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protocols::comparative_modeling::LoopRelaxMover Class Reference

#include <LoopRelaxMover.hh>

Inheritance diagram for protocols::comparative_modeling::LoopRelaxMover:
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Public Member Functions

 LoopRelaxMover ()
 
 LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::Loops const &loops)
 Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
 
 LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::LoopsFileData const &loops_from_file)
 Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
 
 LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::GuardedLoopsFromFileOP guarded_loops)
 GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...
 
void apply (core::pose::Pose &pose) override
 Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used. More...
 
void scorefxns (core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn)
 
void fa_scorefxn (core::scoring::ScoreFunctionOP fa_scorefxn)
 
void cen_scorefxn (core::scoring::ScoreFunctionOP cen_scorefxn)
 
void cmd_line_csts (bool setting)
 
void copy_sidechains (bool setting)
 
void rebuild_filter (core::Real setting)
 
void n_rebuild_tries (core::Size setting)
 
void remodel (std::string val)
 
void intermedrelax (std::string val)
 
void refine (std::string val)
 
void relax (std::string val)
 
void resolve_loopfile_indices (core::pose::Pose const &pose)
 Must be called before the Loops data can be read from. More...
 
void loops (protocols::loops::LoopsOP const val)
 set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor More...
 
void loops_file_data (loops::LoopsFileData const &loopfiledata)
 Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called. More...
 
void frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
 
bool cmd_line_csts () const
 
bool copy_sidechains () const
 
core::Size n_rebuild_tries () const
 
core::Real rebuild_filter () const
 
protocols::loops::LoopsOP get_loops ()
 Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...
 
protocols::loops::LoopsCOP get_loops () const
 Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...
 
std::string remodel () const
 
std::string relax () const
 
std::string intermedrelax () const
 
std::string refine () const
 
utility::vector1
< core::fragment::FragSetOP
frag_libs () const
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void compute_rmsd (bool const c)
 
bool compute_rmsd () const
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) 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...
 
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 set_defaults_ ()
 

Private Attributes

bool cmd_line_csts_
 
bool copy_sidechains_
 
core::Size n_rebuild_tries_
 
core::Real rebuild_filter_
 
std::string remodel_
 
std::string intermedrelax_
 
std::string refine_
 
std::string relax_
 
loops::GuardedLoopsFromFileOP guarded_loops_
 
core::scoring::ScoreFunctionOP cen_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_
 
bool compute_rmsd_
 

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::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( )

References set_defaults_().

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( std::string const &  remodel,
std::string const &  intermedrelax,
std::string const &  refine,
std::string const &  relax,
loops::Loops const &  loops 
)

Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( std::string const &  remodel,
std::string const &  intermedrelax,
std::string const &  refine,
std::string const &  relax,
loops::LoopsFileData const &  loops_from_file 
)

Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( std::string const &  remodel,
std::string const &  intermedrelax,
std::string const &  refine,
std::string const &  relax,
loops::GuardedLoopsFromFileOP  guarded_loops 
)

GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

Member Function Documentation

void protocols::comparative_modeling::LoopRelaxMover::apply ( core::pose::Pose pose)
overridevirtual

Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used.

Implements protocols::moves::Mover.

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::viewer::add_conformation_viewer(), core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), protocols::loops::add_cutpoint_variants(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::loops::loop_mover::LoopMover::add_fragments(), core::scoring::angle_constraint, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), protocols::relax::MiniRelax::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::LoopRebuild::apply(), protocols::minimization_packing::PackRotamersMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::big_bin_constraint, core::id::AtomID::BOGUS_ATOM_ID(), core::scoring::CA_rmsd(), cen_scorefxn_, core::pose::Pose::center(), core::chemical::CENTROID_t, core::scoring::chainbreak, protocols::checkpoint::CheckPointer::checkpoint(), cmd_line_csts(), compute_rmsd(), core::pose::Pose::conformation(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, copy_sidechains(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::chemical::DISULFIDE, core::io::raw_data::DisulfideFile::disulfides(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), fa_scorefxn_, protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), frag_libs(), core::chemical::FULL_ATOM_t, protocols::relax::generate_relax_from_cmd(), protocols::loops::loop_mover::LoopMover::get_checkpoints(), protocols::moves::Mover::get_current_tag(), get_loops(), guarded_loops_, core::chemical::ResidueType::has(), core::conformation::Residue::has_variant_type(), core::pose::initialize_atomid_map(), intermedrelax(), core::pose::Pose::is_fullatom(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::loops::loop_rmsd(), loops(), core::pose::symmetry::make_residue_mask_symmetric(), core::pose::symmetry::make_symmetric_movemap(), protocols::mean_field::max(), protocols::moves::MS_SUCCESS, n_rebuild_tries(), core::scoring::native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), core::conformation::Residue::natoms(), core::scoring::overlap_chainbreak, core::scoring::pair, core::import_pose::PDB_file, protocols::comparative_modeling::pick_loops_chainbreak(), core::import_pose::pose_from_file(), rebuild_filter(), protocols::checkpoint::CheckPointer::recover_checkpoint(), refine(), relax(), remodel(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), core::id::AtomID::set(), protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_(), protocols::moves::Mover::set_current_tag(), protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_(), protocols::moves::Mover::set_last_move_status(), protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::IndependentLoopMover::set_random_order_(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), core::pose::set_ss_from_phipsi(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScore(), core::pose::Pose::size(), core::scoring::superimpose_pose(), core::util::switch_to_residue_type_set(), core::scoring::Energies::total_energies(), protocols::comparative_modeling::TR(), core::pose::virtual_type_for_pose(), and core::conformation::Atom::xyz().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::mpi_refinement::WorkUnit_KicCloser::run().

void protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn ( core::scoring::ScoreFunctionOP  cen_scorefxn)

References cen_scorefxn_.

Referenced by parse_my_tag(), and scorefxns().

protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::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.

void protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( bool  setting)
inline
bool protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( ) const
inline

References cmd_line_csts_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( bool const  c)
inline
bool protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( ) const
inline

References compute_rmsd_.

Referenced by apply(), parse_my_tag(), and set_defaults_().

void protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( bool  setting)
inline

References copy_sidechains_.

bool protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( ) const
inline

References copy_sidechains_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn ( core::scoring::ScoreFunctionOP  fa_scorefxn)
void protocols::comparative_modeling::LoopRelaxMover::frag_libs ( utility::vector1< core::fragment::FragSetOP new_libs)
utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs ( ) const

References frag_libs_.

Referenced by apply().

protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

protocols::loops::LoopsOP protocols::comparative_modeling::LoopRelaxMover::get_loops ( void  )

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

Referenced by protocols::indel::IndelOptimizationMover::apply(), and apply().

protocols::loops::LoopsCOP protocols::comparative_modeling::LoopRelaxMover::get_loops ( void  ) const

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

std::string protocols::comparative_modeling::LoopRelaxMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( std::string  val)
inline
std::string protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( ) const
inline

References intermedrelax_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::loops ( protocols::loops::LoopsOP const  val)

set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor

By setting the loops object directly, the requirement is relaxed that a Pose be first given to the LoopRelax object (through a call to apply() or resolve_loopfile_indices) before the get_loops() function may be called.

References guarded_loops_.

Referenced by protocols::indel::IndelOptimizationMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and apply().

void protocols::comparative_modeling::LoopRelaxMover::loops_file_data ( loops::LoopsFileData const &  loopfiledata)

Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called.

Set the loop file data. This will require that.

References guarded_loops_.

Referenced by protocols::loop_build::LoopBuildMover::setup_loop_definition().

std::string protocols::comparative_modeling::LoopRelaxMover::mover_name ( )
static
void protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( core::Size  setting)
inline

References n_rebuild_tries_.

core::Size protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( ) const
inline

References n_rebuild_tries_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::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 cen_scorefxn(), cen_scorefxn_, cmd_line_csts(), compute_rmsd(), copy_sidechains(), fa_scorefxn(), frag_libs_, guarded_loops_, intermedrelax(), protocols::loops::loops_definers::load_loop_definitions(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries(), core::scoring::parse_score_function(), protocols::loops::read_loop_fragments(), rebuild_filter(), refine(), relax(), and remodel().

void protocols::comparative_modeling::LoopRelaxMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( core::Real  setting)
inline

References rebuild_filter_.

core::Real protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( ) const
inline

References rebuild_filter_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::refine ( std::string  val)
inline
std::string protocols::comparative_modeling::LoopRelaxMover::refine ( ) const
inline

References refine_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::relax ( std::string  val)
inline
std::string protocols::comparative_modeling::LoopRelaxMover::relax ( ) const
inline

References relax_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::remodel ( std::string  val)
inline
std::string protocols::comparative_modeling::LoopRelaxMover::remodel ( ) const
inline

References remodel_.

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::resolve_loopfile_indices ( core::pose::Pose const &  pose)

Must be called before the Loops data can be read from.

References guarded_loops_.

void protocols::comparative_modeling::LoopRelaxMover::scorefxns ( core::scoring::ScoreFunctionOP  cen_scorefxn,
core::scoring::ScoreFunctionOP  fa_scorefxn 
)
void protocols::comparative_modeling::LoopRelaxMover::set_defaults_ ( )
private

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn_
private
bool protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts_
private

Referenced by cmd_line_csts(), and set_defaults_().

bool protocols::comparative_modeling::LoopRelaxMover::compute_rmsd_
private

Referenced by compute_rmsd().

bool protocols::comparative_modeling::LoopRelaxMover::copy_sidechains_
private

Referenced by copy_sidechains(), and set_defaults_().

core::scoring::ScoreFunctionOP protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn_
private

Referenced by apply(), fa_scorefxn(), and set_defaults_().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs_
private

Referenced by frag_libs(), and parse_my_tag().

loops::GuardedLoopsFromFileOP protocols::comparative_modeling::LoopRelaxMover::guarded_loops_
private
std::string protocols::comparative_modeling::LoopRelaxMover::intermedrelax_
private

Referenced by intermedrelax(), and set_defaults_().

core::Size protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries_
private

Referenced by n_rebuild_tries(), and set_defaults_().

core::Real protocols::comparative_modeling::LoopRelaxMover::rebuild_filter_
private

Referenced by rebuild_filter(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::refine_
private

Referenced by refine(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::relax_
private

Referenced by relax(), and set_defaults_().

std::string protocols::comparative_modeling::LoopRelaxMover::remodel_
private

Referenced by remodel(), and set_defaults_().


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