Rosetta 3.4
Public Member Functions | Static Public Member Functions | Friends
protocols::docking::DockingProtocol Class Reference

This is the standard RosettaDock protocol. More...

#include <DockingProtocol.hh>

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

List of all members.

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
 DockingProtocol (Size const rb_jump_in, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionCOP docking_score_low=core::scoring::ScoreFunctionCOP(NULL), core::scoring::ScoreFunctionCOP docking_score_high=core::scoring::ScoreFunctionCOP(NULL))
 DockingProtocol (DockJumps const movable_jumps, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionCOP docking_score_low=core::scoring::ScoreFunctionCOP(NULL), core::scoring::ScoreFunctionCOP docking_score_high=core::scoring::ScoreFunctionCOP(NULL))
void set_default ()
 Assigns default values to primitive members.
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members.
 ~DockingProtocol ()
virtual protocols::moves::MoverOP clone () const
 clone operator, calls the copy constructor
virtual protocols::moves::MoverOP fresh_instance () const
 fresh_instance returns a default-constructed object for the JD2
virtual bool reinitialize_for_new_input () const
 This mover retains state such that a fresh version is needed if the input Pose is about to change.
 DockingProtocol (DockingProtocol const &rhs)
 copy ctor
DockingProtocoloperator= (DockingProtocol const &rhs)
 assignment operator
void set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_low)
 Sets the score function that will be used in the low-resolution phase.
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.
void set_highres_scorefxn (core::scoring::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP 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.
void set_highres_scorefxn (core::scoring::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP docking_scorefxn_pack, core::scoring::ScoreFunctionCOP 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.
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::toolbox::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 ()
virtual void apply (core::pose::Pose &pose)
 main docking protocol
std::string partners () const
virtual std::string get_name () const
 returns the docking partners chain identifiers
DockJumpsmovable_jumps ()
DockJumps const & movable_jumps () const
 returns ref to the jumps vector for docking
core::pack::task::TaskFactory
const & 
task_factory ()
 @ return const ref to the jumps vector for docking
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_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)
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Static Public Member Functions

static void register_options ()
 Associates relevant options with the DockingProtocol class.

Friends

std::ostream & operator<< (std::ostream &out, const DockingProtocol &dp)

Detailed Description

This is the standard RosettaDock protocol.

Detailed: 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().

Referenced by clone(), protocols::docking::DockingProtocolCreator::create_mover(), and fresh_instance().

protocols::docking::DockingProtocol::DockingProtocol ( Size const  rb_jump_in,
bool const  low_res_protocol_only = false,
bool const  docking_local_refine = false,
bool const  autofoldtree = true,
core::scoring::ScoreFunctionCOP  docking_score_low = core::scoring::ScoreFunctionCOP(NULL),
core::scoring::ScoreFunctionCOP  docking_score_high = core::scoring::ScoreFunctionCOP(NULL) 
)
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::ScoreFunctionCOP  docking_score_low = core::scoring::ScoreFunctionCOP(NULL),
core::scoring::ScoreFunctionCOP  docking_score_high = core::scoring::ScoreFunctionCOP(NULL) 
)
protocols::docking::DockingProtocol::~DockingProtocol ( )
protocols::docking::DockingProtocol::DockingProtocol ( DockingProtocol const &  rhs)

copy ctor


Member Function Documentation

void protocols::docking::DockingProtocol::add_additional_task_operaration ( core::pack::task::operation::TaskOperationOP  task_operation)
void protocols::docking::DockingProtocol::add_jump ( core::Size const  jump_number) [inline]
void protocols::docking::DockingProtocol::apply ( core::pose::Pose pose) [virtual]
protocols::moves::MoverOP protocols::docking::DockingProtocol::clone ( ) const [virtual]

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

References DockingProtocol().

protocols::docking::DockingHighResCOP protocols::docking::DockingProtocol::docking_highres_mover ( ) const
protocols::docking::DockingLowResCOP protocols::docking::DockingProtocol::docking_lowres_mover ( ) const
protocols::moves::MoverOP protocols::docking::DockingProtocol::fresh_instance ( ) const [virtual]

fresh_instance returns a default-constructed object for the JD2

Reimplemented from protocols::moves::Mover.

References DockingProtocol().

utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingProtocol::get_additional_task_operarations ( )
virtual std::string protocols::docking::DockingProtocol::get_name ( ) const [inline, virtual]

returns the docking partners chain identifiers

Implements protocols::moves::Mover.

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

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

returns ref to the jumps vector for docking

DockingProtocol & protocols::docking::DockingProtocol::operator= ( DockingProtocol const &  rhs)

assignment operator

void protocols::docking::DockingProtocol::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::get(), protocols::rosetta_scripts::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]

Referenced by parse_my_tag(), and set_partners().

protocols::docking::DockingInitialPerturbationCOP protocols::docking::DockingProtocol::perturber ( ) const
void protocols::docking::DockingProtocol::register_options ( ) [static]

Associates relevant options with the DockingProtocol class.

Reimplemented from protocols::moves::Mover.

bool protocols::docking::DockingProtocol::reinitialize_for_new_input ( ) const [virtual]

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

Assigns default values to primitive members.

void protocols::docking::DockingProtocol::set_design ( bool const  design) [inline]
void protocols::docking::DockingProtocol::set_dock_min ( bool const  dock_min)

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_docking_local_refine ( bool const  docking_local_refine)

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_ensemble1 ( std::string const &  ensemble1) [inline]
void protocols::docking::DockingProtocol::set_ensemble2 ( std::string const &  ensemble2) [inline]
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.

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionCOP  docking_scorefxn_high,
core::scoring::ScoreFunctionCOP  docking_scorefxn_pack,
core::scoring::ScoreFunctionCOP  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.

void protocols::docking::DockingProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionCOP  docking_scorefxn_high,
core::scoring::ScoreFunctionCOP  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.

void protocols::docking::DockingProtocol::set_ignore_default_docking_task ( bool const  ignore_default_docking_task) [inline]

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_inner_cycles ( core::Size  inner_cycles) [inline]
void protocols::docking::DockingProtocol::set_interface_definition_task_operation ( protocols::toolbox::task_operations::InterfaceTaskOperationOP  interface_definition)
void protocols::docking::DockingProtocol::set_low_res_protocol_only ( bool const  low_res_protocol_only)

Referenced by parse_my_tag().

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.

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_movable_jumps ( DockJumps const  jump_numbers) [inline]
void protocols::docking::DockingProtocol::set_no_filters ( bool  no_filters)
void protocols::docking::DockingProtocol::set_outer_cycles ( core::Size  outer_cycles) [inline]
void protocols::docking::DockingProtocol::set_partners ( std::string const &  partners) [inline]

References partners().

Referenced by 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]
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 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::show ( std::ostream &  out = std::cout)

Show the complete setup of the docking protocol

References sync_objects_with_flags().

Referenced by apply().

void protocols::docking::DockingProtocol::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

Referenced by apply(), and show().

core::pack::task::TaskFactory const& protocols::docking::DockingProtocol::task_factory ( ) [inline]

@ return const ref to the jumps vector for docking

Referenced by set_task_factory().

protocols::moves::MoverCOP protocols::docking::DockingProtocol::to_all_atom ( ) const
protocols::simple_moves::SwitchResidueTypeSetMoverCOP protocols::docking::DockingProtocol::to_centroid ( ) const

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const DockingProtocol dp 
) [friend]

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines