Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::hybridization::FoldTreeHybridize Class Reference

#include <FoldTreeHybridize.hh>

Public Member Functions

 FoldTreeHybridize ()
 
 FoldTreeHybridize (core::Size const initial_template_index, utility::vector1< core::pose::PoseOP > const &template_poses, utility::vector1< core::Real > const &template_weights, utility::vector1< protocols::loops::Loops > const &template_chunks, utility::vector1< protocols::loops::Loops > const &template_contigs, core::fragment::FragSetOP fragments_small_in, core::fragment::FragSetOP fragments_big_in)
 
void init ()
 
void setup_for_parser ()
 Extract information from a setup mover. More...
 
void revert_loops_to_original (core::pose::Pose &pose, Loops loops)
 
void set_loops_to_virt_ala (core::pose::Pose &pose, Loops loops)
 
Real gap_distance (Size Seq_gap)
 
void add_gap_constraints_to_pose (core::pose::Pose &pose, Loops const &chunks, int gap_edge_shift=0, Real stdev=0.1)
 
void restore_original_foldtree (core::pose::Pose &pose)
 
void setup_foldtree (core::pose::Pose &pose)
 
numeric::xyzVector< Realcenter_of_mass (core::pose::Pose const &pose)
 
void translate_virt_to_CoM (core::pose::Pose &pose)
 
utility::vector1< core::Realget_residue_weights_for_1mers (core::pose::Pose &pose)
 
utility::vector1< core::Realget_residue_weights_for_small_frags (core::pose::Pose &pose)
 
utility::vector1< core::Realget_residue_weights_for_big_frags (core::pose::Pose &pose)
 
void set_constraint_file (std::string cst_file_in)
 
void set_increase_cycles (core::Real increase_cycles_in)
 
void set_stage1_1_cycles (core::Size stage1_1_cycles_in)
 
void set_stage1_2_cycles (core::Size stage1_2_cycles_in)
 
void set_stage1_3_cycles (core::Size stage1_3_cycles_in)
 
void set_stage1_4_cycles (core::Size stage1_4_cycles_in)
 
void set_add_non_init_chunks (bool add_non_init_chunks_in)
 
void set_domain_assembly (bool domain_assembly_in)
 
void set_add_hetatm (bool add_hetatm_in, core::Real hetatm_self_cst_weight_in, core::Real hetatm_prot_cst_weight_in)
 
void set_frag_1mer_insertion_weight (core::Real frag_1mer_insertion_weight_in)
 
void set_small_frag_insertion_weight (core::Real small_frag_insertion_weight_in)
 
void set_big_frag_insertion_weight (core::Real big_frag_insertion_weight_in)
 
void set_chunk_insertion_weight (core::Real chunk_insertion_weight_in)
 
void set_frag_weight_aligned (core::Real frag_weight_aligned_in)
 
void set_auto_frag_insertion_weight (bool auto_frag_insertion_weight_in)
 
void set_max_registry_shift (core::Size max_registry_shift_in)
 
void set_top_n_big_frag (core::Size top_n_big_frag_in)
 
void set_top_n_small_frag (core::Size top_n_small_frag_in)
 
void set_pairings_file (std::string pairings_file_in)
 
void set_sheets (utility::vector1< core::Size > sheets_in)
 
void set_random_sheets (utility::vector1< core::Size > random_sheets_in)
 
void set_filter_templates (bool filter_templates_in)
 
void set_scorefunction (core::scoring::ScoreFunctionOP const scorefxn)
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory_in)
 
void set_user_csts (utility::vector1< core::Size > user_csts_in)
 
void setup_scorefunctions (core::scoring::ScoreFunctionOP score0, core::scoring::ScoreFunctionOP score1, core::scoring::ScoreFunctionOP score2, core::scoring::ScoreFunctionOP score5, core::scoring::ScoreFunctionOP score3)
 
void apply (core::pose::Pose &pose)
 
std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
utility::vector1< std::pair
< core::Size, core::Size > > 
get_strand_pairs ()
 
std::set< core::Sizeget_pairings_residues ()
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void normalize_template_wts ()
 
void auto_frag_insertion_weight (WeightedFragmentTrialMoverOP &frag_1mer_trial_mover, WeightedFragmentTrialMoverOP &small_frag_trial_mover, WeightedFragmentTrialMoverOP &big_frag_trial_mover)
 
utility::vector1< core::Sizeget_jump_anchors ()
 
void add_strand_pairings ()
 
void add_strand_pairing (core::scoring::dssp::Pairing const &pairing)
 
void filter_templates (std::set< core::Size > const &templates_to_remove)
 
void superimpose_strand_pairings_to_templates (core::pose::Pose &pose)
 
core::Size map_pdb_info_number (const core::pose::Pose &pose, core::Size pdb_res)
 
protocols::simple_moves::ClassicFragmentMoverOP get_pairings_jump_mover ()
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual void parse_my_tag (utility::tag::TagCOP const, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 

Private Attributes

HybridizeSetupOP hybridize_setup_
 
core::Real increase_cycles_
 
core::Size stage1_1_cycles_
 
core::Size stage1_2_cycles_
 
core::Size stage1_3_cycles_
 
core::Size stage1_4_cycles_
 
core::Real frag_1mer_insertion_weight_
 
core::Real small_frag_insertion_weight_
 
core::Real big_frag_insertion_weight_
 
core::Real chunk_insertion_weight_
 
bool add_non_init_chunks_
 
bool domain_assembly_
 
bool add_hetatm_
 
core::Real hetatm_self_cst_weight_
 
core::Real hetatm_prot_cst_weight_
 
core::Real frag_weight_aligned_
 
bool auto_frag_insertion_weight_
 
core::Size max_registry_shift_
 
std::string cst_file_
 
bool initialize_pose_by_templates_
 
bool realign_domains_
 
core::Size initial_template_index_
 
core::scoring::ScoreFunctionOP scorefxn_
 
utility::vector1< core::Realtemplate_wts_
 
utility::vector1
< core::pose::PoseOP
template_poses_
 
utility::vector1
< protocols::loops::Loops
template_chunks_
 
utility::vector1
< protocols::loops::Loops
template_contigs_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_1mer_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_small_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_big_
 
Loops ss_chunks_pose_
 
core::Size top_n_big_frag_
 
core::Size top_n_small_frag_
 
std::string pairings_file_
 
utility::vector1< core::Sizesheets_
 
utility::vector1< core::Sizerandom_sheets_
 
bool filter_templates_
 
std::string target_sequence_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
strand_pairs_
 
std::set< core::Sizestrand_pairings_template_indices_
 
std::set< core::Sizetemplates_with_incorrect_strand_pairings_
 
protocols::jumping::JumpSample jump_sample_
 
core::fragment::FragSetOP jump_frags_
 
std::set< core::Sizefloating_pairs_
 
bool overlap_chainbreaks_
 
HybridizeFoldtreeDynamic foldtree_mover_
 
core::pose::PoseOP native_
 
utility::vector1< boolresidue_sample_template_
 
utility::vector1< boolresidue_sample_abinitio_
 
utility::vector1< core::Sizeresidue_max_registry_shift_
 
core::pack::task::TaskFactoryOP task_factory_
 
utility::vector1< core::Sizeuser_csts_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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 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::hybridization::FoldTreeHybridize::FoldTreeHybridize ( )
protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize ( core::Size const  initial_template_index,
utility::vector1< core::pose::PoseOP > const &  template_poses,
utility::vector1< core::Real > const &  template_weights,
utility::vector1< protocols::loops::Loops > const &  template_chunks,
utility::vector1< protocols::loops::Loops > const &  template_contigs,
core::fragment::FragSetOP  fragments_small_in,
core::fragment::FragSetOP  fragments_big_in 
)

Member Function Documentation

void protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose ( core::pose::Pose pose,
Loops const &  chunks,
int  gap_edge_shift = 0,
Real  stdev = 0.1 
)
void protocols::hybridization::FoldTreeHybridize::add_strand_pairing ( core::scoring::dssp::Pairing const &  pairing)
private
void protocols::hybridization::FoldTreeHybridize::add_strand_pairings ( )
private
void protocols::hybridization::FoldTreeHybridize::apply ( core::pose::Pose pose)
virtual

Implements protocols::moves::Mover.

References protocols::moves::accept_reject, add_hetatm_, protocols::moves::MoverContainer::add_mover(), protocols::hybridization::add_non_protein_cst(), add_strand_pairings(), protocols::hybridization::all_chunks, protocols::moves::RepeatMover::apply(), protocols::moves::WhileMover::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::moves::Mover::apply(), protocols::moves::RandomMover::apply(), protocols::simple_moves::FragmentMover::apply_at_all_positions(), core::scoring::atom_pair_constraint, auto_frag_insertion_weight(), big_frag_insertion_weight_, core::chemical::CENTROID_ROT, core::scoring::ScoreFunction::clone(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), cst_file_, floating_pairs_, frag_1mer_insertion_weight_, frag_libs_1mer_, frag_libs_big_, frag_libs_small_, gdtmm, protocols::hybridization::get_gdtmm(), get_jump_anchors(), protocols::hybridization::get_num_residues_nonvirt(), get_pairings_jump_mover(), get_pairings_residues(), get_residue_weights_for_1mers(), get_residue_weights_for_big_frags(), get_residue_weights_for_small_frags(), core::conformation::Residue::has(), hetatm_prot_cst_weight_, hetatm_self_cst_weight_, hybridize_setup_, I, jumps::increase_chainbreak, increase_cycles_, initial_template_index_, initialize_pose_by_templates_, jumps::invrate_jump_move, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), protocols::moves::TrialMover::keep_stats_type(), core::scoring::linear_chainbreak, max_registry_shift_, numeric::mod(), native_, option, core::scoring::overlap_chainbreak, protocols::forge::methods::overlap_chainbreak(), overlap_chainbreaks_, pack_rotamers(), core::pack::task::TaskFactory::push_back(), protocols::hybridization::random_chunk, protocols::moves::MonteCarlo::recover_low(), core::pose::Pose::remove_constraints(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), residue_max_registry_shift_, residue_sample_abinitio_, residue_sample_template_, restore_original_foldtree(), protocols::moves::MonteCarlo::score_function(), scorefxn_, core::pose::Pose::sequence(), protocols::moves::MonteCarlo::set_autotemp(), protocols::moves::MonteCarlo::set_temperature(), protocols::hybridization::ChunkTrialMover::set_template(), core::pose::setPoseExtraScore(), protocols::hybridization::setup_centroid_constraints(), setup_foldtree(), setup_for_parser(), setup_scorefunctions(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::moves::MonteCarlo::show_counters(), protocols::moves::MonteCarlo::show_scores(), protocols::hybridization::AllResiduesChanged::show_unmoved(), abinitio::skip_convergence_check, small_frag_insertion_weight_, ss_chunks_pose_, stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, cm::hybridize::stage1_4_cenrot_score, stage1_4_cycles_, strand_pairings_template_indices_, superimpose_strand_pairings_to_templates(), target_sequence_, template_chunks_, template_poses_, template_wts_, top_n_big_frag_, core::pose::Pose::total_residue(), protocols::hybridization::TR, translate_virt_to_CoM(), user, and user_csts_.

void protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight ( WeightedFragmentTrialMoverOP frag_1mer_trial_mover,
WeightedFragmentTrialMoverOP small_frag_trial_mover,
WeightedFragmentTrialMoverOP big_frag_trial_mover 
)
private
numeric::xyzVector< Real > protocols::hybridization::FoldTreeHybridize::center_of_mass ( core::pose::Pose const &  pose)
protocols::moves::MoverOP protocols::hybridization::FoldTreeHybridize::clone ( ) const
privatevirtual

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 FoldTreeHybridize().

void protocols::hybridization::FoldTreeHybridize::filter_templates ( std::set< core::Size > const &  templates_to_remove)
private
protocols::moves::MoverOP protocols::hybridization::FoldTreeHybridize::fresh_instance ( ) const
privatevirtual

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.

References FoldTreeHybridize().

Real protocols::hybridization::FoldTreeHybridize::gap_distance ( Size  Seq_gap)
utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::get_jump_anchors ( )
private
std::string protocols::hybridization::FoldTreeHybridize::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

protocols::simple_moves::ClassicFragmentMoverOP protocols::hybridization::FoldTreeHybridize::get_pairings_jump_mover ( )
private
std::set< core::Size > protocols::hybridization::FoldTreeHybridize::get_pairings_residues ( )

References strand_pairs_.

Referenced by apply(), and get_jump_anchors().

utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_1mers ( core::pose::Pose pose)
utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags ( core::pose::Pose pose)
utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_small_frags ( core::pose::Pose pose)
utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::FoldTreeHybridize::get_strand_pairs ( )
inline
void protocols::hybridization::FoldTreeHybridize::init ( void  )
core::Size protocols::hybridization::FoldTreeHybridize::map_pdb_info_number ( const core::pose::Pose pose,
core::Size  pdb_res 
)
private
void protocols::hybridization::FoldTreeHybridize::normalize_template_wts ( )
private
void protocols::hybridization::FoldTreeHybridize::parse_my_tag ( utility::tag::TagCOP const  tag,
basic::datacache::DataMap data,
filters::Filters_map const &  filters,
moves::Movers_map const &  movers,
Pose const &  pose 
)
privatevirtual
void protocols::hybridization::FoldTreeHybridize::restore_original_foldtree ( core::pose::Pose pose)
void protocols::hybridization::FoldTreeHybridize::revert_loops_to_original ( core::pose::Pose pose,
Loops  loops 
)
void protocols::hybridization::FoldTreeHybridize::set_add_hetatm ( bool  add_hetatm_in,
core::Real  hetatm_self_cst_weight_in,
core::Real  hetatm_prot_cst_weight_in 
)
inline

Referenced by setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::set_add_non_init_chunks ( bool  add_non_init_chunks_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_auto_frag_insertion_weight ( bool  auto_frag_insertion_weight_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_big_frag_insertion_weight ( core::Real  big_frag_insertion_weight_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_chunk_insertion_weight ( core::Real  chunk_insertion_weight_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_constraint_file ( std::string  cst_file_in)
inline

Referenced by setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::set_domain_assembly ( bool  domain_assembly_in)
inline

Referenced by setup_for_parser().

void protocols::hybridization::FoldTreeHybridize::set_filter_templates ( bool  filter_templates_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_frag_1mer_insertion_weight ( core::Real  frag_1mer_insertion_weight_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_frag_weight_aligned ( core::Real  frag_weight_aligned_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_increase_cycles ( core::Real  increase_cycles_in)
inline

Referenced by parse_my_tag().

void protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala ( core::pose::Pose pose,
Loops  loops 
)
void protocols::hybridization::FoldTreeHybridize::set_max_registry_shift ( core::Size  max_registry_shift_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_pairings_file ( std::string  pairings_file_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_random_sheets ( utility::vector1< core::Size random_sheets_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_scorefunction ( core::scoring::ScoreFunctionOP const  scorefxn)
inline

Referenced by init(), and parse_my_tag().

void protocols::hybridization::FoldTreeHybridize::set_sheets ( utility::vector1< core::Size sheets_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_small_frag_insertion_weight ( core::Real  small_frag_insertion_weight_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_stage1_1_cycles ( core::Size  stage1_1_cycles_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_stage1_2_cycles ( core::Size  stage1_2_cycles_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_stage1_3_cycles ( core::Size  stage1_3_cycles_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_stage1_4_cycles ( core::Size  stage1_4_cycles_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_task_factory ( core::pack::task::TaskFactoryOP  task_factory_in)

References task_factory_.

void protocols::hybridization::FoldTreeHybridize::set_top_n_big_frag ( core::Size  top_n_big_frag_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_top_n_small_frag ( core::Size  top_n_small_frag_in)
inline
void protocols::hybridization::FoldTreeHybridize::set_user_csts ( utility::vector1< core::Size user_csts_in)
inline
void protocols::hybridization::FoldTreeHybridize::setup_foldtree ( core::pose::Pose pose)
void protocols::hybridization::FoldTreeHybridize::setup_for_parser ( )
void protocols::hybridization::FoldTreeHybridize::setup_scorefunctions ( core::scoring::ScoreFunctionOP  score0,
core::scoring::ScoreFunctionOP  score1,
core::scoring::ScoreFunctionOP  score2,
core::scoring::ScoreFunctionOP  score5,
core::scoring::ScoreFunctionOP  score3 
)
void protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates ( core::pose::Pose pose)
private
void protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM ( core::pose::Pose pose)

Member Data Documentation

bool protocols::hybridization::FoldTreeHybridize::add_hetatm_
private

Referenced by apply(), and init().

bool protocols::hybridization::FoldTreeHybridize::add_non_init_chunks_
private

Referenced by init(), parse_my_tag(), and setup_foldtree().

bool protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight_
private
core::Real protocols::hybridization::FoldTreeHybridize::big_frag_insertion_weight_
private
core::Real protocols::hybridization::FoldTreeHybridize::chunk_insertion_weight_
private

Referenced by auto_frag_insertion_weight(), and init().

std::string protocols::hybridization::FoldTreeHybridize::cst_file_
private

Referenced by apply().

bool protocols::hybridization::FoldTreeHybridize::domain_assembly_
private
bool protocols::hybridization::FoldTreeHybridize::filter_templates_
private
std::set< core::Size > protocols::hybridization::FoldTreeHybridize::floating_pairs_
private
HybridizeFoldtreeDynamic protocols::hybridization::FoldTreeHybridize::foldtree_mover_
private
core::Real protocols::hybridization::FoldTreeHybridize::frag_1mer_insertion_weight_
private
utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_1mer_
private
utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_big_
private
utility::vector1< core::fragment::FragSetOP > protocols::hybridization::FoldTreeHybridize::frag_libs_small_
private
core::Real protocols::hybridization::FoldTreeHybridize::frag_weight_aligned_
private
core::Real protocols::hybridization::FoldTreeHybridize::hetatm_prot_cst_weight_
private

Referenced by apply(), and init().

core::Real protocols::hybridization::FoldTreeHybridize::hetatm_self_cst_weight_
private

Referenced by apply(), and init().

HybridizeSetupOP protocols::hybridization::FoldTreeHybridize::hybridize_setup_
private
core::Real protocols::hybridization::FoldTreeHybridize::increase_cycles_
private

Referenced by apply(), and init().

core::Size protocols::hybridization::FoldTreeHybridize::initial_template_index_
private
bool protocols::hybridization::FoldTreeHybridize::initialize_pose_by_templates_
private

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

core::fragment::FragSetOP protocols::hybridization::FoldTreeHybridize::jump_frags_
private
protocols::jumping::JumpSample protocols::hybridization::FoldTreeHybridize::jump_sample_
private
core::Size protocols::hybridization::FoldTreeHybridize::max_registry_shift_
private

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

core::pose::PoseOP protocols::hybridization::FoldTreeHybridize::native_
private

Referenced by apply(), and init().

bool protocols::hybridization::FoldTreeHybridize::overlap_chainbreaks_
private

Referenced by apply(), and init().

std::string protocols::hybridization::FoldTreeHybridize::pairings_file_
private
utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::random_sheets_
private
bool protocols::hybridization::FoldTreeHybridize::realign_domains_
private
utility::vector1<core::Size> protocols::hybridization::FoldTreeHybridize::residue_max_registry_shift_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<bool> protocols::hybridization::FoldTreeHybridize::residue_sample_abinitio_
private
utility::vector1<bool> protocols::hybridization::FoldTreeHybridize::residue_sample_template_
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::FoldTreeHybridize::scorefxn_
private

Referenced by apply(), and setup_scorefunctions().

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::sheets_
private
core::Real protocols::hybridization::FoldTreeHybridize::small_frag_insertion_weight_
private
Loops protocols::hybridization::FoldTreeHybridize::ss_chunks_pose_
private

Referenced by apply().

core::Size protocols::hybridization::FoldTreeHybridize::stage1_1_cycles_
private

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

core::Size protocols::hybridization::FoldTreeHybridize::stage1_2_cycles_
private

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

core::Size protocols::hybridization::FoldTreeHybridize::stage1_3_cycles_
private

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

core::Size protocols::hybridization::FoldTreeHybridize::stage1_4_cycles_
private

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

std::set< core::Size > protocols::hybridization::FoldTreeHybridize::strand_pairings_template_indices_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::FoldTreeHybridize::strand_pairs_
private
std::string protocols::hybridization::FoldTreeHybridize::target_sequence_
private

Referenced by add_strand_pairing(), and apply().

core::pack::task::TaskFactoryOP protocols::hybridization::FoldTreeHybridize::task_factory_
private

Referenced by set_task_factory().

utility::vector1< protocols::loops::Loops > protocols::hybridization::FoldTreeHybridize::template_chunks_
private
utility::vector1< protocols::loops::Loops > protocols::hybridization::FoldTreeHybridize::template_contigs_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::FoldTreeHybridize::template_poses_
private
utility::vector1< core::Real > protocols::hybridization::FoldTreeHybridize::template_wts_
private
std::set< core::Size > protocols::hybridization::FoldTreeHybridize::templates_with_incorrect_strand_pairings_
private
core::Size protocols::hybridization::FoldTreeHybridize::top_n_big_frag_
private
core::Size protocols::hybridization::FoldTreeHybridize::top_n_small_frag_
private

Referenced by auto_frag_insertion_weight(), and init().

utility::vector1< core::Size > protocols::hybridization::FoldTreeHybridize::user_csts_
private

Referenced by apply().


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