Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::frag_picker::nonlocal::NonlocalFrags Class Reference

#include <NonlocalFrags.hh>

Inheritance diagram for protocols::frag_picker::nonlocal::NonlocalFrags:
Inheritance graph

Public Member Functions

 NonlocalFrags ()
 Constructs a new mover. More...
void apply (core::pose::Pose &pose) override
 Finds interacting non-local fragment pairs. More...
std::string get_name () const override
 Returns the name of this mover. More...
protocols::moves::MoverOP clone () const override
 Creates a copy of this instance. More...
protocols::moves::MoverOP fresh_instance () const override
 Creates a new instance by calling the no-argument constructor. 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...
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 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions

static void register_options ()
 Registers applicable options. More...
- 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 initialize ()
bool recover_checkpoint (std::string const &tag, core::pose::Pose &pose)
void write_checkpoint (std::string const &tag, std::string const &data)
void read_checkpoint_file ()

Private Attributes

bool single_chain_
bool relax_input_
bool relax_input_with_coordinate_constraints_
core::Size relax_frags_repeats_
std::string checkpointfile_
std::map< std::string, std::string > checkpoints_map_
utility::vector1< core::Sizefrag_sizes_
core::Size min_seq_sep_
core::Real ca_dist_squared_
core::Size min_contacts_per_res_
core::Real max_rmsd_after_relax_
core::Real max_ddg_score_
bool output_frags_pdbs_
bool output_idealized_

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

◆ NonlocalFrags()

protocols::frag_picker::nonlocal::NonlocalFrags::NonlocalFrags ( )

Constructs a new mover.

References initialize().

Member Function Documentation

◆ apply()

void protocols::frag_picker::nonlocal::NonlocalFrags::apply ( core::pose::Pose pose)

Finds interacting non-local fragment pairs.

Implements protocols::moves::Mover.

References core::pose::add_comment(), core::scoring::angle_constraint, protocols::idealize::IdealizeMover::apply(), core::scoring::atom_pair_constraint, ca_dist_squared_, core::scoring::CA_rmsd(), core::conformation::Residue::chain(), protocols::idealize::IdealizeMover::chainbreaks(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::create_subpose(), protocols::jd2::current_input_tag(), protocols::jd2::JobDistributor::current_job(), protocols::jd2::current_output_name(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::pose::Pose::dump_pdb(), protocols::idealize::IdealizeMover::fast(), frag_sizes_, protocols::relax::generate_relax_from_cmd(), protocols::jd2::JobDistributor::get_instance(), core::scoring::get_score_function(), core::conformation::Residue::has(), core::conformation::Conformation::insert_chain_ending(), core::conformation::Residue::is_protein(), protocols::jd2::JobDistributor::job_outputter(), max_ddg_score_, max_rmsd_after_relax_, min_contacts_per_res_, min_seq_sep_, core::kinematics::FoldTree::new_jump(), output_frags_pdbs_, output_idealized_, core::pose::Pose::pdb_info(), recover_checkpoint(), relax_frags_repeats_, relax_input_, relax_input_with_coordinate_constraints_, core::pose::Pose::replace_residue(), core::scoring::res_type_constraint, core::pose::Pose::residue(), protocols::hybridization::score, core::kinematics::FoldTree::set_jump_atoms(), single_chain_, core::pose::Pose::size(), protocols::frag_picker::nonlocal::TR(), write_checkpoint(), and core::conformation::Residue::xyz().

◆ clone()

protocols::moves::MoverOP protocols::frag_picker::nonlocal::NonlocalFrags::clone ( ) const

Creates a copy of this instance.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::frag_picker::nonlocal::NonlocalFrags::fresh_instance ( ) const

Creates a new instance by calling the no-argument constructor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::frag_picker::nonlocal::NonlocalFrags::get_name ( ) const

Returns the name of this mover.

Implements protocols::moves::Mover.

◆ initialize()

void protocols::frag_picker::nonlocal::NonlocalFrags::initialize ( )

◆ read_checkpoint_file()

void protocols::frag_picker::nonlocal::NonlocalFrags::read_checkpoint_file ( )

◆ recover_checkpoint()

bool protocols::frag_picker::nonlocal::NonlocalFrags::recover_checkpoint ( std::string const &  tag,
core::pose::Pose pose 

◆ register_options()

void protocols::frag_picker::nonlocal::NonlocalFrags::register_options ( )

Registers applicable options.

◆ write_checkpoint()

void protocols::frag_picker::nonlocal::NonlocalFrags::write_checkpoint ( std::string const &  tag,
std::string const &  data 

Member Data Documentation

◆ ca_dist_squared_

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::ca_dist_squared_

Referenced by apply(), and initialize().

◆ checkpointfile_

std::string protocols::frag_picker::nonlocal::NonlocalFrags::checkpointfile_

◆ checkpoints_map_

std::map< std::string, std::string > protocols::frag_picker::nonlocal::NonlocalFrags::checkpoints_map_

◆ frag_sizes_

utility::vector1<core::Size> protocols::frag_picker::nonlocal::NonlocalFrags::frag_sizes_

Referenced by apply(), and initialize().

◆ max_ddg_score_

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::max_ddg_score_

Referenced by apply(), and initialize().

◆ max_rmsd_after_relax_

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::max_rmsd_after_relax_

Referenced by apply(), and initialize().

◆ min_contacts_per_res_

core::Size protocols::frag_picker::nonlocal::NonlocalFrags::min_contacts_per_res_

Referenced by apply(), and initialize().

◆ min_seq_sep_

core::Size protocols::frag_picker::nonlocal::NonlocalFrags::min_seq_sep_

Referenced by apply(), and initialize().

◆ output_frags_pdbs_

bool protocols::frag_picker::nonlocal::NonlocalFrags::output_frags_pdbs_

Referenced by apply(), and initialize().

◆ output_idealized_

bool protocols::frag_picker::nonlocal::NonlocalFrags::output_idealized_

Referenced by apply(), and initialize().

◆ relax_frags_repeats_

core::Size protocols::frag_picker::nonlocal::NonlocalFrags::relax_frags_repeats_

Referenced by apply(), and initialize().

◆ relax_input_

bool protocols::frag_picker::nonlocal::NonlocalFrags::relax_input_

Referenced by apply(), and initialize().

◆ relax_input_with_coordinate_constraints_

bool protocols::frag_picker::nonlocal::NonlocalFrags::relax_input_with_coordinate_constraints_

Referenced by apply(), and initialize().

◆ single_chain_

bool protocols::frag_picker::nonlocal::NonlocalFrags::single_chain_

Referenced by apply(), and initialize().

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