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protocols::swa::protein::StepWiseProteinResidueSampler Class Reference

#include <StepWiseProteinResidueSampler.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinResidueSampler:
Inheritance graph
Collaboration diagram for protocols::swa::protein::StepWiseProteinResidueSampler:
Collaboration graph

Public Member Functions

 StepWiseProteinResidueSampler (utility::vector1< Size > const &moving_residues, utility::vector1< core::id::TorsionID > const &which_torsions, utility::vector1< utility::vector1< core::Real > > const &main_chain_torsion_set_lists)
 StepWiseProteinResidueSampler (utility::vector1< Size > const &moving_residues, utility::vector1< core::id::TorsionID > const &which_torsions, utility::vector1< utility::vector1< core::Real > > const &main_chain_torsion_set_lists, Size const which_jump, utility::vector1< core::kinematics::Jump > const &jumps)
 ~StepWiseProteinResidueSampler ()
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void set_silent_file (std::string const &setting)
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
void set_use_green_packer (bool const &setting)
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
void set_do_prepack (bool const &setting)
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
core::io::silent::SilentFileDataOPsilent_file_data ()
- 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

Private Member Functions

void sample_residues (core::pose::Pose &pose)
void quick_output (core::pose::Pose &pose, std::string const &tag)
void initialize_moving_residues_including_junction (Size const &nres)
void initialize_green_packer (core::Size const &nres)
void initialize_for_regular_packer (core::pose::Pose &pose)
void figure_out_neighbors (core::pose::Pose &pose, utility::vector1< bool > &residues_allowed_to_be_packed)
void reinstate_side_chain_angles (core::pose::Pose &pose, core::pose::Pose const &src_pose)
void apply_regular_packer (core::pose::Pose &pose)

Private Attributes

utility::vector1< Size > const moving_residues_
< core::id::TorsionID > const 
< utility::vector1< core::Real > > 
core::scoring::ScoreFunctionOP scorefxn_
protocols::simple_moves::GreenPackerOP green_packer_
bool use_green_packer_
bool use_packer_instead_of_rotamer_trials_
bool pack_at_neighbors_only_
bool do_prepack_
core::pack::task::PackerTaskOP pack_task_
core::pose::PoseOP pose_prepack_
std::string silent_file_
core::io::silent::SilentFileDataOP sfd_
utility::vector1< core::Sizecalc_rms_res_
Size const which_jump_
< core::kinematics::Jump

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 std::list< std::string > Strings
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::swa::protein::StepWiseProteinResidueSampler::StepWiseProteinResidueSampler ( utility::vector1< Size > const &  moving_residues,
utility::vector1< core::id::TorsionID > const &  which_torsions,
utility::vector1< utility::vector1< core::Real > > const &  main_chain_torsion_set_lists 
protocols::swa::protein::StepWiseProteinResidueSampler::StepWiseProteinResidueSampler ( utility::vector1< Size > const &  moving_residues,
utility::vector1< core::id::TorsionID > const &  which_torsions,
utility::vector1< utility::vector1< core::Real > > const &  main_chain_torsion_set_lists,
Size const  which_jump,
utility::vector1< core::kinematics::Jump > const &  jumps 
protocols::swa::protein::StepWiseProteinResidueSampler::~StepWiseProteinResidueSampler ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinResidueSampler::apply ( core::pose::Pose pose_to_visualize)
void protocols::swa::protein::StepWiseProteinResidueSampler::apply_regular_packer ( core::pose::Pose pose)
void protocols::swa::protein::StepWiseProteinResidueSampler::figure_out_neighbors ( core::pose::Pose pose,
utility::vector1< bool > &  residues_allowed_to_be_packed 
std::string protocols::swa::protein::StepWiseProteinResidueSampler::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinResidueSampler::initialize_for_regular_packer ( core::pose::Pose pose)
void protocols::swa::protein::StepWiseProteinResidueSampler::initialize_green_packer ( core::Size const &  nres)

References green_packer_, moving_residues_, scorefxn_, and protocols::TR().

Referenced by apply().

void protocols::swa::protein::StepWiseProteinResidueSampler::initialize_moving_residues_including_junction ( Size const &  nres)
void protocols::swa::protein::StepWiseProteinResidueSampler::quick_output ( core::pose::Pose pose,
std::string const &  tag 
void protocols::swa::protein::StepWiseProteinResidueSampler::reinstate_side_chain_angles ( core::pose::Pose pose,
core::pose::Pose const &  src_pose 
void protocols::swa::protein::StepWiseProteinResidueSampler::sample_residues ( core::pose::Pose pose)
void protocols::swa::protein::StepWiseProteinResidueSampler::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

void protocols::swa::protein::StepWiseProteinResidueSampler::set_do_prepack ( bool const &  setting)

References do_prepack_.

void protocols::swa::protein::StepWiseProteinResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

void protocols::swa::protein::StepWiseProteinResidueSampler::set_silent_file ( std::string const &  setting)

References silent_file_.

void protocols::swa::protein::StepWiseProteinResidueSampler::set_use_green_packer ( bool const &  setting)

References use_green_packer_.

void protocols::swa::protein::StepWiseProteinResidueSampler::set_use_packer_instead_of_rotamer_trials ( bool const &  setting)
core::io::silent::SilentFileDataOP & protocols::swa::protein::StepWiseProteinResidueSampler::silent_file_data ( )

References sfd_.

Member Data Documentation

utility::vector1< core::Size > protocols::swa::protein::StepWiseProteinResidueSampler::calc_rms_res_
bool protocols::swa::protein::StepWiseProteinResidueSampler::do_prepack_
protocols::simple_moves::GreenPackerOP protocols::swa::protein::StepWiseProteinResidueSampler::green_packer_
utility::vector1< core::kinematics::Jump > protocols::swa::protein::StepWiseProteinResidueSampler::jumps_
utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinResidueSampler::main_chain_torsion_set_lists_
utility::vector1< Size > const protocols::swa::protein::StepWiseProteinResidueSampler::moving_residues_
bool protocols::swa::protein::StepWiseProteinResidueSampler::pack_at_neighbors_only_

Referenced by apply_regular_packer().

core::pack::task::PackerTaskOP protocols::swa::protein::StepWiseProteinResidueSampler::pack_task_
core::pose::PoseOP protocols::swa::protein::StepWiseProteinResidueSampler::pose_prepack_
core::scoring::ScoreFunctionOP protocols::swa::protein::StepWiseProteinResidueSampler::scorefxn_
core::io::silent::SilentFileDataOP protocols::swa::protein::StepWiseProteinResidueSampler::sfd_
std::string protocols::swa::protein::StepWiseProteinResidueSampler::silent_file_

Referenced by sample_residues(), and set_silent_file().

bool protocols::swa::protein::StepWiseProteinResidueSampler::use_green_packer_
bool protocols::swa::protein::StepWiseProteinResidueSampler::use_packer_instead_of_rotamer_trials_
Size const protocols::swa::protein::StepWiseProteinResidueSampler::which_jump_

Referenced by sample_residues().

utility::vector1< core::id::TorsionID > const protocols::swa::protein::StepWiseProteinResidueSampler::which_torsions_

Referenced by sample_residues().

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