Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
protocols::antibody::snugdock::SnugDockProtocol Class Reference

#include <SnugDockProtocol.hh>

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

Public Member Functions

 SnugDockProtocol ()
 default constructor More...
 SnugDockProtocol (SnugDockProtocol const &rhs)
 copy constructor More...
SnugDockProtocoloperator= (SnugDockProtocol const &rhs)
 assignment operator More...
 ~SnugDockProtocol () override
void apply (Pose &) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. 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...
bool auto_generate_kink_constraint () const
void auto_generate_kink_constraint (bool const setting)
bool high_res_kink_constraint () const
void high_res_kink_constraint (bool const setting)
bool low_res_kink_constraint () const
void low_res_kink_constraint (bool const setting)
bool constrain_vlvh_qq () const
void constrain_vlvh_qq (bool const setting)
void show (std::ostream &out=std::cout) const override
 Outputs details about the Mover, including current settings. More...
core::pack::task::TaskFactoryOP repack_tf_from_residue_sets (Pose const &pose, std::set< core::Size > const &ab_residues, std::set< core::Size > const &ag_residues)
void setup_ab_ag_foldtree (Pose &pose, AntibodyInfoOP antibody_info)
core::conformation::ResidueOP place_VRT_at_residue_COM (Pose const &pose, utility::vector1< bool > residues)
core::conformation::ResidueOP place_VRT_at_residue_COM (Pose const &pose, core::Size start, core::Size stop)
- 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 SnugDockProtocol 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. More...

Private Member Functions

void setup_objects (Pose &pose)
void setup_loop_refinement_movers ()
void update_fold_tree_from_bool_vector ()
void init ()
void init_for_equal_operator_and_copy_constructor (SnugDockProtocol &lhs, SnugDockProtocol const &rhs)
void init_from_options ()
void set_default ()
docking::DockingProtocolOP docking () const
protocols::loop_modeler::LoopModelerOP refine_loop () const

Private Attributes

AntibodyInfoOP antibody_info_
core::pose::PDBInfoOP pdb_info_
std::map< protocols::antibody::CDRNameEnum, loops::LoopCDR_loops_
bool ab_has_light_chain_
core::Size vh_vl_jump_
std::set< core::Sizeab_residues_
std::set< core::Sizeag_residues_
core::pack::task::TaskFactoryOP tf_
protocols::loop_modeler::LoopModelerOP low_res_refine_cdr_h2_
protocols::loop_modeler::LoopModelerOP low_res_refine_cdr_h3_
docking::DockingProtocolOP docking_
bool auto_generate_kink_constraint_
bool high_res_kink_constraint_
bool low_res_kink_constraint_
bool constrain_vlvh_qq_


std::ostream & operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)

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::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

◆ SnugDockProtocol() [1/2]

protocols::antibody::snugdock::SnugDockProtocol::SnugDockProtocol ( )

default constructor

References init().

◆ SnugDockProtocol() [2/2]

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

◆ ~SnugDockProtocol()

protocols::antibody::snugdock::SnugDockProtocol::~SnugDockProtocol ( )

Member Function Documentation

◆ apply()

void protocols::antibody::snugdock::SnugDockProtocol::apply ( Pose )

◆ auto_generate_kink_constraint() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint ( ) const

◆ auto_generate_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint ( bool const  setting)

◆ clone()

protocols::moves::MoverOP protocols::antibody::snugdock::SnugDockProtocol::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.

◆ constrain_vlvh_qq() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq ( ) const

References constrain_vlvh_qq_.

Referenced by init_from_options(), and setup_objects().

◆ constrain_vlvh_qq() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq ( bool const  setting)

References constrain_vlvh_qq_.

◆ docking()

docking::DockingProtocolOP protocols::antibody::snugdock::SnugDockProtocol::docking ( ) const

References docking_.

Referenced by apply(), and setup_objects().

◆ fresh_instance()

protocols::moves::MoverOP protocols::antibody::snugdock::SnugDockProtocol::fresh_instance ( ) const

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

Each derived class must specify its name.

Implements protocols::moves::Mover.

References protocols::moves::Mover::type().

Referenced by apply(), setup_loop_refinement_movers(), and setup_objects().

◆ high_res_kink_constraint() [1/2]

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

◆ high_res_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint ( bool const  setting)

◆ init()

void protocols::antibody::snugdock::SnugDockProtocol::init ( void  )

◆ init_for_equal_operator_and_copy_constructor()

void protocols::antibody::snugdock::SnugDockProtocol::init_for_equal_operator_and_copy_constructor ( SnugDockProtocol lhs,
SnugDockProtocol const &  rhs 

◆ init_from_options()

void protocols::antibody::snugdock::SnugDockProtocol::init_from_options ( )

◆ low_res_kink_constraint() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint ( ) const

◆ low_res_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint ( bool const  setting)

◆ operator=()

SnugDockProtocol & protocols::antibody::snugdock::SnugDockProtocol::operator= ( SnugDockProtocol const &  rhs)

assignment operator

References init_for_equal_operator_and_copy_constructor().

◆ place_VRT_at_residue_COM() [1/2]

core::conformation::ResidueOP protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM ( Pose const &  pose,
core::Size  start,
core::Size  stop 

◆ place_VRT_at_residue_COM() [2/2]

core::conformation::ResidueOP protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM ( Pose const &  pose,
utility::vector1< bool >  residues 

◆ refine_loop()

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::refine_loop ( ) const

◆ register_options()

void protocols::antibody::snugdock::SnugDockProtocol::register_options ( )

◆ reinitialize_for_new_input()

bool protocols::antibody::snugdock::SnugDockProtocol::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.

◆ repack_tf_from_residue_sets()

core::pack::task::TaskFactoryOP protocols::antibody::snugdock::SnugDockProtocol::repack_tf_from_residue_sets ( Pose const &  pose,
std::set< core::Size > const &  ab_residues,
std::set< core::Size > const &  ag_residues 

◆ set_default()

void protocols::antibody::snugdock::SnugDockProtocol::set_default ( )

◆ setup_ab_ag_foldtree()

void protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree ( Pose pose,
AntibodyInfoOP  antibody_info 

◆ setup_loop_refinement_movers()

void protocols::antibody::snugdock::SnugDockProtocol::setup_loop_refinement_movers ( )

◆ setup_objects()

void protocols::antibody::snugdock::SnugDockProtocol::setup_objects ( Pose pose)

◆ show()

void protocols::antibody::snugdock::SnugDockProtocol::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.

References core::conformation::membrane::out.

Referenced by apply().

◆ update_fold_tree_from_bool_vector()

void protocols::antibody::snugdock::SnugDockProtocol::update_fold_tree_from_bool_vector ( )

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<< ( std::ostream &  out,
SnugDockProtocol const &  snugdockprotocol 

Member Data Documentation

◆ ab_has_light_chain_

bool protocols::antibody::snugdock::SnugDockProtocol::ab_has_light_chain_

◆ ab_residues_

std::set< core::Size > protocols::antibody::snugdock::SnugDockProtocol::ab_residues_

◆ ag_residues_

std::set< core::Size > protocols::antibody::snugdock::SnugDockProtocol::ag_residues_

◆ antibody_info_

AntibodyInfoOP protocols::antibody::snugdock::SnugDockProtocol::antibody_info_

◆ auto_generate_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint_

◆ CDR_loops_

std::map<protocols::antibody::CDRNameEnum,loops::Loop> protocols::antibody::snugdock::SnugDockProtocol::CDR_loops_

◆ constrain_vlvh_qq_

bool protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq_

Referenced by constrain_vlvh_qq(), and set_default().

◆ docking_

docking::DockingProtocolOP protocols::antibody::snugdock::SnugDockProtocol::docking_

◆ high_res_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint_

◆ low_res_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint_

◆ low_res_refine_cdr_h2_

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::low_res_refine_cdr_h2_

◆ low_res_refine_cdr_h3_

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::low_res_refine_cdr_h3_

◆ pdb_info_

core::pose::PDBInfoOP protocols::antibody::snugdock::SnugDockProtocol::pdb_info_

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::snugdock::SnugDockProtocol::tf_

Referenced by setup_objects().

◆ vh_vl_jump_

core::Size protocols::antibody::snugdock::SnugDockProtocol::vh_vl_jump_

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