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protocols::symmetric_docking::SymDockProtocol Class Reference

Main Symmetric Docking protocol class. More...

#include <SymDockProtocol.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockProtocol:
Inheritance graph

Public Types

- 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

Public Member Functions

 SymDockProtocol ()
 Default Constructor for Symmetric Docking Protocol. More...
 SymDockProtocol (bool const fullatom, bool const local_refine, bool const view=false)
 Custom Constructor - Symmetric docking protocol. More...
 SymDockProtocol (bool const fullatom, bool const local_refine, bool const view, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)
 Custom Constructor - Symmetric Docking Protocol. More...
 ~SymDockProtocol () override
 Destructor. More...
void register_options ()
 Register Options from the Commandline. More...
void set_default ()
 Setup options based on constructors. More...
void set_dock_rtmin (bool dock_rtmin_in)
 Setters for Protocol Options. More...
void set_sc_min (bool sc_min_in)
void set_max_repeats (core::Size const max_repeats_in)
void set_dock_ppk (bool dock_ppk_in)
void set_fullatom (bool const fullatom_in)
void set_local_refine (bool const local_refine_in)
void set_view (bool view_in)
void set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_score_low_in)
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in)
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in, core::scoring::ScoreFunctionOP docking_score_pack_in)
bool docking_lowres_filter (core::pose::Pose &pose)
bool docking_highres_filter (core::pose::Pose &pose)
core::Real calc_interaction_energy (core::pose::Pose &pose)
 Calculate Interaction energy between partners. More...
core::Real calc_rms (core::pose::Pose &pose)
 Calculate RMSD from partner to symmetric starting structure. More...
core::Real calc_Irms (core::pose::Pose &pose)
 Calculate interface RMSD of one chain to symmetric starting structure assuming correct native chain order. More...
core::Real calc_fnat (core::pose::Pose &pose, core::scoring::ScoreFunctionOP dock_scorefxn)
 Calculate fraction of native contacts recovered for one chain assuming correct native chain order. More...
bool calc_res_contact (core::conformation::ResidueOP const rsd1, core::conformation::ResidueOP const rsd2, core::Real const dist_cutoff)
 Calculate whether two residues are within a distance cutoff of each other. More...
core::Real calc_CAPRI_rank (core::Real const Irmsd, core::Real const Lrmsd, core::Real const Fnat)
 Calculate fraction of native contacts recovered for one chain assuming correct native chain order. More...
void recover_sidechains (core::pose::Pose &pose, const core::pose::Pose &native_pose)
 Recover sidechains from the native pose. More...
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 Set Task Factory for Packing. More...
void design (bool const des)
 Turn on Design of partner 2 during docking - not thoroughly tested. More...
bool design () const
void hurry (bool const hurry)
 Skip population of the score map. More...
core::pack::task::TaskFactoryOP task_factory () const
 Methods for task factory? More...
core::pack::task::TaskFactoryOPtask_factory ()
void score_only (core::pose::Pose &pose)
 Only score the pose using docking config. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 RosettaScripts Methods //////. More...
void apply (core::pose::Pose &pose) override
 Mover Methods /////////. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. 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...
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
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 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 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 classic_mcm_protocol (core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const
 Classic MCM Protocol for symmetric docking protocol. More...
protocols::moves::MoverOP make_dockmcm_mover (core::pose::Pose const &pose, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const
 Setup Docking Monte Carlo mover. More...

Private Attributes

bool fullatom_
 Data about the protocol. More...
bool local_refine_
bool rtmin_
bool sc_min_
core::Size max_repeats_
bool dock_ppk_
utility::vector1< core::Sizemovable_jumps_
 Jumps for symmetric rigid body transformations. More...
bool autofoldtree_
 Modified Docking foldtree for symmetry. More...
bool view_
 Initialize the graphics viewer (opengl) More...
bool design_
 Allow design of partner 2 during docking. More...
bool passed_lowres_filter_
 Filters for structures during protocols. More...
bool passed_highres_filter_
bool hurry_
 Sip population of the score map. More...
std::map< std::string, core::Realscore_map_
 For scorefile output. More...
core::scoring::ScoreFunctionOP docking_score_low_
 Scorefunctions used during the protocol. More...
core::scoring::ScoreFunctionOP docking_score_high_
core::scoring::ScoreFunctionOP docking_score_high_min_
core::scoring::ScoreFunctionOP docking_score_pack_
moves::MonteCarloOP mc_
 Monte carlo object. More...
protocols::symmetric_docking::SymDockingLowResOP docking_low_
 Child protocols - low resolution and high resolution docking & for packing. More...
protocols::symmetric_docking::SymDockingHiResOP docking_high_
core::pack::task::TaskFactoryOP init_task_factory_
 Used to restrict packer task during docking. More...

Additional Inherited Members

- 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

Main Symmetric Docking protocol class.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( )

Default Constructor for Symmetric Docking Protocol.

References register_options(), and set_default().

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( bool const  fullatom,
bool const  local_refine,
bool const  view = false 

Custom Constructor - Symmetric docking protocol.

Custom protocol - specify if input pose is fullatom, local refinement and use graphics viewer

References register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( bool const  fullatom,
bool const  local_refine,
bool const  view,
core::scoring::ScoreFunctionOP  docking_score_low,
core::scoring::ScoreFunctionOP  docking_score_high 

Custom Constructor - Symmetric Docking Protocol.

Custom protocol - specify if input pose is fullatom, local refinement and use graphics viewer. Also specify custom scoring functions for low and high resolution stages

References docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

protocols::symmetric_docking::SymDockProtocol::~SymDockProtocol ( )


Member Function Documentation

void protocols::symmetric_docking::SymDockProtocol::apply ( core::pose::Pose pose)

Mover Methods /////////.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::constraint_movers::ConstraintSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::symmetry::SymDockingInitialPerturbation::apply(), calc_CAPRI_rank(), calc_fnat(), calc_interaction_energy(), calc_Irms(), calc_rms(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::data(), core::pack::interaction_graph::debug, design_, docking_high_, docking_highres_filter(), docking_low_, docking_lowres_filter(), docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, core::scoring::fa_rep, core::scoring::fa_sol, core::chemical::FA_STANDARD, fullatom_, protocols::moves::Mover::get_input_pose(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), core::scoring::get_score_function(), hurry_, init_task_factory_, core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), local_refine_, core::chemical::element::N, core::scoring::pair, passed_highres_filter_, passed_lowres_filter_, recover_sidechains(), protocols::relax::relax_pose(), core::scoring::rms, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, score_only(), core::scoring::score_type_from_name(), protocols::moves::Mover::set_input_pose(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), protocols::medal::to_centroid(), and protocols::symmetric_docking::TR().

core::Real protocols::symmetric_docking::SymDockProtocol::calc_CAPRI_rank ( core::Real const  Irmsd,
core::Real const  Lrmsd,
core::Real const  Fnat 

Calculate fraction of native contacts recovered for one chain assuming correct native chain order.

References protocols::symmetric_docking::TR().

Referenced by apply().

core::Real protocols::symmetric_docking::SymDockProtocol::calc_fnat ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  dock_scorefxn 
core::Real protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy ( core::pose::Pose pose)
core::Real protocols::symmetric_docking::SymDockProtocol::calc_Irms ( core::pose::Pose pose)
bool protocols::symmetric_docking::SymDockProtocol::calc_res_contact ( core::conformation::ResidueOP const  rsd1,
core::conformation::ResidueOP const  rsd2,
core::Real const  dist_cutoff 

Calculate whether two residues are within a distance cutoff of each other.

Referenced by calc_fnat().

core::Real protocols::symmetric_docking::SymDockProtocol::calc_rms ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockProtocol::classic_mcm_protocol ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo,
core::Size  num_cycles,
core::Size  repack_every_Nth 
) const

Classic MCM Protocol for symmetric docking protocol.

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::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.

References docking_score_high_, docking_score_low_, fullatom_, local_refine_, and view_.

void protocols::symmetric_docking::SymDockProtocol::design ( bool const  des)

Turn on Design of partner 2 during docking - not thoroughly tested.

I think this is just copied over from regular docking protocol?

References design_.

bool protocols::symmetric_docking::SymDockProtocol::design ( ) const

References design_.

Referenced by set_default().

bool protocols::symmetric_docking::SymDockProtocol::docking_highres_filter ( core::pose::Pose pose)
bool protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter ( core::pose::Pose pose)
std::string protocols::symmetric_docking::SymDockProtocol::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::symmetric_docking::SymDockProtocol::hurry ( bool const  hurry)

Skip population of the score map.

References hurry_.

Referenced by set_default().

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::make_dockmcm_mover ( core::pose::Pose const &  pose,
protocols::moves::MoverOP  repack_mover,
protocols::moves::MoverOP  rigbod_mover,
core::kinematics::MoveMapOP  movemap,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo 
) const

Setup Docking Monte Carlo mover.

std::string protocols::symmetric_docking::SymDockProtocol::mover_name ( )
void protocols::symmetric_docking::SymDockProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
void protocols::symmetric_docking::SymDockProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::symmetric_docking::SymDockProtocol::recover_sidechains ( core::pose::Pose pose,
const core::pose::Pose native_pose 

Recover sidechains from the native pose.

References protocols::simple_moves::ReturnSidechainMover::apply(), docking_score_pack_, rtmin_, and protocols::symmetric_docking::TR().

Referenced by apply().

void protocols::symmetric_docking::SymDockProtocol::register_options ( )
void protocols::symmetric_docking::SymDockProtocol::score_only ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockProtocol::set_default ( )
void protocols::symmetric_docking::SymDockProtocol::set_dock_ppk ( bool  dock_ppk_in)

References dock_ppk_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin ( bool  dock_rtmin_in)

Setters for Protocol Options.

References rtmin_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_fullatom ( bool const  fullatom_in)
void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_high_in)
void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_high_in,
core::scoring::ScoreFunctionOP  docking_score_pack_in 
void protocols::symmetric_docking::SymDockProtocol::set_local_refine ( bool const  local_refine_in)
void protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_low_in)

References docking_low_, and docking_score_low_.

Referenced by parse_my_tag().

void protocols::symmetric_docking::SymDockProtocol::set_max_repeats ( core::Size const  max_repeats_in)

References max_repeats_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_sc_min ( bool  sc_min_in)

References sc_min_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_view ( bool  view_in)

References view_.

Referenced by parse_my_tag(), and SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

Set Task Factory for Packing.

References init_task_factory_.

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::task_factory ( ) const

Methods for task factory?

References init_task_factory_.

Referenced by parse_my_tag().

core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockProtocol::task_factory ( )

References init_task_factory_.

Member Data Documentation

bool protocols::symmetric_docking::SymDockProtocol::autofoldtree_

Modified Docking foldtree for symmetry.

bool protocols::symmetric_docking::SymDockProtocol::design_

Allow design of partner 2 during docking.

Referenced by apply(), and design().

bool protocols::symmetric_docking::SymDockProtocol::dock_ppk_

Referenced by set_default(), and set_dock_ppk().

protocols::symmetric_docking::SymDockingHiResOP protocols::symmetric_docking::SymDockProtocol::docking_high_

Referenced by apply(), and set_highres_scorefxn().

protocols::symmetric_docking::SymDockingLowResOP protocols::symmetric_docking::SymDockProtocol::docking_low_

Child protocols - low resolution and high resolution docking & for packing.

Referenced by apply(), and set_lowres_scorefxn().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_min_
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_low_

Scorefunctions used during the protocol.

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), set_default(), set_lowres_scorefxn(), and SymDockProtocol().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_pack_
bool protocols::symmetric_docking::SymDockProtocol::fullatom_

Data about the protocol.

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::hurry_

Sip population of the score map.

Referenced by apply(), and hurry().

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::init_task_factory_

Used to restrict packer task during docking.

Referenced by apply(), and task_factory().

bool protocols::symmetric_docking::SymDockProtocol::local_refine_

Referenced by apply(), clone(), and set_local_refine().

core::Size protocols::symmetric_docking::SymDockProtocol::max_repeats_

Referenced by set_max_repeats().

moves::MonteCarloOP protocols::symmetric_docking::SymDockProtocol::mc_

Monte carlo object.

utility::vector1<core::Size> protocols::symmetric_docking::SymDockProtocol::movable_jumps_

Jumps for symmetric rigid body transformations.

bool protocols::symmetric_docking::SymDockProtocol::passed_highres_filter_

Referenced by apply(), set_default(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::passed_lowres_filter_

Filters for structures during protocols.

Referenced by apply(), set_default(), and set_local_refine().

bool protocols::symmetric_docking::SymDockProtocol::rtmin_
bool protocols::symmetric_docking::SymDockProtocol::sc_min_

Referenced by set_sc_min().

std::map< std::string, core::Real > protocols::symmetric_docking::SymDockProtocol::score_map_

For scorefile output.

Referenced by apply(), and docking_highres_filter().

bool protocols::symmetric_docking::SymDockProtocol::view_

Initialize the graphics viewer (opengl)

Referenced by clone(), and set_view().

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