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protocols::enzdes::EnzdesFixBBProtocol Class Reference

#include <EnzdesFixBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFixBBProtocol:
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Collaboration diagram for protocols::enzdes::EnzdesFixBBProtocol:
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Public Member Functions

 EnzdesFixBBProtocol ()
 
 ~EnzdesFixBBProtocol ()
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
 EnzdesBaseProtocol ()
 
utility::vector1< Sizecatalytic_res (core::pose::Pose const &pose) const
 
std::set< Size > const & design_targets (core::pose::Pose const &pose) 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
 
virtual void remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)
 
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 ()
 
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::constraints::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 ~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
 
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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
static void register_options ()
 

Protected Attributes

bool start_from_random_rb_conf_
 
- 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_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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)
 

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFixBBProtocol::EnzdesFixBBProtocol ( )
protocols::enzdes::EnzdesFixBBProtocol::~EnzdesFixBBProtocol ( )

Member Function Documentation

void protocols::enzdes::EnzdesFixBBProtocol::apply ( core::pose::Pose pose)
virtual
std::string protocols::enzdes::EnzdesFixBBProtocol::get_name ( ) const
virtual

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

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

void protocols::enzdes::EnzdesFixBBProtocol::register_options ( )
static

Member Data Documentation

bool protocols::enzdes::EnzdesFixBBProtocol::start_from_random_rb_conf_
protected

Referenced by apply().


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