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protocols::docking::DockingProtocol Class Reference

This is the standard RosettaDock protocol. More...

#include <DockingProtocol.hh>

Inheritance diagram for protocols::docking::DockingProtocol:
Inheritance graph
[legend]

Public Member Functions

 DockingProtocol ()
 empty constructor fills values with the expected defaults rb_jump will be assigned as 1 (meaning the first jump will be used as the jump across which all rigid-body perturbations will occur More...
 
 DockingProtocol (core::Size const rb_jump_in, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr))
 
 DockingProtocol (DockJumps const movable_jumps, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr))
 
void set_default ()
 Assigns default values to primitive members. More...
 
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. More...
 
 ~DockingProtocol () override
 
protocols::moves::MoverOP clone () const override
 clone operator, calls the copy constructor More...
 
protocols::moves::MoverOP fresh_instance () const override
 fresh_instance returns a default-constructed object for the 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...
 
 DockingProtocol (DockingProtocol const &rhs)
 copy ctor More...
 
DockingProtocoloperator= (DockingProtocol const &rhs)
 assignment operator More...
 
void set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_low)
 Sets the score function that will be used in the low-resolution phase. More...
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high)
 Sets the score function that will be used in the high-resolution phase. The same score function will be used for evaluating moves, packing and discriminating. More...
 
core::scoring::ScoreFunctionCOP get_highres_scorefxn () const
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack)
 Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing. More...
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack, core::scoring::ScoreFunctionOP docking_scorefxn_output)
 Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating. More...
 
void set_sc_min (bool sc_min)
 
void set_rt_min (bool rt_min)
 
void set_dock_min (bool const dock_min)
 
void set_no_filters (bool no_filters)
 
void set_low_res_protocol_only (bool const low_res_protocol_only)
 
void set_docking_local_refine (bool const docking_local_refine)
 
void set_use_legacy_protocol (bool const use_legacy_protocol)
 
void set_cst_weight (core::Real const cst_weight)
 
void set_use_constraints (bool const use_csts)
 
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::TaskOperationOP
get_additional_task_operarations ()
 
void apply (core::pose::Pose &pose) override
 main docking protocol More...
 
std::string partners () const
 returns the docking partners chain identifiers More...
 
DockJumpsmovable_jumps ()
 returns ref to the jumps vector for docking More...
 
DockJumps const & movable_jumps () const
 returns a const ref to the jumps vector for docking More...
 
core::pack::task::TaskFactory
const & 
task_factory ()
 
protocols::simple_moves::SwitchResidueTypeSetMoverCOP to_centroid () const
 
protocols::moves::MoverCOP to_all_atom () const
 
protocols::docking::DockingLowResCOP docking_lowres_mover () const
 
protocols::docking::DockingHighResCOP docking_highres_mover () const
 
protocols::docking::DockingInitialPerturbationCOP perturber () const
 
void set_docking_highres_mover (protocols::docking::DockingHighResOP docking_highres_mover)
 
void add_additional_low_resolution_step (protocols::moves::MoverOP additional_low_resolution_mover)
 
void set_autofoldtree (bool const autofoldtree)
 
void set_partners (std::string const &partners)
 
void set_inner_cycles (core::Size inner_cycles)
 
void set_outer_cycles (core::Size outer_cycles)
 
void set_design (bool const design)
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void set_ignore_default_docking_task (bool const ignore_default_docking_task)
 
void set_movable_jumps (DockJumps const jump_numbers)
 
void set_reporting (bool report)
 
void set_ensemble1 (std::string const &ensemble1)
 
void set_ensemble2 (std::string const &ensemble2)
 
void set_recover_sidechains_filename (std::string const &file)
 
void add_jump (core::Size const jump_number)
 
void show (std::ostream &out=std::cout) const override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- 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
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void register_options ()
 Associates relevant options with the DockingProtocol 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 init_from_options ()
 Assigns user specified values to primitive members using command line options. More...
 
bool is_ensemble_prepacked (std::string ensemble_filename)
 Verifies ensembles are prepacked to prevent seg faults. More...
 
void finalize_setup (core::pose::Pose &pose)
 Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...
 
void init (DockJumps const movable_jumps, bool const low_res_protocol_only_, bool const docking_local_refine, bool const autofoldtree, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)
 Sets up the instance of DockingProtocol and initializes all members based on values passed in at construction or via the command line. More...
 
void initForEqualOperatorAndCopyConstructor (DockingProtocol &lhs, DockingProtocol const &rhs)
 
void setup_objects ()
 
void setup_constraints (core::pose::Pose &pose)
 setup the constrainta for each application of the docking protocol More...
 
void add_constraints_to_scorefunction ()
 add distance constraint to the docking score functions More...
 
void check_high_res_protocol ()
 

Private Attributes

bool user_defined_
 information about the mode More...
 
bool low_res_protocol_only_
 
bool reporting_
 
bool autofoldtree_
 
bool flags_and_objects_are_in_sync_
 
bool first_apply_with_current_setup_
 
bool sc_min_
 
bool rt_min_
 
bool dock_min_
 
bool if_ensemble_
 
bool no_filters_
 
bool use_legacy_protocol_
 
bool docking_local_refine_
 
bool use_csts_
 
core::Real cst_weight_
 
core::Real cst_fa_weight_
 
core::Real score_cutoff_
 
core::kinematics::FoldTree fold_tree_
 
std::string partners_
 
std::string previous_sequence_
 
core::SSize lowres_inner_cycles_
 
core::SSize lowres_outer_cycles_
 
DockJumps movable_jumps_
 jumps that rigid_body transformations can occur over More...
 
core::scoring::ScoreFunctionOP docking_scorefxn_low_
 
core::scoring::ScoreFunctionOP docking_scorefxn_high_
 
core::scoring::ScoreFunctionOP docking_scorefxn_pack_
 
core::scoring::ScoreFunctionOP docking_scorefxn_output_
 
protocols::moves::MonteCarloOP mc_
 
protocols::docking::DockingLowResFilterOP lowres_filter_
 
protocols::docking::DockingHighResFilterOP highres_filter_
 
protocols::docking::DockingLowResOP docking_lowres_mover_
 
protocols::docking::DockingHighResOP docking_highres_mover_
 
protocols::docking::DockingInitialPerturbationOP perturber_
 
protocols::simple_moves::SwitchResidueTypeSetMoverOP to_centroid_
 
protocols::moves::MoverOP to_all_atom_
 
protocols::docking::DockingEnsembleOP ensemble1_
 
protocols::docking::DockingEnsembleOP ensemble2_
 
std::string ensemble1_filename_
 
std::string ensemble2_filename_
 
protocols::constraint_movers::ConstraintSetMoverOP docking_constraint_
 
protocols::simple_moves::ReturnSidechainMoverOP recover_sidechains_
 
protocols::moves::SequenceMoverOP additional_low_resolution_steps_
 
std::string recover_sidechains_filename_
 
core::pack::task::TaskFactoryOP init_task_factory_
 
bool design_
 
bool ignore_default_docking_task_
 

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...
 

Detailed Description

This is the standard RosettaDock protocol.

RosettaDock protocol based on [refs...Gray2003, Wang2005, Chaudhury 2007 ... ]

Constructor & Destructor Documentation

protocols::docking::DockingProtocol::DockingProtocol ( )

empty constructor fills values with the expected defaults rb_jump will be assigned as 1 (meaning the first jump will be used as the jump across which all rigid-body perturbations will occur

References core::init::init().

protocols::docking::DockingProtocol::DockingProtocol ( core::Size const  rb_jump_in,
bool const  low_res_protocol_only = false,
bool const  docking_local_refine = false,
bool const  autofoldtree = true,
core::scoring::ScoreFunctionOP  docking_score_low = core::scoring::ScoreFunctionOP( nullptr ),
core::scoring::ScoreFunctionOP  docking_score_high = core::scoring::ScoreFunctionOP( nullptr ) 
)

References init(), and user_defined_.

protocols::docking::DockingProtocol::DockingProtocol ( DockJumps const  movable_jumps,
bool const  low_res_protocol_only = false,
bool const  docking_local_refine = false,
bool const  autofoldtree = true,
core::scoring::ScoreFunctionOP  docking_score_low = core::scoring::ScoreFunctionOP( nullptr ),
core::scoring::ScoreFunctionOP  docking_score_high = core::scoring::ScoreFunctionOP( nullptr ) 
)

References init(), and user_defined_.

protocols::docking::DockingProtocol::~DockingProtocol ( )
overridedefault
protocols::docking::DockingProtocol::DockingProtocol ( DockingProtocol const &  rhs)

Member Function Documentation

void protocols::docking::DockingProtocol::add_additional_low_resolution_step ( protocols::moves::MoverOP  additional_low_resolution_mover)
void protocols::docking::DockingProtocol::add_additional_task_operaration ( core::pack::task::operation::TaskOperationOP  task_operation)
void protocols::docking::DockingProtocol::add_constraints_to_scorefunction ( )
private
void protocols::docking::DockingProtocol::add_jump ( core::Size const  jump_number)
inline

References movable_jumps_.

void protocols::docking::DockingProtocol::apply ( core::pose::Pose pose)
overridevirtual

main docking protocol

Main function for docking. Includes the following steps: 0) prepack mode: prepare a starting structure for later runs OR: 1) perturbation of decoy (see docking_perturb_decoy): changes orientation of docking partners 2) low-resolution search: refine structure with rigid-body, centroid-mode MC cycles 3) high-resolution search: further refinement of structure in fullatom mode

Implements protocols::moves::Mover.

Reimplemented in protocols::docking::stateless::SaneDockingProtocol.

References core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::jd2::add_string_real_pair_to_current_job(), additional_low_resolution_steps_, protocols::docking::calc_CAPRI_rank(), protocols::docking::calc_Fnat(), protocols::docking::calc_interaction_energy(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_Lrmsd(), cst_fa_weight_, cst_weight_, docking_constraint_, docking_highres_mover_, docking_lowres_mover_, docking_scorefxn_high_, docking_scorefxn_output_, core::pose::Pose::energies(), ensemble1_, ensemble2_, protocols::moves::FAIL_RETRY, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, core::pose::Pose::fold_tree(), fold_tree_, protocols::moves::Mover::get_native_pose(), highres_filter_, core::pose::Pose::is_fullatom(), lowres_filter_, movable_jumps_, protocols::moves::MS_SUCCESS, core::scoring::pair, perturber_, previous_sequence_, recover_sidechains_, reporting_, core::pose::Pose::sequence(), protocols::moves::Mover::set_last_move_status(), protocols::moves::Mover::set_native_pose(), setup_constraints(), show(), sync_objects_with_flags(), to_all_atom_, to_centroid_, core::scoring::Energies::total_energies(), core::scoring::total_score, protocols::docking::TR(), and protocols::jd2::write_score_tracer().

Referenced by protocols::docking::stateless::SaneDockingProtocol::apply().

void protocols::docking::DockingProtocol::check_high_res_protocol ( )
private
protocols::moves::MoverOP protocols::docking::DockingProtocol::clone ( ) const
overridevirtual

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

protocols::docking::DockingHighResCOP protocols::docking::DockingProtocol::docking_highres_mover ( ) const
protocols::docking::DockingLowResCOP protocols::docking::DockingProtocol::docking_lowres_mover ( ) const

References docking_lowres_mover_.

void protocols::docking::DockingProtocol::finalize_setup ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::docking::DockingProtocol::fresh_instance ( ) const
overridevirtual

fresh_instance returns a default-constructed object for the JD2

Reimplemented from protocols::moves::Mover.

utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingProtocol::get_additional_task_operarations ( )
core::scoring::ScoreFunctionCOP protocols::docking::DockingProtocol::get_highres_scorefxn ( ) const
inline
std::string protocols::docking::DockingProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::docking::stateless::SaneDockingProtocol.

References mover_name().

void protocols::docking::DockingProtocol::init ( DockJumps const  movable_jumps,
bool const  low_res_protocol_only_,
bool const  docking_local_refine,
bool const  autofoldtree,
core::scoring::ScoreFunctionOP  docking_score_low,
core::scoring::ScoreFunctionOP  docking_score_high 
)
private
void protocols::docking::DockingProtocol::init_from_options ( )
private
void protocols::docking::DockingProtocol::initForEqualOperatorAndCopyConstructor ( DockingProtocol lhs,
DockingProtocol const &  rhs 
)
private
bool protocols::docking::DockingProtocol::is_ensemble_prepacked ( std::string  ensemble_filename)
private

Verifies ensembles are prepacked to prevent seg faults.

Referenced by finalize_setup().

DockJumps& protocols::docking::DockingProtocol::movable_jumps ( )
inline

returns ref to the jumps vector for docking

References movable_jumps_.

Referenced by init().

DockJumps const& protocols::docking::DockingProtocol::movable_jumps ( ) const
inline

returns a const ref to the jumps vector for docking

References movable_jumps_.

std::string protocols::docking::DockingProtocol::mover_name ( )
static
DockingProtocol & protocols::docking::DockingProtocol::operator= ( DockingProtocol const &  rhs)

assignment operator

References initForEqualOperatorAndCopyConstructor().

void protocols::docking::DockingProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References clone(), core::pack::task::parse_task_operations(), partners(), set_dock_min(), set_docking_local_refine(), set_highres_scorefxn(), set_ignore_default_docking_task(), set_low_res_protocol_only(), set_lowres_scorefxn(), set_partners(), and set_task_factory().

std::string protocols::docking::DockingProtocol::partners ( ) const
inline

returns the docking partners chain identifiers

References partners_.

Referenced by parse_my_tag(), and set_partners().

protocols::docking::DockingInitialPerturbationCOP protocols::docking::DockingProtocol::perturber ( ) const

References perturber_.

void protocols::docking::DockingProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::DockingProtocol::register_options ( )
static
bool protocols::docking::DockingProtocol::reinitialize_for_new_input ( ) const
overridevirtual

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::docking::DockingProtocol::set_additional_task_operarations ( utility::vector1< core::pack::task::operation::TaskOperationOP additional_task_operations)
void protocols::docking::DockingProtocol::set_autofoldtree ( bool const  autofoldtree)
inline

References autofoldtree_.

void protocols::docking::DockingProtocol::set_cst_weight ( core::Real const  cst_weight)

Set the constraint weight for both centroid and full atom constraints to the same value

References cst_fa_weight_, cst_weight_, and flags_and_objects_are_in_sync_.

void protocols::docking::DockingProtocol::set_default ( )
void protocols::docking::DockingProtocol::set_design ( bool const  design)
inline

References design_.

void protocols::docking::DockingProtocol::set_dock_min ( bool const  dock_min)

References dock_min_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_docking_highres_mover ( protocols::docking::DockingHighResOP  docking_highres_mover)
void protocols::docking::DockingProtocol::set_docking_local_refine ( bool const  docking_local_refine)
void protocols::docking::DockingProtocol::set_ensemble1 ( std::string const &  ensemble1)
inline

References ensemble1_filename_.

Referenced by init_from_options().

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

References ensemble2_filename_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_high)

Sets the score function that will be used in the high-resolution phase. The same score function will be used for evaluating moves, packing and discriminating.

References docking_highres_mover_, docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

Referenced by add_constraints_to_scorefunction(), parse_my_tag(), and set_docking_highres_mover().

void protocols::docking::DockingProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_high,
core::scoring::ScoreFunctionOP  docking_scorefxn_pack 
)

Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing.

References docking_highres_mover_, docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::DockingProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_high,
core::scoring::ScoreFunctionOP  docking_scorefxn_pack,
core::scoring::ScoreFunctionOP  docking_scorefxn_output 
)

Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating.

References docking_highres_mover_, docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::DockingProtocol::set_ignore_default_docking_task ( bool const  ignore_default_docking_task)
inline
void protocols::docking::DockingProtocol::set_inner_cycles ( core::Size  inner_cycles)
inline

References lowres_inner_cycles_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_interface_definition_task_operation ( protocols::simple_task_operations::InterfaceTaskOperationOP  interface_definition)
void protocols::docking::DockingProtocol::set_low_res_protocol_only ( bool const  low_res_protocol_only)
void protocols::docking::DockingProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP  docking_scorefxn_low)

Sets the score function that will be used in the low-resolution phase.

References docking_lowres_mover_, and docking_scorefxn_low_.

Referenced by add_constraints_to_scorefunction(), finalize_setup(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_movable_jumps ( DockJumps const  jump_numbers)
inline

References movable_jumps_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_no_filters ( bool  no_filters)
void protocols::docking::DockingProtocol::set_outer_cycles ( core::Size  outer_cycles)
inline

References lowres_outer_cycles_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_partners ( std::string const &  partners)
inline

References partners(), and partners_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_recover_sidechains_filename ( std::string const &  file)
inline
void protocols::docking::DockingProtocol::set_reporting ( bool  report)
inline

References reporting_.

void protocols::docking::DockingProtocol::set_rt_min ( bool  rt_min)
void protocols::docking::DockingProtocol::set_sc_min ( bool  sc_min)
void protocols::docking::DockingProtocol::set_task_factory ( core::pack::task::TaskFactoryOP  task_factory)
inline

References init_task_factory_, and task_factory().

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_use_constraints ( bool const  use_csts)
void protocols::docking::DockingProtocol::set_use_legacy_protocol ( bool const  use_legacy_protocol)
void protocols::docking::DockingProtocol::setup_constraints ( core::pose::Pose pose)
private

setup the constrainta for each application of the docking protocol

References add_constraints_to_scorefunction(), core::pose::Pose::constraint_set(), cst_weight_, lowres_filter_, and protocols::docking::TR().

Referenced by apply(), and finalize_setup().

void protocols::docking::DockingProtocol::setup_objects ( )
private
void protocols::docking::DockingProtocol::show ( std::ostream &  out = std::cout) const
overridevirtual
void protocols::docking::DockingProtocol::sync_objects_with_flags ( )
core::pack::task::TaskFactory const& protocols::docking::DockingProtocol::task_factory ( )
inline

References init_task_factory_.

Referenced by set_task_factory().

protocols::moves::MoverCOP protocols::docking::DockingProtocol::to_all_atom ( ) const

References to_all_atom_.

protocols::simple_moves::SwitchResidueTypeSetMoverCOP protocols::docking::DockingProtocol::to_centroid ( ) const

References to_centroid_.

Member Data Documentation

protocols::moves::SequenceMoverOP protocols::docking::DockingProtocol::additional_low_resolution_steps_
private
bool protocols::docking::DockingProtocol::autofoldtree_
private
core::Real protocols::docking::DockingProtocol::cst_fa_weight_
private
core::Real protocols::docking::DockingProtocol::cst_weight_
private
bool protocols::docking::DockingProtocol::design_
private
bool protocols::docking::DockingProtocol::dock_min_
private
protocols::constraint_movers::ConstraintSetMoverOP protocols::docking::DockingProtocol::docking_constraint_
private
protocols::docking::DockingHighResOP protocols::docking::DockingProtocol::docking_highres_mover_
private
bool protocols::docking::DockingProtocol::docking_local_refine_
private
protocols::docking::DockingLowResOP protocols::docking::DockingProtocol::docking_lowres_mover_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_high_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_low_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_output_
private
core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_pack_
private
protocols::docking::DockingEnsembleOP protocols::docking::DockingProtocol::ensemble1_
private
std::string protocols::docking::DockingProtocol::ensemble1_filename_
private
protocols::docking::DockingEnsembleOP protocols::docking::DockingProtocol::ensemble2_
private
std::string protocols::docking::DockingProtocol::ensemble2_filename_
private
bool protocols::docking::DockingProtocol::first_apply_with_current_setup_
private
bool protocols::docking::DockingProtocol::flags_and_objects_are_in_sync_
private
core::kinematics::FoldTree protocols::docking::DockingProtocol::fold_tree_
private
protocols::docking::DockingHighResFilterOP protocols::docking::DockingProtocol::highres_filter_
private
bool protocols::docking::DockingProtocol::if_ensemble_
private
bool protocols::docking::DockingProtocol::ignore_default_docking_task_
private
core::pack::task::TaskFactoryOP protocols::docking::DockingProtocol::init_task_factory_
private
bool protocols::docking::DockingProtocol::low_res_protocol_only_
private
protocols::docking::DockingLowResFilterOP protocols::docking::DockingProtocol::lowres_filter_
private
core::SSize protocols::docking::DockingProtocol::lowres_inner_cycles_
private
core::SSize protocols::docking::DockingProtocol::lowres_outer_cycles_
private
protocols::moves::MonteCarloOP protocols::docking::DockingProtocol::mc_
private
DockJumps protocols::docking::DockingProtocol::movable_jumps_
private
bool protocols::docking::DockingProtocol::no_filters_
private
std::string protocols::docking::DockingProtocol::partners_
private
protocols::docking::DockingInitialPerturbationOP protocols::docking::DockingProtocol::perturber_
private
std::string protocols::docking::DockingProtocol::previous_sequence_
private
protocols::simple_moves::ReturnSidechainMoverOP protocols::docking::DockingProtocol::recover_sidechains_
private
std::string protocols::docking::DockingProtocol::recover_sidechains_filename_
private
bool protocols::docking::DockingProtocol::reporting_
private
bool protocols::docking::DockingProtocol::rt_min_
private
bool protocols::docking::DockingProtocol::sc_min_
private
core::Real protocols::docking::DockingProtocol::score_cutoff_
private
protocols::moves::MoverOP protocols::docking::DockingProtocol::to_all_atom_
private
protocols::simple_moves::SwitchResidueTypeSetMoverOP protocols::docking::DockingProtocol::to_centroid_
private
bool protocols::docking::DockingProtocol::use_csts_
private
bool protocols::docking::DockingProtocol::use_legacy_protocol_
private
bool protocols::docking::DockingProtocol::user_defined_
private

information about the mode

Referenced by DockingProtocol(), init(), and initForEqualOperatorAndCopyConstructor().


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