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

Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application. More...

#include <AntibodyDesignMover.hh>

Public Member Functions

 AntibodyDesignMover ()
 
virtual ~AntibodyDesignMover ()
 
virtual string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
void set_graft_designer (AntibodyGraftDesignMoverOP graft_designer)
 
void set_sequence_designer (AntibodySeqDesignMoverOP seq_designer)
 
void set_modeler (AntibodyDesignModelerOP modeler)
 
void set_scorefxn (ScoreFunctionOP scorefxn)
 
void set_design_scorefxn (ScoreFunctionOP design_scorefxn)
 
void set_ab_info (AntibodyInfoOP ab_info)
 
void set_use_graft_designer (bool setting)
 Use low-resolution graft designer for structural sampling. Default true. More...
 
void set_use_sequence_designer (bool setting)
 Use high-resolution sequence designer for sequence sampling. Default true. More...
 
void set_do_post_graft_design_modeling (bool setting)
 Run dock/min modeling step after the graft design step if run. More...
 
void set_do_post_design_modeling (bool setting)
 Run dock/min modeling step after sequence design if run. More...
 
virtual void apply (core::pose::Pose &pose)
 
- 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 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 read_command_line_design_options ()
 Sets command line driven CDR design. This is mainly for testing, but makes the whole algorithm controllable without a specific instruction file. More...
 
void setup_scorefxn (ScoreFunctionOP scorefxn)
 Set constraint and chainbreak score on scorefunction if not already set. More...
 
void model_post_graft (core::pose::Pose &pose)
 Post-graft step modeling. If no graft step, no need to do post-graft modeling. Default false. More...
 
void model_post_design (core::pose::Pose &pose)
 Post-design step modeling. Less aggressive, more high resolution. Default false. More...
 
void read_options ()
 
void init_on_new_input (core::pose::Pose const &pose)
 
void output_ensemble (vector1< core::pose::PoseOP > ensemble, Size range_start, Size range_end, std::string prefix)
 Used to output ongoing current ensembles during the protocol. Specify a range in the vector to output. More...
 
void add_cluster_comments_to_pose (core::pose::Pose &pose)
 add cluster info to the pose. Needs to go into pose and not jd2 due to Ensemble generation. More...
 

Private Attributes

AntibodyGraftDesignMoverOP graft_designer_
 
AntibodySeqDesignMoverOP seq_designer_
 
AntibodyDesignModelerOP modeler_
 
ScoreFunctionOP scorefxn_
 
ScoreFunctionOP design_scorefxn_
 
AntibodyInfoOP ab_info_
 
AntibodyDatabaseManagerOP cdr_db_parser_
 
bool run_graft_designer_
 
bool run_sequence_designer_
 
bool run_post_graft_modeling_
 
bool run_post_design_modeling_
 
bool post_graft_ensemble_output_
 

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
protocols::filters::Filters_map 
Filters_map
 
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...
 

Detailed Description

Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( )
protocols::antibody::design::AntibodyDesignMover::~AntibodyDesignMover ( )
virtual

Member Function Documentation

void protocols::antibody::design::AntibodyDesignMover::add_cluster_comments_to_pose ( core::pose::Pose pose)
private
void protocols::antibody::design::AntibodyDesignMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::clone ( ) const
virtual

Return a clone of the Mover object.

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 AntibodyDesignMover().

std::string protocols::antibody::design::AntibodyDesignMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::antibody::design::AntibodyDesignMover::init_on_new_input ( core::pose::Pose const &  pose)
private
void protocols::antibody::design::AntibodyDesignMover::model_post_design ( core::pose::Pose pose)
private

Post-design step modeling. Less aggressive, more high resolution. Default false.

References protocols::antibody::AHO_Scheme, core::scoring::ScoreFunction::clone(), modeler_, protocols::antibody::North, and scorefxn_.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::model_post_graft ( core::pose::Pose pose)
private

Post-graft step modeling. If no graft step, no need to do post-graft modeling. Default false.

References protocols::moves::MonteCarlo::boltzmann(), mc, modeler_, protocols::moves::MonteCarlo::recover_low(), scorefxn_, and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::output_ensemble ( vector1< core::pose::PoseOP ensemble,
core::Size  range_start,
core::Size  range_end,
std::string  prefix 
)
private

Used to output ongoing current ensembles during the protocol. Specify a range in the vector to output.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_outputter(), tag, utility::to_string(), and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::read_command_line_design_options ( )
private

Sets command line driven CDR design. This is mainly for testing, but makes the whole algorithm controllable without a specific instruction file.

References ab_info_, protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, protocols::antibody::AntibodyInfo::get_CDR_name_enum(), graft_designer_, option, seq_designer_, and user.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::read_options ( )
private
void protocols::antibody::design::AntibodyDesignMover::set_ab_info ( AntibodyInfoOP  ab_info)

References ab_info_.

void protocols::antibody::design::AntibodyDesignMover::set_design_scorefxn ( ScoreFunctionOP  design_scorefxn)

References design_scorefxn_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_do_post_design_modeling ( bool  setting)

Run dock/min modeling step after sequence design if run.

References run_post_design_modeling_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_do_post_graft_design_modeling ( bool  setting)

Run dock/min modeling step after the graft design step if run.

References run_post_graft_modeling_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_graft_designer ( AntibodyGraftDesignMoverOP  graft_designer)

References graft_designer_.

void protocols::antibody::design::AntibodyDesignMover::set_modeler ( AntibodyDesignModelerOP  modeler)

References modeler_.

void protocols::antibody::design::AntibodyDesignMover::set_scorefxn ( ScoreFunctionOP  scorefxn)

References scorefxn_.

Referenced by AntibodyDesignMover().

void protocols::antibody::design::AntibodyDesignMover::set_sequence_designer ( AntibodySeqDesignMoverOP  seq_designer)

References seq_designer_.

void protocols::antibody::design::AntibodyDesignMover::set_use_graft_designer ( bool  setting)

Use low-resolution graft designer for structural sampling. Default true.

References run_graft_designer_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_use_sequence_designer ( bool  setting)

Use high-resolution sequence designer for sequence sampling. Default true.

References run_sequence_designer_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::setup_scorefxn ( ScoreFunctionOP  scorefxn)
private

Set constraint and chainbreak score on scorefunction if not already set.

References chainbreak, and dihedral_constraint.

Referenced by apply().

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::ab_info_
private
AntibodyDatabaseManagerOP protocols::antibody::design::AntibodyDesignMover::cdr_db_parser_
private

Referenced by AntibodyDesignMover().

ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::design_scorefxn_
private

Referenced by apply(), and set_design_scorefxn().

AntibodyGraftDesignMoverOP protocols::antibody::design::AntibodyDesignMover::graft_designer_
private
AntibodyDesignModelerOP protocols::antibody::design::AntibodyDesignMover::modeler_
private
bool protocols::antibody::design::AntibodyDesignMover::post_graft_ensemble_output_
private

Referenced by apply(), and read_options().

bool protocols::antibody::design::AntibodyDesignMover::run_graft_designer_
private

Referenced by apply(), and set_use_graft_designer().

bool protocols::antibody::design::AntibodyDesignMover::run_post_design_modeling_
private
bool protocols::antibody::design::AntibodyDesignMover::run_post_graft_modeling_
private
bool protocols::antibody::design::AntibodyDesignMover::run_sequence_designer_
private

Referenced by apply(), and set_use_sequence_designer().

ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_
private
AntibodySeqDesignMoverOP protocols::antibody::design::AntibodyDesignMover::seq_designer_
private

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