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protocols::flexpep_docking::FlexPepDockingProtocol Class Reference

#include <FlexPepDockingProtocol.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingProtocol:
Inheritance graph
[legend]

Public Member Functions

 FlexPepDockingProtocol (core::Size const rb_jump_in=1)
 constructor More...
 
 FlexPepDockingProtocol (core::Size const rb_jump_in, bool const fullatom, bool const view=false)
 
 ~FlexPepDockingProtocol () override
 
void set_default ()
 setup that is called from constructor More...
 
void view (bool view_in)
 setter More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) 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...
 
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 setup_foldtree (core::pose::Pose &pose)
 setup the peptide docking fold tree More...
 
void minimize_only (core::pose::Pose &pose, const std::string &min_type, const float min_func_tol)
 
void prepack_only (core::pose::Pose &pose, bool ppk_receptor, bool ppk_peptide)
 prepack protocol for flexpepdock More...
 
void set_receptor_constraints (core::pose::Pose &pose)
 
void set_allowed_moves ()
 
void random_peptide_phi_psi_perturbation (core::pose::Pose &pose)
 
void extend_peptide (core::pose::Pose &pose)
 
void place_peptide_on_binding_site (core::pose::Pose &pose)
 
void flip_in_pcs (core::pose::Pose &pose)
 
void SlideIntoContact (core::pose::Pose &pose, core::Vector translate_axis)
 
void random_rb_pert (core::pose::Pose &pose)
 
void small_moves (core::pose::Pose &pose)
 
void shear_moves (core::pose::Pose &pose)
 
void backrub_move (core::pose::Pose &pose)
 
void polyAla (core::pose::Pose &pose)
 
bool check_filters (core::pose::Pose &pose)
 
void calcMetrics (core::pose::Pose &pose)
 
void randomlySlidePeptideJump (core::pose::Pose &pose)
 
void torsions_monte_carlo_minimize (core::pose::Pose &pose, const int cycles, const std::string &min_type, const float minimization_threshold, const float min_func_tol)
 
void rigidbody_monte_carlo_minimize (core::pose::Pose &pose, const int cycles, const std::string &min_type, const float trans_magnitude, const float rot_magnitude, const float minimization_threshold, const float func_tol)
 
void peptide_random_loop_model (core::pose::Pose &pose)
 
void markInterfaceBySideChainContacts (ObjexxFCL::FArray1D_bool &native_interface_residues, core::Size distance) const
 
void markNativeInterface (ObjexxFCL::FArray1D_bool &superpos_partner, ObjexxFCL::FArray1D_bool &native_interface_residues, bool mark_receptor_interface) const
 
void addLowResStatistics (core::pose::Pose const &start_pose, core::pose::Pose &pose_after_lowres) const
 
void storeJobStatistics (core::pose::Pose const &start_pose, core::pose::Pose &pose_after_lowres, core::pose::Pose &final_pose)
 
void hires_fpdock_protocol (core::pose::Pose &pose)
 

Private Attributes

bool fullatom_
 information about the mode More...
 
core::Size rb_jump_
 the jump number across which to do rigid_body transformations More...
 
bool view_
 whether or not to initialize the viewer (for opengl) More...
 
bool is_fail_
 
FlexPepDockingFlags flags_
 
core::Size nres_receptor_
 
core::Size nres_peptide_
 
moves::MonteCarloOP mc_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP scorefxn_lowres_
 
FlexPepDockingPoseMetrics fpdock_metrics_
 
std::map< std::string, core::Realif_metrics_
 
core::pack::task::TaskFactoryOP allprotein_tf_
 
core::pack::task::TaskFactoryOP interface_tf_
 
protocols::minimization_packing::PackRotamersMoverOP interface_packer_
 
core::kinematics::MoveMapOP movemap_
 
core::kinematics::MoveMapOP movemap_minimizer_
 
protocols::comparative_modeling::LoopRelaxMoverOP loop_relax_mover_
 
bool is_trimmed_loops_
 

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

protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol ( core::Size const  rb_jump_in = 1)

constructor

References set_default().

Referenced by clone().

protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol ( core::Size const  rb_jump_in,
bool const  fullatom,
bool const  view = false 
)

References fullatom_, set_default(), view(), and view_.

protocols::flexpep_docking::FlexPepDockingProtocol::~FlexPepDockingProtocol ( )
overridedefault

Member Function Documentation

void protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics ( core::pose::Pose const &  start_pose,
core::pose::Pose pose_after_lowres 
) const
private
void protocols::flexpep_docking::FlexPepDockingProtocol::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline(), protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), backrub_move(), protocols::flexpep_docking::FlexPepDockingFlags::backrub_opt, check_filters(), protocols::flexpep_docking::FlexPepDockingFlags::clone(), core::pose::Pose::conformation(), protocols::flexpep_docking::FlexPepDockingFlags::design_peptide, protocols::flexpep_docking::FlexPepDockingFlags::extend, extend_peptide(), flags_, flip_in_pcs(), core::pose::Pose::fold_tree(), fpdock_metrics_, protocols::moves::Mover::get_native_pose(), hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio, protocols::flexpep_docking::FlexPepDockingFlags::lowres_preoptimize, protocols::flexpep_docking::FlexPepDockingFlags::min_only, protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb, minimize_only(), movemap_, protocols::flexpep_docking::FlexPepDockingFlags::no_prepack1, protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2, core::import_pose::PDB_file, protocols::flexpep_docking::FlexPepDockingFlags::pep_refine, protocols::flexpep_docking::FlexPepDockingFlags::peptide_anchors, protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model, protocols::flexpep_docking::FlexPepDockingFlags::place_peptide, place_peptide_on_binding_site(), core::import_pose::pose_from_file(), protocols::flexpep_docking::FlexPepDockingFlags::ppk_only, prepack_only(), random_peptide_phi_psi_perturbation(), protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert, random_rb_pert(), protocols::flexpep_docking::FlexPepDockingFlags::randomRBstart, rb_jump_, protocols::flexpep_docking::FlexPepDockingFlags::rbMCM, protocols::flexpep_docking::FlexPepDockingFlags::recal_foldtree, protocols::flexpep_docking::FlexPepDockingFlags::receptor_anchor_pos, protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct(), core::pose::Pose::residue(), protocols::flexpep_docking::FlexPepDockingFlags::sample_pc, scorefxn_, scorefxn_lowres_, set_allowed_moves(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::set_flags(), protocols::moves::Mover::set_native_pose(), set_receptor_constraints(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), setup_foldtree(), SlideIntoContact(), protocols::flexpep_docking::FlexPepDockingFlags::slideintocontact, storeJobStatistics(), protocols::flexpep_docking::FlexPepDockingFlags::torsionsMCM, protocols::TR(), protocols::flexpep_docking::FlexPepDockingFlags::updateChains(), protocols::flexpep_docking::FlexPepDockingFlags::valid_anchors(), protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct(), view_, and core::conformation::Residue::xyz().

void protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::calcMetrics ( core::pose::Pose pose)
private
bool protocols::flexpep_docking::FlexPepDockingProtocol::check_filters ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::flexpep_docking::FlexPepDockingProtocol::clone ( ) const
overridevirtual

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 flags_, FlexPepDockingProtocol(), fullatom_, rb_jump_, scorefxn_, and view_.

void protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs ( core::pose::Pose pose)
private
std::string protocols::flexpep_docking::FlexPepDockingProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts ( ObjexxFCL::FArray1D_bool &  native_interface_residues,
core::Size  distance 
) const
private
void protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface ( ObjexxFCL::FArray1D_bool &  superpos_partner,
ObjexxFCL::FArray1D_bool &  native_interface_residues,
bool  mark_receptor_interface 
) const
private
void protocols::flexpep_docking::FlexPepDockingProtocol::minimize_only ( core::pose::Pose pose,
const std::string &  min_type,
const float  min_func_tol 
)
private
std::string protocols::flexpep_docking::FlexPepDockingProtocol::mover_name ( )
static
void protocols::flexpep_docking::FlexPepDockingProtocol::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 protocols::flexpep_docking::FlexPepDockingFlags::backrub_opt, protocols::flexpep_docking::FlexPepDockingFlags::boost_fa_atr, core::import_pose::centroid_pose_from_pdb(), protocols::flexpep_docking::FlexPepDockingFlags::design_peptide, protocols::flexpep_docking::FlexPepDockingFlags::extend, flags_, protocols::flexpep_docking::FlexPepDockingFlags::frag3_weight, protocols::flexpep_docking::FlexPepDockingFlags::frag5_weight, protocols::flexpep_docking::FlexPepDockingFlags::frag9_weight, protocols::flexpep_docking::FlexPepDockingFlags::hb_filter, protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter, protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio, protocols::flexpep_docking::FlexPepDockingFlags::lowres_preoptimize, protocols::flexpep_docking::FlexPepDockingFlags::mcm_cycles, protocols::flexpep_docking::FlexPepDockingFlags::min_only, protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb, protocols::flexpep_docking::FlexPepDockingFlags::no_prepack1, protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2, core::scoring::parse_score_function(), core::import_pose::PDB_file, protocols::flexpep_docking::FlexPepDockingFlags::pep_refine, protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model, protocols::flexpep_docking::FlexPepDockingFlags::place_peptide, core::import_pose::pose_from_file(), protocols::flexpep_docking::FlexPepDockingFlags::ppk_only, protocols::flexpep_docking::FlexPepDockingFlags::pSer2Asp_centroid, protocols::flexpep_docking::FlexPepDockingFlags::pSer2Glu_centroid, protocols::flexpep_docking::FlexPepDockingFlags::ramp_fa_rep, protocols::flexpep_docking::FlexPepDockingFlags::ramp_rama, protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert, protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert_size, protocols::flexpep_docking::FlexPepDockingFlags::randomRBstart, protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size, protocols::flexpep_docking::FlexPepDockingFlags::rb_trans_size, protocols::flexpep_docking::FlexPepDockingFlags::rbMCM, protocols::flexpep_docking::FlexPepDockingFlags::recal_foldtree, protocols::flexpep_docking::FlexPepDockingFlags::rep_ramp_cycles, protocols::flexpep_docking::FlexPepDockingFlags::sample_pc, protocols::flexpep_docking::FlexPepDockingFlags::score_filter, protocols::flexpep_docking::FlexPepDockingFlags::score_only, scorefxn_, scorefxn_lowres_, protocols::moves::Mover::set_native_pose(), protocols::flexpep_docking::FlexPepDockingFlags::set_peptide_chain(), protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain(), protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_peptide(), protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_receptor(), protocols::flexpep_docking::FlexPepDockingFlags::slideintocontact, protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range, and protocols::flexpep_docking::FlexPepDockingFlags::torsionsMCM.

void protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::polyAla ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only ( core::pose::Pose pose,
bool  ppk_receptor,
bool  ppk_peptide 
)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::random_rb_pert ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize ( core::pose::Pose pose,
const int  cycles,
const std::string &  min_type,
const float  trans_magnitude,
const float  rot_magnitude,
const float  minimization_threshold,
const float  func_tol 
)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves ( )
private
void protocols::flexpep_docking::FlexPepDockingProtocol::set_default ( )
void protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::shear_moves ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::SlideIntoContact ( core::pose::Pose pose,
core::Vector  translate_axis 
)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::small_moves ( core::pose::Pose pose)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics ( core::pose::Pose const &  start_pose,
core::pose::Pose pose_after_lowres,
core::pose::Pose final_pose 
)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize ( core::pose::Pose pose,
const int  cycles,
const std::string &  min_type,
const float  minimization_threshold,
const float  min_func_tol 
)
private
void protocols::flexpep_docking::FlexPepDockingProtocol::view ( bool  view_in)
inline

setter

References view_.

Referenced by FlexPepDockingProtocol().

Member Data Documentation

core::pack::task::TaskFactoryOP protocols::flexpep_docking::FlexPepDockingProtocol::allprotein_tf_
private
FlexPepDockingFlags protocols::flexpep_docking::FlexPepDockingProtocol::flags_
private
FlexPepDockingPoseMetrics protocols::flexpep_docking::FlexPepDockingProtocol::fpdock_metrics_
private
bool protocols::flexpep_docking::FlexPepDockingProtocol::fullatom_
private

information about the mode

Referenced by clone(), FlexPepDockingProtocol(), and set_default().

std::map< std::string, core::Real > protocols::flexpep_docking::FlexPepDockingProtocol::if_metrics_
private

Referenced by set_default(), and storeJobStatistics().

protocols::minimization_packing::PackRotamersMoverOP protocols::flexpep_docking::FlexPepDockingProtocol::interface_packer_
private
core::pack::task::TaskFactoryOP protocols::flexpep_docking::FlexPepDockingProtocol::interface_tf_
private
bool protocols::flexpep_docking::FlexPepDockingProtocol::is_fail_
private
bool protocols::flexpep_docking::FlexPepDockingProtocol::is_trimmed_loops_
private
protocols::comparative_modeling::LoopRelaxMoverOP protocols::flexpep_docking::FlexPepDockingProtocol::loop_relax_mover_
private
moves::MonteCarloOP protocols::flexpep_docking::FlexPepDockingProtocol::mc_
private
core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingProtocol::movemap_
private
core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingProtocol::movemap_minimizer_
private
core::Size protocols::flexpep_docking::FlexPepDockingProtocol::nres_peptide_
private
core::Size protocols::flexpep_docking::FlexPepDockingProtocol::nres_receptor_
private
core::Size protocols::flexpep_docking::FlexPepDockingProtocol::rb_jump_
private
core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingProtocol::scorefxn_
private
core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingProtocol::scorefxn_lowres_
private
bool protocols::flexpep_docking::FlexPepDockingProtocol::view_
private

whether or not to initialize the viewer (for opengl)

Referenced by apply(), clone(), FlexPepDockingProtocol(), set_default(), and view().


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