Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD Class Reference

#include <LoopMover_CCD.hh>

Inheritance diagram for protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD:
Inheritance graph
[legend]

Public Member Functions

 LoopMover_Perturb_CCD ()
 
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in)
 
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn, core::fragment::FragSetOP fragset)
 
 ~LoopMover_Perturb_CCD () override
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
void set_default_settings ()
 
virtual protocols::loops::LoopsCOP get_loops () const
 
virtual
core::scoring::ScoreFunctionOP 
get_scorefxn () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::loops::loop_mover::IndependentLoopMover
 IndependentLoopMover ()
 
 IndependentLoopMover (LoopsOP loops_in)
 
 IndependentLoopMover (utility::vector1< bool > const &selection)
 
 IndependentLoopMover (LoopsFileData const &lfd)
 
 IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops)
 
 ~IndependentLoopMover () override
 
void set_defaults ()
 
void apply (core::pose::Pose &pose) override
 Apply the loop-build protocol to the input pose. More...
 
void set_build_attempts_ (int value)
 Accessors: More...
 
void set_grow_attempts_ (int value)
 
void set_accept_aborted_loops_ (bool value)
 
void set_strict_loops (bool value)
 
void set_random_order_ (bool value)
 
void set_build_all_loops_ (bool value)
 
void set_loop_combine_rate_ (core::Real value)
 
int get_build_attempts () const
 
int get_grow_attempts () const
 
bool get_accept_aborted_loops () const
 
bool get_strict_loops () const
 
bool get_random_order () const
 
bool get_build_all_loops () const
 
bool get_loop_combine_rate () const
 
bool get_all_loops_closed () const
 
LoopResult get_last_LoopResult () const
 
- Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
 LoopMover ()
 
 LoopMover (protocols::loops::LoopsOP loops_in)
 
 LoopMover (protocols::loops::LoopsFileData const &loops_from_file)
 
 LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 
 LoopMover (LoopMover const &rhs)
 copy ctor More...
 
LoopMoveroperator= (LoopMover const &rhs)
 assignment operator More...
 
 ~LoopMover () override
 
void set_guarded_loops_not_in_charge ()
 Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...
 
void set_scorefxn (const core::scoring::ScoreFunctionOP score_in)
 
const
core::scoring::ScoreFunctionOP
scorefxn () const
 
void loops (protocols::loops::LoopsOP lptr)
 Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...
 
void loops (LoopsFileData const &loop_file_data)
 Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...
 
void loops (protocols::loops::loops_definers::LoopsDefinerOP setting)
 
void loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 Set the guarded_loops pointer. More...
 
protocols::loops::LoopsCOP loops () const
 Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
 
protocols::loops::LoopsOP loops ()
 non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
 
const utility::vector1
< core::fragment::FragSetOP > & 
frag_libs () const
 
core::conformation::torsion_bin_string torsion_features_string (core::pose::Pose const &pose) const
 create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object). More...
 
virtual void set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
 Extend a loop. More...
 
void add_fragments (core::fragment::FragSetOP fragset)
 add a fragment set More...
 
void clear_fragments ()
 clear the list of fragment sets More...
 
MoveMapOP const & false_movemap () const
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
 
void false_movemap (MoveMapOP const &mm)
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
 
checkpoint::CheckPointerOPget_checkpoints ()
 
- 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual 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...
 

Protected Member Functions

loop_mover::LoopResult model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop) override
 
basic::Tracer & tr () const override
 
- Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
core::Size enforce_false_movemap (MoveMapOP &mm) const
 import the false_movemap's explicit False settings into the given MoveMap More...
 
void set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
 allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...
 
bool use_loops_from_observer_cache () const
 
void set_use_loops_from_observer_cache (bool const loops_from_observer_cache)
 
void resolve_loop_indices (core::pose::Pose const &p)
 Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. More...
 
- 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...
 

Protected Attributes

std::vector
< core::fragment::FragSetOP
frag_libs_
 

Additional Inherited Members

- Public Types inherited from protocols::loops::loop_mover::LoopMover
typedef core::kinematics::MoveMapOP MoveMapOP
 
- 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
 

Detailed Description

the main function to model one single loop in centroid mode. The modeling algorithm is fragment_ccd_min_trial, which consists of perturbing the loop conformation by fragment insertion , then close the loop by CCD loop closure, then minimize the loop conformation and finally subject it to Monte Carlo acceptance or rejection. The loop conformation will be initialized as extended conformation if it is specified in the loop definition, resembling ab initio loop modeling in real practice. The loop has to be long enough for inserting certain length of fragments.

Constructor & Destructor Documentation

protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD ( )
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD ( protocols::loops::LoopsOP  loops_in)
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn 
)
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn,
core::fragment::FragSetOP  fragset 
)
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::~LoopMover_Perturb_CCD ( )
overridedefault

Member Function Documentation

protocols::moves::MoverOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::clone ( ) const
overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

protocols::loops::LoopsCOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::get_loops ( void  ) const
virtual
std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::loops::loop_mover::IndependentLoopMover.

References mover_name().

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::get_scorefxn ( ) const
virtual
loop_mover::LoopResult protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop ( core::pose::Pose pose,
protocols::loops::Loop const &  loop 
)
overrideprotectedvirtual

Implements protocols::loops::loop_mover::IndependentLoopMover.

References protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), protocols::moves::MonteCarlo::boltzmann(), protocols::loops::ccd_close_loops(), core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, core::pose::Pose::fold_tree(), frag_libs_, protocols::moves::Mover::get_native_pose(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::Residue::is_bonded(), core::kinematics::FoldTree::is_cutpoint(), protocols::loops::Loop::is_extended(), core::pose::symmetry::is_symmetric(), protocols::loops::Loop::is_terminal(), protocols::loops::loop_rmsd(), protocols::loops::loops_set_move_map(), core::conformation::Residue::lower_connect_atom(), protocols::moves::MonteCarlo::lowest_score_pose(), protocols::mean_field::min(), core::conformation::membrane::out, protocols::moves::MonteCarlo::recover_low(), core::pose::Pose::residue(), protocols::loops::loop_mover::LoopMover::scorefxn(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_scores(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_mover::Success, core::scoring::Energies::total_energies(), tr(), core::conformation::Residue::upper_connect_atom(), and core::scoring::EMapVector::weighted_string_of().

std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::mover_name ( )
static
void protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::set_default_settings ( )
inline

Referenced by LoopMover_Perturb_CCD().

void protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References get_loops(), and get_scorefxn().

Referenced by protocols::loops::loop_mover::perturb::operator<<().

basic::Tracer & protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::tr ( ) const
overrideprotectedvirtual

Member Data Documentation

std::vector< core::fragment::FragSetOP > protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::frag_libs_
protected

Referenced by model_loop().


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