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protocols::antibody2::GraftCDRLoopsProtocol Class Reference

#include <GraftCDRLoopsProtocol.hh>

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

Public Types

typedef std::map< std::string,
- 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

Public Member Functions

 GraftCDRLoopsProtocol ()
 ~GraftCDRLoopsProtocol ()
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
void set_default ()
 Assigns default values to primitive members. More...
virtual void apply (core::pose::Pose &pose)
void set_graft_l1 (bool graft_l1)
void set_graft_l2 (bool graft_l2)
void set_graft_l3 (bool graft_l3)
void set_graft_h1 (bool graft_h1)
void set_graft_h2 (bool graft_h2)
void set_graft_h3 (bool graft_h3)
void set_h3_stem_graft (bool h3_stem_graft)
void set_packonly_after_graft (bool setting)
void set_camelid (bool camelid)
void set_camelid_constraints (bool camelid_constraints)
void set_benchmark (bool benchmark)
void set_cst_weight (core::Real cst_weight)
void set_sc_min (bool scmin)
void set_rt_min (bool rtmin)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void display_constraint_residues (core::pose::Pose &pose)
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 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

Static Public Member Functions

static void register_options ()
 Associates relevant options with the AntibodyModeler class. More...
- 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...

Private Member Functions

void finalize_setup (core::pose::Pose &pose)
void init ()
void setup_objects ()
void init_from_options ()

Private Attributes

bool graft_l1_
bool graft_l2_
bool graft_l3_
bool graft_h1_
bool graft_h2_
bool graft_h3_
bool h3_no_stem_graft_
bool packonly_after_graft_
bool camelid_
bool camelid_constraints_
bool sc_min_
bool rt_min_
bool benchmark_
core::Real cst_weight_
core::scoring::ScoreFunctionOP scorefxn_pack_
AntibodyInfoOP ab_info_
Ab_TemplateInfoOP ab_t_info_
pack::task::TaskFactoryOP tf_
protocols::moves::SequenceMoverOP graft_sequence_


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

Additional Inherited Members

- 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::antibody2::GraftCDRLoopsProtocol::GraftCDRLoopsProtocol ( )

References init().

Referenced by clone().

protocols::antibody2::GraftCDRLoopsProtocol::~GraftCDRLoopsProtocol ( )

Member Function Documentation

void protocols::antibody2::GraftCDRLoopsProtocol::apply ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::antibody2::GraftCDRLoopsProtocol::clone ( ) const

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References GraftCDRLoopsProtocol().

void protocols::antibody2::GraftCDRLoopsProtocol::display_constraint_residues ( core::pose::Pose pose)
void protocols::antibody2::GraftCDRLoopsProtocol::finalize_setup ( core::pose::Pose pose)
std::string protocols::antibody2::GraftCDRLoopsProtocol::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody2::GraftCDRLoopsProtocol::init ( void  )
void protocols::antibody2::GraftCDRLoopsProtocol::init_from_options ( )
void protocols::antibody2::GraftCDRLoopsProtocol::register_options ( )

Associates relevant options with the AntibodyModeler class.

Referenced by init().

void protocols::antibody2::GraftCDRLoopsProtocol::set_benchmark ( bool  benchmark)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_camelid ( bool  camelid)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_camelid_constraints ( bool  camelid_constraints)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_cst_weight ( core::Real  cst_weight)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_default ( )
void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h1 ( bool  graft_h1)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h2 ( bool  graft_h2)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h3 ( bool  graft_h3)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l1 ( bool  graft_l1)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l2 ( bool  graft_l2)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l3 ( bool  graft_l3)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_h3_stem_graft ( bool  h3_stem_graft)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_packonly_after_graft ( bool  setting)

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_rt_min ( bool  rtmin)
void protocols::antibody2::GraftCDRLoopsProtocol::set_sc_min ( bool  scmin)
void protocols::antibody2::GraftCDRLoopsProtocol::setup_objects ( )
void protocols::antibody2::GraftCDRLoopsProtocol::show ( std::ostream &  out = std::cout)

Show the complete setup of the docking protocol

Friends And Related Function Documentation

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

Member Data Documentation

AntibodyInfoOP protocols::antibody2::GraftCDRLoopsProtocol::ab_info_
Ab_TemplateInfoOP protocols::antibody2::GraftCDRLoopsProtocol::ab_t_info_

Referenced by finalize_setup(), and setup_objects().

bool protocols::antibody2::GraftCDRLoopsProtocol::benchmark_

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::camelid_
bool protocols::antibody2::GraftCDRLoopsProtocol::camelid_constraints_

Referenced by apply(), and set_default().

core::Real protocols::antibody2::GraftCDRLoopsProtocol::cst_weight_

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h1_
bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h2_
bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h3_
bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l1_
bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l2_
bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l3_
protocols::moves::SequenceMoverOP protocols::antibody2::GraftCDRLoopsProtocol::graft_sequence_
bool protocols::antibody2::GraftCDRLoopsProtocol::h3_no_stem_graft_

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::packonly_after_graft_

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::rt_min_

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::sc_min_

Referenced by finalize_setup(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody2::GraftCDRLoopsProtocol::scorefxn_pack_

Referenced by setup_objects().

pack::task::TaskFactoryOP protocols::antibody2::GraftCDRLoopsProtocol::tf_

Referenced by finalize_setup(), and setup_objects().

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