Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::packer::StepWisePacker Class Reference

#include <StepWisePacker.hh>

Inheritance diagram for protocols::stepwise::modeler::packer::StepWisePacker:
Inheritance graph

Public Member Functions

 StepWisePacker (utility::vector1< core::Size > const &working_moving_residues)
 ~StepWisePacker () override
void apply (core::pose::Pose &pose) override
 Apply the minimizer to one pose. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void do_packing (core::pose::Pose &pose)
void reset (core::pose::Pose const &pose)
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
void do_prepack (core::pose::Pose &pose)
void set_allow_virtual_side_chains (bool const &setting)
bool allow_virtual_side_chains () const
void set_allow_virtual_o2prime_hydrogens (bool const &setting)
bool allow_virtual_o2prime_hydrogens () const
void set_pack_all_side_chains (bool const &setting)
bool pack_all_side_chains () const
void set_pack_o2prime_hydrogens (bool const &setting)
bool pack_o2prime_hydrogens () const
bool working_pack_res_was_inputted () const
void set_pack_protein_side_chains (bool const &setting)
void set_working_pack_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const & working_pack_res () const
utility::vector1< core::Size > const & previous_working_pack_res () const
void figure_out_neighbors (core::pose::Pose &pose)
- 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

void reinstate_side_chain_angles (core::pose::Pose &pose, core::pose::Pose const &src_pose)
void setup_pack_task (core::pose::Pose const &pose)

Private Attributes

utility::vector1< core::Size > const working_moving_res_list_
core::scoring::ScoreFunctionCOP scorefxn_
bool use_packer_instead_of_rotamer_trials_
bool allow_virtual_side_chains_
bool allow_virtual_o2prime_hydrogens_
bool pack_o2prime_hydrogens_
core::pack::task::PackerTaskOP pack_task_
core::pose::PoseOP pose_init_
utility::vector1< core::Sizeworking_pack_res_
utility::vector1< core::Sizeprevious_working_pack_res_
bool working_pack_res_was_inputted_
bool pack_all_side_chains_
bool pack_protein_side_chains_

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
- 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

◆ StepWisePacker()

protocols::stepwise::modeler::packer::StepWisePacker::StepWisePacker ( utility::vector1< core::Size > const &  working_moving_residues)

◆ ~StepWisePacker()

protocols::stepwise::modeler::packer::StepWisePacker::~StepWisePacker ( )

Member Function Documentation

◆ allow_virtual_o2prime_hydrogens()

bool protocols::stepwise::modeler::packer::StepWisePacker::allow_virtual_o2prime_hydrogens ( ) const

◆ allow_virtual_side_chains()

bool protocols::stepwise::modeler::packer::StepWisePacker::allow_virtual_side_chains ( ) const

◆ apply()

void protocols::stepwise::modeler::packer::StepWisePacker::apply ( core::pose::Pose pose)

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References do_packing(), figure_out_neighbors(), pose_init_, reinstate_side_chain_angles(), and setup_pack_task().

Referenced by do_prepack().

◆ do_packing()

void protocols::stepwise::modeler::packer::StepWisePacker::do_packing ( core::pose::Pose pose)

◆ do_prepack()

void protocols::stepwise::modeler::packer::StepWisePacker::do_prepack ( core::pose::Pose pose)

◆ figure_out_neighbors()

void protocols::stepwise::modeler::packer::StepWisePacker::figure_out_neighbors ( core::pose::Pose pose)

◆ get_name()

std::string protocols::stepwise::modeler::packer::StepWisePacker::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ pack_all_side_chains()

bool protocols::stepwise::modeler::packer::StepWisePacker::pack_all_side_chains ( ) const

References pack_all_side_chains_.

◆ pack_o2prime_hydrogens()

bool protocols::stepwise::modeler::packer::StepWisePacker::pack_o2prime_hydrogens ( ) const

◆ previous_working_pack_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::packer::StepWisePacker::previous_working_pack_res ( ) const

◆ reinstate_side_chain_angles()

void protocols::stepwise::modeler::packer::StepWisePacker::reinstate_side_chain_angles ( core::pose::Pose pose,
core::pose::Pose const &  src_pose 

◆ reset()

void protocols::stepwise::modeler::packer::StepWisePacker::reset ( core::pose::Pose const &  pose)

◆ set_allow_virtual_o2prime_hydrogens()

void protocols::stepwise::modeler::packer::StepWisePacker::set_allow_virtual_o2prime_hydrogens ( bool const &  setting)

◆ set_allow_virtual_side_chains()

void protocols::stepwise::modeler::packer::StepWisePacker::set_allow_virtual_side_chains ( bool const &  setting)

◆ set_pack_all_side_chains()

void protocols::stepwise::modeler::packer::StepWisePacker::set_pack_all_side_chains ( bool const &  setting)

References pack_all_side_chains_.

◆ set_pack_o2prime_hydrogens()

void protocols::stepwise::modeler::packer::StepWisePacker::set_pack_o2prime_hydrogens ( bool const &  setting)

◆ set_pack_protein_side_chains()

void protocols::stepwise::modeler::packer::StepWisePacker::set_pack_protein_side_chains ( bool const &  setting)

◆ set_scorefxn()

void protocols::stepwise::modeler::packer::StepWisePacker::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

◆ set_use_packer_instead_of_rotamer_trials()

void protocols::stepwise::modeler::packer::StepWisePacker::set_use_packer_instead_of_rotamer_trials ( bool const &  setting)

◆ set_working_pack_res()

void protocols::stepwise::modeler::packer::StepWisePacker::set_working_pack_res ( utility::vector1< core::Size > const &  setting)

References working_pack_res_.

◆ setup_pack_task()

void protocols::stepwise::modeler::packer::StepWisePacker::setup_pack_task ( core::pose::Pose const &  pose)

◆ working_pack_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::packer::StepWisePacker::working_pack_res ( ) const

References working_pack_res_.

◆ working_pack_res_was_inputted()

bool protocols::stepwise::modeler::packer::StepWisePacker::working_pack_res_was_inputted ( ) const

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

bool protocols::stepwise::modeler::packer::StepWisePacker::allow_virtual_o2prime_hydrogens_

◆ allow_virtual_side_chains_

bool protocols::stepwise::modeler::packer::StepWisePacker::allow_virtual_side_chains_

◆ pack_all_side_chains_

bool protocols::stepwise::modeler::packer::StepWisePacker::pack_all_side_chains_

◆ pack_o2prime_hydrogens_

bool protocols::stepwise::modeler::packer::StepWisePacker::pack_o2prime_hydrogens_

◆ pack_protein_side_chains_

bool protocols::stepwise::modeler::packer::StepWisePacker::pack_protein_side_chains_

◆ pack_task_

core::pack::task::PackerTaskOP protocols::stepwise::modeler::packer::StepWisePacker::pack_task_

Referenced by do_packing(), and setup_pack_task().

◆ pose_init_

core::pose::PoseOP protocols::stepwise::modeler::packer::StepWisePacker::pose_init_

Referenced by apply(), do_prepack(), and reset().

◆ previous_working_pack_res_

utility::vector1< core::Size > protocols::stepwise::modeler::packer::StepWisePacker::previous_working_pack_res_

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::packer::StepWisePacker::scorefxn_

Referenced by do_packing(), and set_scorefxn().

◆ use_packer_instead_of_rotamer_trials_

bool protocols::stepwise::modeler::packer::StepWisePacker::use_packer_instead_of_rotamer_trials_

◆ working_moving_res_list_

utility::vector1< core::Size > const protocols::stepwise::modeler::packer::StepWisePacker::working_moving_res_list_

Referenced by do_prepack(), and figure_out_neighbors().

◆ working_pack_res_

utility::vector1< core::Size > protocols::stepwise::modeler::packer::StepWisePacker::working_pack_res_

◆ working_pack_res_was_inputted_

bool protocols::stepwise::modeler::packer::StepWisePacker::working_pack_res_was_inputted_

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