std::string protocols::antibody2::CDRsMinPackMin::min_type_

Referenced by finalize_setup(), and init().

bool protocols::antibody2::CDRsMinPackMin::rt_min_
bool protocols::antibody2::CDRsMinPackMin::sc_min_
core::Real protocols::antibody2::CDRsMinPackMin::Temperature_

Referenced by finalize_setup(), and init().

core::pack::task::TaskFactoryOP protocols::antibody2::CDRsMinPackMin::tf_
bool protocols::antibody2::CDRsMinPackMin::turnoff_minimization_

Referenced by finalize_setup(), and init().

core::Size protocols::antibody2::CDRsMinPackMin::update_rounds_

Referenced by apply(), finalize_setup(), and init().

bool protocols::antibody2::CDRsMinPackMin::user_defined_

Referenced by CDRsMinPackMin(), and init().

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