Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::docking::DockingEnsemblePrepackProtocol Class Reference

#include <DockingEnsemblePrepackProtocol.hh>

Inheritance diagram for protocols::docking::DockingEnsemblePrepackProtocol:
Inheritance graph

Public Member Functions

 DockingEnsemblePrepackProtocol ()
 Default constructor. More...
 ~DockingEnsemblePrepackProtocol () override
void setup_defaults ()
 Assigns default values to members. More...
void setup_pack_operation_movers ()
 Instantiates and configures movers used by DockingEnsemblePrepackProtocol. More...
utility::vector1< char > get_pose_chains (core::pose::Pose &)
 Returns a vector1 of the pdb chains in a pose, in order. More...
void check_ensemble_member_compatibility ()
 Ensures all members of either ensemble are compatible with one another. More...
void move_away (core::pose::Pose &pose)
void move_back (core::pose::Pose &pose)
void apply (core::pose::Pose &) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_ensemble1 (std::string const &ensemble1)
void set_ensemble2 (std::string const &ensemble2)
void set_spanfile1 (std::string const &spanfile1)
void set_spanfile2 (std::string const &spanfile2)
- 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)
utility::vector1< core::pack::task::operation::TaskOperationOPget_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 MoverOP clone () const
 Return a clone of the Mover object. 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...
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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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...

Private Member Functions

std::string copy_ensemble (std::string const &inputfile_name)
void finalize_setup (core::pose::Pose &)
 Performs setup that requires a pose. More...
void register_options ()
void init_from_options ()

Private Attributes

utility::vector1< rigid::RigidBodyTransMoverOPtrans_away_vec_
utility::vector1< rigid::RigidBodyTransMoverOPtrans_back_vec_
core::Real trans_magnitude_
bool membrane_
 membrane for translating in the membrane plane More...
bool movers_setup_
protocols::minimization_packing::RotamerTrialsMinMoverOP rtmin_mover_
protocols::minimization_packing::PackRotamersMoverOP prepack_full_repack_
SidechainMinMoverOP scmin_mover_
protocols::moves::SequenceMoverOP pack_operations_
DockingEnsembleOP ensemble1_
DockingEnsembleOP ensemble2_
std::string ensemble1_filename_
std::string ensemble2_filename_
std::string span1_filename_
std::string span2_filename_

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
- 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::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...

Constructor & Destructor Documentation

◆ DockingEnsemblePrepackProtocol()

protocols::docking::DockingEnsemblePrepackProtocol::DockingEnsemblePrepackProtocol ( )

Default constructor.

References init_from_options(), register_options(), and setup_defaults().

◆ ~DockingEnsemblePrepackProtocol()

protocols::docking::DockingEnsemblePrepackProtocol::~DockingEnsemblePrepackProtocol ( )

Member Function Documentation

◆ apply()

void protocols::docking::DockingEnsemblePrepackProtocol::apply ( core::pose::Pose )

◆ check_ensemble_member_compatibility()

void protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility ( )

◆ copy_ensemble()

std::string protocols::docking::DockingEnsemblePrepackProtocol::copy_ensemble ( std::string const &  inputfile_name)

Referenced by set_ensemble1(), and set_ensemble2().

◆ finalize_setup()

void protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup ( core::pose::Pose pose)

◆ get_name()

std::string protocols::docking::DockingEnsemblePrepackProtocol::get_name ( ) const

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

Implements protocols::docking::DockingHighRes.

◆ get_pose_chains()

utility::vector1< char > protocols::docking::DockingEnsemblePrepackProtocol::get_pose_chains ( core::pose::Pose pose)

Returns a vector1 of the pdb chains in a pose, in order.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by check_ensemble_member_compatibility().

◆ init_from_options()

void protocols::docking::DockingEnsemblePrepackProtocol::init_from_options ( )

◆ move_away()

void protocols::docking::DockingEnsemblePrepackProtocol::move_away ( core::pose::Pose pose)

◆ move_back()

void protocols::docking::DockingEnsemblePrepackProtocol::move_back ( core::pose::Pose pose)

◆ register_options()

void protocols::docking::DockingEnsemblePrepackProtocol::register_options ( )

◆ set_ensemble1()

void protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble1 ( std::string const &  ensemble1)

References copy_ensemble(), and ensemble1_filename_.

Referenced by init_from_options().

◆ set_ensemble2()

void protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble2 ( std::string const &  ensemble2)

References copy_ensemble(), and ensemble2_filename_.

Referenced by init_from_options().

◆ set_spanfile1()

void protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile1 ( std::string const &  spanfile1)

References span1_filename_.

Referenced by init_from_options().

◆ set_spanfile2()

void protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile2 ( std::string const &  spanfile2)

References span2_filename_.

Referenced by init_from_options().

◆ setup_defaults()

void protocols::docking::DockingEnsemblePrepackProtocol::setup_defaults ( )

◆ setup_pack_operation_movers()

void protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers ( )

Member Data Documentation

◆ ensemble1_

DockingEnsembleOP protocols::docking::DockingEnsemblePrepackProtocol::ensemble1_

◆ ensemble1_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::ensemble1_filename_

◆ ensemble2_

DockingEnsembleOP protocols::docking::DockingEnsemblePrepackProtocol::ensemble2_

◆ ensemble2_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::ensemble2_filename_

◆ membrane_

bool protocols::docking::DockingEnsemblePrepackProtocol::membrane_

membrane for translating in the membrane plane

Referenced by apply(), finalize_setup(), init_from_options(), move_away(), move_back(), and setup_defaults().

◆ movers_setup_

bool protocols::docking::DockingEnsemblePrepackProtocol::movers_setup_

◆ pack_operations_

protocols::moves::SequenceMoverOP protocols::docking::DockingEnsemblePrepackProtocol::pack_operations_

◆ prepack_full_repack_

protocols::minimization_packing::PackRotamersMoverOP protocols::docking::DockingEnsemblePrepackProtocol::prepack_full_repack_

◆ rtmin_mover_

protocols::minimization_packing::RotamerTrialsMinMoverOP protocols::docking::DockingEnsemblePrepackProtocol::rtmin_mover_

◆ scmin_mover_

SidechainMinMoverOP protocols::docking::DockingEnsemblePrepackProtocol::scmin_mover_

◆ span1_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::span1_filename_

◆ span2_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::span2_filename_

◆ trans_away_vec_

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingEnsemblePrepackProtocol::trans_away_vec_

◆ trans_back_vec_

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingEnsemblePrepackProtocol::trans_back_vec_

◆ trans_magnitude_

core::Real protocols::docking::DockingEnsemblePrepackProtocol::trans_magnitude_

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