#include <StepWisePacker.hh>

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

[legend]

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 Strings &	info ()
	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::Size >	working_pack_res_

utility::vector1< core::Size >	previous_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 ( )

overridedefault

Member Function Documentation

◆ allow_virtual_o2prime_hydrogens()

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

inline

References allow_virtual_o2prime_hydrogens_.

◆ allow_virtual_side_chains()

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

inline

References allow_virtual_side_chains_.

◆ apply()

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

overridevirtual

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 )

References core::pack::pack_rotamers(), pack_task_, previous_working_pack_res_, core::pack::rotamer_trials(), scorefxn_, use_packer_instead_of_rotamer_trials_, and working_pack_res_.

Referenced by apply().

◆ do_prepack()

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

References protocols::stepwise::modeler::packer::SideChainCopier::apply(), apply(), pack_o2prime_hydrogens_, pose_init_, core::pose::Pose::remove_constraints(), reset(), protocols::stepwise::modeler::split_pose(), working_moving_res_list_, and working_pack_res_.

◆ figure_out_neighbors()

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

References protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::stepwise::modeler::get_all_residues(), pack_all_side_chains_, pack_protein_side_chains_, working_moving_res_list_, working_pack_res_, and working_pack_res_was_inputted_.

Referenced by apply().

◆ get_name()

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

overridevirtual

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

inline

References pack_all_side_chains_.

◆ pack_o2prime_hydrogens()

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

inline

References pack_o2prime_hydrogens_.

◆ previous_working_pack_res()

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

inline

References previous_working_pack_res_.

◆ reinstate_side_chain_angles()

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

private

References protocols::stepwise::modeler::packer::SideChainCopier::apply(), pack_o2prime_hydrogens_, and previous_working_pack_res_.

Referenced by apply().

◆ reset()

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

References core::pose::Pose::clone(), protocols::stepwise::modeler::get_all_residues(), pose_init_, and previous_working_pack_res_.

Referenced by do_prepack().

◆ set_allow_virtual_o2prime_hydrogens()

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

inline

References allow_virtual_o2prime_hydrogens_.

◆ set_allow_virtual_side_chains()

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

inline

References allow_virtual_side_chains_.

◆ set_pack_all_side_chains()

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

inline

References pack_all_side_chains_.

◆ set_pack_o2prime_hydrogens()

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

inline

References pack_o2prime_hydrogens_.

◆ set_pack_protein_side_chains()

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

inline

References pack_protein_side_chains_.

◆ 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 )

inline

References use_packer_instead_of_rotamer_trials_.

◆ set_working_pack_res()

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

inline

References working_pack_res_.

◆ setup_pack_task()

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

private

References allow_virtual_o2prime_hydrogens_, allow_virtual_side_chains_, core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), pack_o2prime_hydrogens_, pack_task_, core::pose::Pose::residue(), core::pose::Pose::size(), and working_pack_res_.

Referenced by apply().

◆ working_pack_res()

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

inline

References working_pack_res_.

◆ working_pack_res_was_inputted()

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

inline

References working_pack_res_was_inputted_.

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

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

private

Referenced by allow_virtual_o2prime_hydrogens(), set_allow_virtual_o2prime_hydrogens(), and setup_pack_task().

◆ allow_virtual_side_chains_

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

private

Referenced by allow_virtual_side_chains(), set_allow_virtual_side_chains(), and setup_pack_task().

◆ pack_all_side_chains_

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

private

Referenced by figure_out_neighbors(), pack_all_side_chains(), and set_pack_all_side_chains().

◆ pack_o2prime_hydrogens_

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

private

Referenced by do_prepack(), pack_o2prime_hydrogens(), reinstate_side_chain_angles(), set_pack_o2prime_hydrogens(), and setup_pack_task().

◆ pack_protein_side_chains_

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

private

Referenced by figure_out_neighbors(), and set_pack_protein_side_chains().

◆ pack_task_

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

private

Referenced by do_packing(), and setup_pack_task().

◆ pose_init_

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

private

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

◆ previous_working_pack_res_

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

private

Referenced by do_packing(), previous_working_pack_res(), reinstate_side_chain_angles(), and reset().

◆ scorefxn_

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

private

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_

private

Referenced by do_packing(), and set_use_packer_instead_of_rotamer_trials().

◆ working_moving_res_list_

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

private

Referenced by do_prepack(), and figure_out_neighbors().

◆ working_pack_res_

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

private

Referenced by do_packing(), do_prepack(), figure_out_neighbors(), set_working_pack_res(), setup_pack_task(), and working_pack_res().

◆ working_pack_res_was_inputted_

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

private

Referenced by figure_out_neighbors(), and working_pack_res_was_inputted().

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

src/protocols/stepwise/modeler/packer/StepWisePacker.hh
src/protocols/stepwise/modeler/packer/StepWisePacker.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWisePacker()

◆ ~StepWisePacker()

Member Function Documentation

◆ allow_virtual_o2prime_hydrogens()

◆ allow_virtual_side_chains()

◆ apply()

◆ do_packing()

◆ do_prepack()

◆ figure_out_neighbors()

◆ get_name()

◆ pack_all_side_chains()

◆ pack_o2prime_hydrogens()

◆ previous_working_pack_res()

◆ reinstate_side_chain_angles()

◆ reset()

◆ set_allow_virtual_o2prime_hydrogens()

◆ set_allow_virtual_side_chains()

◆ set_pack_all_side_chains()

◆ set_pack_o2prime_hydrogens()

◆ set_pack_protein_side_chains()

◆ set_scorefxn()

◆ set_use_packer_instead_of_rotamer_trials()

◆ set_working_pack_res()

◆ setup_pack_task()

◆ working_pack_res()

◆ working_pack_res_was_inputted()

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

◆ allow_virtual_side_chains_

◆ pack_all_side_chains_

◆ pack_o2prime_hydrogens_

◆ pack_protein_side_chains_

◆ pack_task_

◆ pose_init_

◆ previous_working_pack_res_

◆ scorefxn_

◆ use_packer_instead_of_rotamer_trials_

◆ working_moving_res_list_

◆ working_pack_res_

◆ working_pack_res_was_inputted_