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protocols::enzdes::EnzdesFlexBBProtocol Class Reference

#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexBBProtocol:
Inheritance graph
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Public Member Functions

 EnzdesFlexBBProtocol ()
 
 ~EnzdesFlexBBProtocol () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 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) override
 
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)
 
- Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
 EnzdesBaseProtocol ()
 
utility::vector1< core::Sizecatalytic_res (core::pose::Pose const &pose) const
 
std::set< core::Size > const & design_targets (core::pose::Pose const &pose) const
 
utility::vector1< core::Sizerb_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
 
- Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
 LigandBaseProtocol ()
 
 ~LigandBaseProtocol () override
 
LigandBaseProtocolOP shared_from_this ()
 
core::scoring::ScoreFunctionOP get_scorefxn ()
 
core::scoring::ScoreFunctionCOP get_scorefxn () const
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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 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 void register_options ()
 
- Static Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
static void register_options ()
 
- Static Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
static core::Size get_ligand_jump_id (core::pose::Pose const &pose)
 
static core::Size get_ligand_id (core::pose::Pose const &pose)
 Return the residue sequence number for our ligand. More...
 
static core::Size get_ligand_id (core::pose::Pose const &pose, core::Size jump_id)
 Return the residue sequence number for our ligand. 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...
 

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)
 
- Protected Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
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)
 
- Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
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)
 
- 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

utility::vector1
< EnzdesFlexibleRegionOP
flex_regions_
 
- Protected Attributes inherited from protocols::enzdes::EnzdesBaseProtocol
core::scoring::ScoreFunctionOP reduced_sfxn_
 
std::set< core::Sizedesign_targets_
 
bool include_all_design_targets_in_design_interface_
 
- Protected Attributes inherited from protocols::ligand_docking::LigandBaseProtocol
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_
 

Private Attributes

toolbox::match_enzdes_util::EnzdesLoopsFileCOP enz_loops_file_
 
utility::vector1< core::Sizefragment_counters_
 
core::pose::Pose pack_region_ala_pose_
 
utility::vector1< core::Realnative_fragment_bb_energies_
 
protocols::backrub::BackrubMoverOP brub_mover_
 
protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP kinematic_mover_
 
core::Real mc_kt_low_
 
core::Real mc_kt_high_
 
core::Size brub_min_atoms_
 
core::Size brub_max_atoms_
 
core::Size loop_ensemble_size_
 
core::Size loopgen_trials_
 
utility::vector1< std::string > brub_pivot_atoms_
 
bool minimize_cats_
 
core::kinematics::MoveMapOP catmin_movemap_
 
protocols::minimization_packing::MinMoverOP catmin_mover_
 
core::scoring::ScoreFunctionOP catmin_sfxn_
 

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
 

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFlexBBProtocol::EnzdesFlexBBProtocol ( )
protocols::enzdes::EnzdesFlexBBProtocol::~EnzdesFlexBBProtocol ( )
overridedefault

Member Function Documentation

void protocols::enzdes::EnzdesFlexBBProtocol::add_flexible_region ( core::Size  start,
core::Size  end,
core::pose::Pose const &  pose,
bool  clear_existing 
)
void protocols::enzdes::EnzdesFlexBBProtocol::apply ( core::pose::Pose )
overridevirtual
bool protocols::enzdes::EnzdesFlexBBProtocol::assemble_next_best_loop_combination ( core::pose::Pose pose)
protected

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 
)
EnzdesFlexibleRegionCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_flexible_region ( core::Size  region) const
inline

References flex_regions_.

toolbox::match_enzdes_util::EnzdesLoopsFileCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file ( ) const
inline

References enz_loops_file_.

void protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
void protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
void protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
std::string protocols::enzdes::EnzdesFlexBBProtocol::get_name ( ) const
overridevirtual

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::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::type().

Referenced by modified_task().

bool protocols::enzdes::EnzdesFlexBBProtocol::hack_assemble_next_loop_combination ( core::pose::Pose pose)
protected

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
bool protocols::enzdes::EnzdesFlexBBProtocol::is_remodelable ( core::Size  seqpos) const
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 
)
bool protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file ( core::pose::Pose const &  pose)
protected
void protocols::enzdes::EnzdesFlexBBProtocol::register_options ( )
static
void protocols::enzdes::EnzdesFlexBBProtocol::remap_resid ( core::pose::Pose const &  pose,
core::id::SequenceMapping const &  smap 
)
overridevirtual
void protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region ( core::pose::Pose const &  pose,
core::Size  region 
)
protected
void protocols::enzdes::EnzdesFlexBBProtocol::test_flexbb_rotamer_sets ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task 
)

Member Data Documentation

core::Size protocols::enzdes::EnzdesFlexBBProtocol::brub_max_atoms_
private
core::Size protocols::enzdes::EnzdesFlexBBProtocol::brub_min_atoms_
private
protocols::backrub::BackrubMoverOP protocols::enzdes::EnzdesFlexBBProtocol::brub_mover_
private
utility::vector1< std::string > protocols::enzdes::EnzdesFlexBBProtocol::brub_pivot_atoms_
private
core::kinematics::MoveMapOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_movemap_
private
protocols::minimization_packing::MinMoverOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_mover_
private
core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_sfxn_
private
toolbox::match_enzdes_util::EnzdesLoopsFileCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file_
private
utility::vector1< EnzdesFlexibleRegionOP > protocols::enzdes::EnzdesFlexBBProtocol::flex_regions_
protected
utility::vector1< core::Size > protocols::enzdes::EnzdesFlexBBProtocol::fragment_counters_
private
protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP protocols::enzdes::EnzdesFlexBBProtocol::kinematic_mover_
private
core::Size protocols::enzdes::EnzdesFlexBBProtocol::loop_ensemble_size_
private
core::Size protocols::enzdes::EnzdesFlexBBProtocol::loopgen_trials_
private
core::Real protocols::enzdes::EnzdesFlexBBProtocol::mc_kt_high_
private
core::Real protocols::enzdes::EnzdesFlexBBProtocol::mc_kt_low_
private
bool protocols::enzdes::EnzdesFlexBBProtocol::minimize_cats_
private
utility::vector1< core::Real > protocols::enzdes::EnzdesFlexBBProtocol::native_fragment_bb_energies_
private
core::pose::Pose protocols::enzdes::EnzdesFlexBBProtocol::pack_region_ala_pose_
private

Referenced by apply().


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