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Rosetta
2016.11
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#include <EnzdesFlexBBProtocol.hh>
Public Member Functions | |
EnzdesFlexBBProtocol () | |
~EnzdesFlexBBProtocol () | |
void | apply (core::pose::Pose &pose) |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
bool | is_flexible (core::Size seqpos) const |
bool | is_remodelable (core::Size seqpos) const |
void | get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions) const |
core::pack::task::PackerTaskOP | modified_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task) |
void | test_flexbb_rotamer_sets (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) |
void | remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap) |
void | add_flexible_region (core::Size start, core::Size end, core::pose::Pose const &pose, bool clear_existing) |
EnzdesFlexibleRegionCOP | enz_flexible_region (core::Size region) const |
toolbox::match_enzdes_util::EnzdesLoopsFileCOP | enz_loops_file () const |
void | generate_ensemble_for_region (core::pose::Pose &pose, core::Size region) |
bool | minimize_flexible_region (core::pose::Pose &pose, core::Size region, core::scoring::ScoreFunctionCOP scorefxn, std::set< core::Size > const &chi_to_move, bool const including_CA_angles, core::Real min_tolerance) |
void | generate_alc_ensemble_for_region (core::pose::Pose &pose, core::Size region) |
void | generate_backrub_ensemble_for_region (core::pose::Pose &pose, core::Size region) |
void | determine_flexible_regions (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) |
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EnzdesBaseProtocol () | |
utility::vector1< Size > | catalytic_res (core::pose::Pose const &pose) const |
std::set< Size > const & | design_targets (core::pose::Pose const &pose) const |
utility::vector1< core::Size > | rb_min_jumps () const |
void | rb_min_jumps (utility::vector1< core::Size > const ) |
bool | is_catalytic_position (core::pose::Pose const &pose, core::Size const seqpos) const |
core::chemical::ResidueTypeSetCAP | restype_set () const |
void | generate_explicit_ligand_rotamer_poses (core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx) |
core::scoring::ScoreFunctionCOP | reduced_scorefxn () const |
core::scoring::ScoreFunctionOP | reduced_scorefxn () |
core::Real | design_targets_score (core::pose::Pose const &pose) const |
void | remove_enzdes_constraints (core::pose::Pose &pose, bool keep_covalent) const |
void | add_pregenerated_enzdes_constraints (core::pose::Pose &pose) const |
void | cst_minimize (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false) const |
core::pack::task::PackerTaskOP | create_enzdes_pack_task (core::pose::Pose &pose, bool design=true) |
void | setup_sequence_recovery_cache (core::pose::Pose &pose, core::pack::task::PackerTask const &task) const |
void | set_all_jumps_minimizable (bool const &setting) |
void | set_minimize_options (bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false) |
void | set_fix_cataa (bool const &setting) |
core::kinematics::MoveMapOP | create_enzdes_movemap (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false) const |
void | enzdes_pack (core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native) const |
void | set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn) |
void | setup_bbmin_ft_and_csts (core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id) const |
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LigandBaseProtocol () | |
virtual | ~LigandBaseProtocol () |
core::scoring::ScoreFunctionOP | get_scorefxn () |
core::scoring::ScoreFunctionCOP | get_scorefxn () const |
core::Size | get_ligand_jump_id (core::pose::Pose const &pose) const |
core::Size | get_ligand_id (core::pose::Pose const &pose) const |
Return the residue sequence number for our ligand. More... | |
core::Size | get_ligand_id (core::pose::Pose const &pose, core::Size jump_id) const |
Return the residue sequence number for our ligand. More... | |
void | restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const |
void | reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const |
reorders a fold tree such that movement in the mobile regions will More... | |
void | get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const |
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Mover () | |
virtual | ~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... | |
Mover (Mover const &other) | |
Mover & | operator= (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... | |
virtual 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) |
virtual MoverOP | clone () const |
Return a clone of the Mover object. More... | |
virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
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 Strings & | info () |
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... | |
virtual MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. 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... | |
Static Public Member Functions | |
static void | register_options () |
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static void | register_options () |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Protected Member Functions | |
bool | assemble_next_best_loop_combination (core::pose::Pose &pose) |
bool | hack_assemble_next_loop_combination (core::pose::Pose &pose) |
bool | recover_loops_from_file (core::pose::Pose const &pose) |
void | setup_catalytic_residue_minimization_for_region (core::pose::Pose const &pose, core::Size region) |
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void | setup_enzdes_constraints (core::pose::Pose &pose, bool allow_missing_remark_blocks) const |
void | enable_constraint_scoreterms () |
void | disable_constraint_scoreterms () |
function to disable constraint scoring terms: : this will leave eventual covalent connections set up by EnzConstraintIO untouched. More... | |
bool | exchange_ligands_in_pose (core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx) |
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core::scoring::ScoreFunctionOP | make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight) |
core::Vector | choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >) |
void | move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts) |
void | move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid) |
core::kinematics::MoveMapOP | make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const |
core::pack::task::PackerTaskOP | make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const |
Shared machinery for the next two. More... | |
core::pack::task::PackerTaskOP | make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const |
Receptor (interface?) plus ligand. More... | |
core::pack::task::PackerTaskOP | make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const |
Just ligand, not the receptor. More... | |
void | find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const |
void | find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const |
core::scoring::constraints::ConstraintOP | restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const |
void | setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms) |
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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 | |
utility::vector1 < EnzdesFlexibleRegionOP > | flex_regions_ |
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core::scoring::ScoreFunctionOP | reduced_sfxn_ |
std::set< core::Size > | design_targets_ |
bool | include_all_design_targets_in_design_interface_ |
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bool | use_soft_rep_ |
core::scoring::ScoreFunctionOP | scorefxn_ |
core::scoring::ScoreFunctionOP | hard_scorefxn_ |
core::scoring::ScoreFunctionOP | soft_scorefxn_ |
core::Real | sc_interface_padding_ |
core::Real | bb_interface_cutoff_ |
core::pack::rotamer_set::UnboundRotamersOperationOP | unboundrot_ |
Additional Inherited Members | |
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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::string > | Strings |
protocols::enzdes::EnzdesFlexBBProtocol::EnzdesFlexBBProtocol | ( | ) |
protocols::enzdes::EnzdesFlexBBProtocol::~EnzdesFlexBBProtocol | ( | ) |
void protocols::enzdes::EnzdesFlexBBProtocol::add_flexible_region | ( | core::Size | start, |
core::Size | end, | ||
core::pose::Pose const & | pose, | ||
bool | clear_existing | ||
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Reimplemented from protocols::ligand_docking::LigandBaseProtocol.
References protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), determine_flexible_regions(), core::fragment::dump_frames_as_pdb(), protocols::enzdes::EnzdesBaseProtocol::enable_constraint_scoreterms(), protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(), core::scoring::fa_sol, flex_regions_, fragment_counters_, generate_ensemble_for_region(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), core::conformation::Residue::is_ligand(), core::scoring::mm_bend, modified_task(), pack_region_ala_pose_, core::pose::Pose::pdb_info(), recover_loops_from_file(), protocols::enzdes::enzutil::recreate_task(), core::pose::Pose::residue(), protocols::ligand_docking::LigandBaseProtocol::scorefxn_, protocols::moves::Mover::set_native_pose(), protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints(), protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn_, core::pose::Pose::total_residue(), protocols::enzdes::tr(), and core::pose::Pose::update_residue_neighbors().
Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().
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figure out which combination of loop conformations is the next most promising one
References flex_regions_, fragment_counters_, and protocols::enzdes::tr().
void protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions | ( | core::pose::Pose const & | pose, |
core::pack::task::PackerTaskCOP | task | ||
) |
References enz_loops_file_, flex_regions_, fragment_counters_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::moves::Mover::get_self_ptr(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), core::conformation::Residue::is_polymer(), protocols::loops::Loops::loop_file_name(), protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector(), core::pose::Pose::observer_cache(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::datacache::CacheableObserverType::SPECIAL_SEGMENTS_OBSERVER, core::pose::Pose::total_residue(), protocols::enzdes::tr(), protocols::loops::Loops::v_begin(), and protocols::loops::Loops::v_end().
Referenced by apply().
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References flex_regions_.
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References enz_loops_file_.
void protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region | ( | core::pose::Pose & | pose, |
core::Size | region | ||
) |
References apply(), protocols::moves::MonteCarlo::boltzmann(), catmin_mover_, core::pose::Pose::energies(), flex_regions_, kinematic_mover_, protocols::moves::MonteCarlo::last_accepted_pose(), loop_ensemble_size_, loopgen_trials_, protocols::moves::MonteCarlo::lowest_score_pose(), mc_kt_high_, mc_kt_low_, minimize_cats_, protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::enzdes::EnzdesBaseProtocol::restype_set(), protocols::hybridization::score, protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_counters(), protocols::loops::start, protocols::loops::stop, core::scoring::Energies::total_energies(), core::scoring::total_score, and protocols::enzdes::tr().
Referenced by generate_ensemble_for_region().
void protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region | ( | core::pose::Pose & | pose, |
core::Size | region | ||
) |
References apply(), protocols::moves::MonteCarlo::boltzmann(), brub_max_atoms_, brub_min_atoms_, brub_mover_, brub_pivot_atoms_, catmin_mover_, flex_regions_, protocols::moves::MonteCarlo::last_accepted_pose(), loop_ensemble_size_, loopgen_trials_, protocols::moves::MonteCarlo::lowest_score_pose(), mc_kt_high_, mc_kt_low_, minimize_cats_, protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::enzdes::EnzdesBaseProtocol::restype_set(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_counters(), protocols::loops::start, and protocols::enzdes::tr().
Referenced by generate_ensemble_for_region().
void protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region | ( | core::pose::Pose & | pose, |
core::Size | region | ||
) |
References core::chemical::ResidueType::aa(), core::chemical::aa_pro, brub_mover_, catmin_movemap_, catmin_mover_, core::pose::Pose::chain(), core::scoring::fa_rep, flex_regions_, core::pose::Pose::fold_tree(), generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), kinematic_mover_, loop_ensemble_size_, loopgen_trials_, minimize_cats_, core::kinematics::FoldTree::new_jump(), protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), core::pose::Pose::residue_type(), setup_catalytic_residue_minimization_for_region(), core::pose::Pose::total_residue(), and protocols::enzdes::tr().
Referenced by apply().
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Each derived class must specify its name. The class name.
Reimplemented from protocols::enzdes::EnzdesBaseProtocol.
void protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues | ( | core::pose::Pose const & | pose, |
utility::vector1< bool > & | residue_positions | ||
) | const |
As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.
References core::pose::Pose::energies(), core::chemical::ResidueType::is_disulfide_bonded(), is_flexible(), is_remodelable(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().
Referenced by modified_task().
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returns false if the last combination is reached, true otherwise
References flex_regions_, and fragment_counters_.
bool protocols::enzdes::EnzdesFlexBBProtocol::is_flexible | ( | core::Size | seqpos | ) | const |
References flex_regions_, and protocols::loops::start.
Referenced by get_tenA_neighbor_residues(), and modified_task().
bool protocols::enzdes::EnzdesFlexBBProtocol::is_remodelable | ( | core::Size | seqpos | ) | const |
References flex_regions_, and protocols::loops::start.
Referenced by get_tenA_neighbor_residues(), and modified_task().
bool protocols::enzdes::EnzdesFlexBBProtocol::minimize_flexible_region | ( | core::pose::Pose & | pose, |
core::Size | region, | ||
core::scoring::ScoreFunctionCOP | scorefxn, | ||
std::set< core::Size > const & | chi_to_move, | ||
bool const | including_CA_angles, | ||
core::Real | min_tolerance | ||
) |
References flex_regions_.
core::pack::task::PackerTaskOP protocols::enzdes::EnzdesFlexBBProtocol::modified_task | ( | core::pose::Pose const & | pose, |
core::pack::task::PackerTask const & | orig_task | ||
) |
References core::chemical::aa_cys, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), core::pack::task::PackerTask::design_residue(), core::chemical::DISULFIDE, get_tenA_neighbor_residues(), core::conformation::Residue::has_variant_type(), core::pack::task::PackerTask::IGEdgeReweights(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), is_flexible(), is_remodelable(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rotamer_operations(), core::pack::task::ResidueLevelTask::rotamer_set_operation_begin(), core::pack::task::ResidueLevelTask::rotamer_set_operation_end(), core::pose::Pose::total_residue(), and protocols::enzdes::tr().
Referenced by apply().
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References protocols::moves::Mover::register_options().
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Reimplemented from protocols::enzdes::EnzdesBaseProtocol.
References flex_regions_, and protocols::enzdes::EnzdesBaseProtocol::remap_resid().
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References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, catmin_movemap_, catmin_mover_, catmin_sfxn_, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::fa_dun, core::scoring::fa_rep, flex_regions_, protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), protocols::loops::start, and protocols::enzdes::tr().
Referenced by generate_ensemble_for_region().
void protocols::enzdes::EnzdesFlexBBProtocol::test_flexbb_rotamer_sets | ( | core::pose::Pose const & | pose, |
core::pack::task::PackerTaskCOP | task | ||
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Referenced by generate_backrub_ensemble_for_region().
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Referenced by generate_backrub_ensemble_for_region().
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Referenced by EnzdesFlexBBProtocol(), generate_backrub_ensemble_for_region(), and generate_ensemble_for_region().
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Referenced by EnzdesFlexBBProtocol(), and generate_backrub_ensemble_for_region().
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Referenced by generate_ensemble_for_region(), and setup_catalytic_residue_minimization_for_region().
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Referenced by setup_catalytic_residue_minimization_for_region().
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Referenced by determine_flexible_regions(), and enz_loops_file().
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Referenced by add_flexible_region(), apply(), assemble_next_best_loop_combination(), determine_flexible_regions(), enz_flexible_region(), EnzdesFlexBBProtocol(), generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), generate_ensemble_for_region(), hack_assemble_next_loop_combination(), is_flexible(), is_remodelable(), minimize_flexible_region(), recover_loops_from_file(), remap_resid(), and setup_catalytic_residue_minimization_for_region().
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Referenced by generate_alc_ensemble_for_region(), and generate_ensemble_for_region().
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Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().
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Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().
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Referenced by apply().