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protocols::antibody::snugdock::SnugDock Class Reference

MoveSet step of Snugdock as described in: More...

#include <SnugDock.hh>

Inheritance diagram for protocols::antibody::snugdock::SnugDock:
Inheritance graph

Public Member Functions

 SnugDock ()
 default constructor More...
 SnugDock (SnugDock const &rhs)
 copy constructor More...
SnugDockoperator= (SnugDock const &rhs)
 assignment operator More...
 ~SnugDock () override
void apply (Pose &) override
 Main Method. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 fresh_instance returns a default-constructed object for JD2 More...
bool reinitialize_for_new_input () const override
 This mover retains state such that a fresh version is needed if the input Pose is about to change. More...
void debug ()
core::Size number_of_high_resolution_cycles () const
void number_of_high_resolution_cycles (core::Size const number_of_high_resolution_cycles)
void set_antibody_info (AntibodyInfoOP antibody_info)
void set_CDR_loops (std::map< protocols::antibody::CDRNameEnum, loops::Loop > cdr_loops)
void set_ab_has_light_chain (bool ab_has_light_chain)
void set_vh_vl_jump (bool vh_vl_jump)
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
bool high_res_kink_constraint () const
void high_res_kink_constraint (bool const setting)
void show (std::ostream &out=std::cout) const override
 Outputs details about the Mover, including current settings. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::docking::DockingHighRes
 DockingHighRes ()
 Default constructor. More...
 DockingHighRes (core::Size const rb_jump)
 Constructor with one argument - the jump number to dock over. More...
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 DockingHighRes (DockingHighRes const &old_instance)
 ~DockingHighRes () override
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
void set_ignore_default_task (bool ignore_default_task)
bool ignore_default_task ()
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)
DockJumpsmovable_jumps ()
DockJumps const & movable_jumps () const
void set_movable_jumps (DockJumps movable_jumps)
core::pack::task::TaskFactoryCOP task_factory ()
void set_sc_min (bool sc_min)
void set_rt_min (bool rt_min)
void set_partners (std::string partners)
std::string get_partners () const
void set_interface_definition_task_operation (protocols::simple_task_operations::InterfaceTaskOperationOP interface_definition)
void set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)
void add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)
< core::pack::task::operation::TaskOperationOP
get_additional_task_operarations ()
bool sc_min ()
bool rt_min ()
std::string partners ()
core::scoring::ScoreFunctionOP scorefxn () const
core::scoring::ScoreFunctionOP scorefxn_pack () const
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
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...
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...
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...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
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...
virtual core::Real last_proposal_density_ratio ()
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions

static void register_options ()
 Associates relevant options with the SnugDock class. More...
static std::string mover_name ()
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
- 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...

Private Member Functions

void setup_objects (Pose const &pose)
void set_default ()
void init ()
void init_for_equal_operator_and_copy_constructor (SnugDock &lhs, SnugDock const &rhs)
void init_from_options ()
protocols::loop_modeler::LoopModelerOP refine_loop () const

Private Attributes

AntibodyInfoOP antibody_info_
moves::MonteCarloOP mc_
< protocols::antibody::CDRNameEnum,
bool ab_has_light_chain_
core::Size vh_vl_jump_
core::pack::task::TaskFactoryOP tf_
moves::MoverContainerOP high_resolution_step_
antibody::CDRsMinPackMinOP pre_minimization_
bool debug_
bool high_res_kink_constraint_
core::Size number_of_high_resolution_cycles_


std::ostream & operator<< (std::ostream &out, SnugDock const &snugdock)

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::string > Strings
- Protected Member Functions inherited from protocols::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP tf2 ()
- 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

MoveSet step of Snugdock as described in:

Sircar A, Gray JJ (2010) SnugDock: Paratope Structural Optimization duringAntibody-Antigen Docking Compensates for Errors in Antibody Homology Models. PLoS Comput Biol 6(1): e1000644. doi:10.1371/journal.pcbi.1000644

This is the main high resolution step of the overall SnugDock protocol. See the Show method for a complete description of the algorithm.

Constructor & Destructor Documentation

protocols::antibody::snugdock::SnugDock::SnugDock ( )

default constructor

References init().

protocols::antibody::snugdock::SnugDock::SnugDock ( SnugDock const &  rhs)

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::antibody::snugdock::SnugDock::~SnugDock ( )

Member Function Documentation

void protocols::antibody::snugdock::SnugDock::apply ( Pose )
protocols::moves::MoverOP protocols::antibody::snugdock::SnugDock::clone ( ) const

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.

void protocols::antibody::snugdock::SnugDock::debug ( )
protocols::moves::MoverOP protocols::antibody::snugdock::SnugDock::fresh_instance ( ) const

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

std::string protocols::antibody::snugdock::SnugDock::get_name ( ) const

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

Implements protocols::docking::DockingHighRes.

References mover_name().

Referenced by apply(), and setup_objects().

bool protocols::antibody::snugdock::SnugDock::high_res_kink_constraint ( ) const

References high_res_kink_constraint_.

Referenced by setup_objects().

void protocols::antibody::snugdock::SnugDock::high_res_kink_constraint ( bool const  setting)
void protocols::antibody::snugdock::SnugDock::init ( void  )
void protocols::antibody::snugdock::SnugDock::init_for_equal_operator_and_copy_constructor ( SnugDock lhs,
SnugDock const &  rhs 
void protocols::antibody::snugdock::SnugDock::init_from_options ( )

References number_of_high_resolution_cycles().

Referenced by init().

std::string protocols::antibody::snugdock::SnugDock::mover_name ( )
Size protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles ( ) const
void protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles ( core::Size const  number_of_high_resolution_cycles)
SnugDock & protocols::antibody::snugdock::SnugDock::operator= ( SnugDock const &  rhs)

assignment operator

References init_for_equal_operator_and_copy_constructor().

void protocols::antibody::snugdock::SnugDock::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDock::refine_loop ( ) const

Referenced by setup_objects().

void protocols::antibody::snugdock::SnugDock::register_options ( )
bool protocols::antibody::snugdock::SnugDock::reinitialize_for_new_input ( ) const

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::moves::Mover.

void protocols::antibody::snugdock::SnugDock::set_ab_has_light_chain ( bool  ab_has_light_chain)

References ab_has_light_chain_.

void protocols::antibody::snugdock::SnugDock::set_antibody_info ( AntibodyInfoOP  antibody_info)

References antibody_info_.

void protocols::antibody::snugdock::SnugDock::set_CDR_loops ( std::map< protocols::antibody::CDRNameEnum, loops::Loop cdr_loops)

References CDR_loops_.

void protocols::antibody::snugdock::SnugDock::set_default ( )
void protocols::antibody::snugdock::SnugDock::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

void protocols::antibody::snugdock::SnugDock::set_vh_vl_jump ( bool  vh_vl_jump)

References vh_vl_jump_.

void protocols::antibody::snugdock::SnugDock::setup_objects ( Pose const &  pose)
void protocols::antibody::snugdock::SnugDock::show ( std::ostream &  output = std::cout) const

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

Referenced by apply().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
SnugDock const &  snugdock 

Member Data Documentation

bool protocols::antibody::snugdock::SnugDock::ab_has_light_chain_
AntibodyInfoOP protocols::antibody::snugdock::SnugDock::antibody_info_
std::map<protocols::antibody::CDRNameEnum,loops::Loop> protocols::antibody::snugdock::SnugDock::CDR_loops_

Referenced by set_CDR_loops(), and setup_objects().

bool protocols::antibody::snugdock::SnugDock::debug_
bool protocols::antibody::snugdock::SnugDock::high_res_kink_constraint_
moves::MoverContainerOP protocols::antibody::snugdock::SnugDock::high_resolution_step_
moves::MonteCarloOP protocols::antibody::snugdock::SnugDock::mc_
core::Size protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles_
antibody::CDRsMinPackMinOP protocols::antibody::snugdock::SnugDock::pre_minimization_
core::pack::task::TaskFactoryOP protocols::antibody::snugdock::SnugDock::tf_

Referenced by set_task_factory(), and setup_objects().

core::Size protocols::antibody::snugdock::SnugDock::vh_vl_jump_

Referenced by set_vh_vl_jump(), and setup_objects().

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