#include <StepWiseProteinMinimizer.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer:

[legend]

Public Member Functions
	StepWiseProteinMinimizer (utility::vector1< core::pose::PoseOP > const &pose_list, utility::vector1< core::Size > const &moving_residues)

	~StepWiseProteinMinimizer () override

void	apply (core::pose::Pose &pose_to_visualize) 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	set_min_tolerance (core::Real const &setting)

void	set_min_type (std::string const &setting)

void	set_fixed_res (utility::vector1< core::Size > const &fixed_res)

void	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)

core::Size const &	num_pose_minimize () const

void	set_num_pose_minimize (core::Size const &setting)

void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

void	set_move_takeoff_torsions (bool const value)

void	set_rescore_only (bool const &setting)

void	set_move_jumps_between_chains (bool const &setting)

void	set_cartesian (bool const setting)

void	set_use_coordinate_constraints (bool const &setting)

bool	use_coordinate_constraints () const

utility::vector1< core::pose::PoseOP >	pose_list () 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 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	initialize_parameters ()

void	let_neighboring_chis_minimize (core::kinematics::MoveMap &mm, core::pose::Pose &pose)

bool	pose_has_chainbreak (core::pose::Pose const &pose)

Private Attributes
utility::vector1< core::Size > const &	moving_residues_

utility::vector1< core::Size >	fixed_res_

utility::vector1< core::Size >	calc_rms_res_

bool	move_takeoff_torsions_

bool	rescore_only_

bool	move_jumps_between_chains_

bool	cartesian_

core::scoring::ScoreFunctionOP	fa_scorefxn_

utility::vector1< core::pose::PoseOP >	pose_list_

std::string	min_type_

core::Real	min_tolerance_

bool	use_coordinate_constraints_

core::Size	num_pose_minimize_

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

◆ StepWiseProteinMinimizer()

protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::StepWiseProteinMinimizer	(	utility::vector1< core::pose::PoseOP > const &	pose_list,
		utility::vector1< core::Size > const &	moving_residues
	)

References initialize_parameters().

◆ ~StepWiseProteinMinimizer()

protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::~StepWiseProteinMinimizer ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply ( core::pose::Pose & pose_to_visualize )

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References core::scoring::constraints::add_coordinate_constraints(), cartesian_, core::pose::Pose::clone(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::disulfide_bonds(), core::chemical::element::F, fa_scorefxn_, protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), core::conformation::Conformation::fix_disulfides(), fixed_res_, let_neighboring_chis_minimize(), core::scoring::linear_chainbreak, min_tolerance_, min_type_, move_takeoff_torsions_, core::optimization::MinimizerOptions::nblist_auto_update(), num_pose_minimize_, protocols::stepwise::legacy::modeler::protein::output_pose_list(), pose_has_chainbreak(), pose_list_, rescore_only_, core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::pose::Pose::size(), protocols::TR(), and use_coordinate_constraints_.

◆ get_name()

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ initialize_parameters()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::initialize_parameters ( )

private

References cartesian_, min_tolerance_, min_type_, move_jumps_between_chains_, move_takeoff_torsions_, num_pose_minimize_, rescore_only_, and use_coordinate_constraints_.

Referenced by StepWiseProteinMinimizer().

◆ let_neighboring_chis_minimize()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose &	pose
	)

private

References core::chemical::rna::CHI, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), moving_residues_, core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_chi(), and core::chemical::VIRTUAL_RESIDUE_VARIANT.

Referenced by apply().

◆ num_pose_minimize()

core::Size const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::num_pose_minimize ( ) const

inline

References num_pose_minimize_.

◆ pose_has_chainbreak()

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_has_chainbreak ( core::pose::Pose const & pose )

private

References core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by apply().

◆ pose_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_list ( ) const

inline

References pose_list_.

◆ set_calc_rms_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_calc_rms_res ( utility::vector1< core::Size > const & calc_rms_res )

References calc_rms_res_.

◆ set_cartesian()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_cartesian ( bool const setting )

References cartesian_, and min_type_.

◆ set_fixed_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_fixed_res ( utility::vector1< core::Size > const & fixed_res )

References fixed_res_.

◆ set_min_tolerance()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_min_tolerance ( core::Real const & setting )

References min_tolerance_.

◆ set_min_type()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_min_type ( std::string const & setting )

References min_type_.

◆ set_move_jumps_between_chains()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_move_jumps_between_chains ( bool const & setting )

inline

References move_jumps_between_chains_.

◆ set_move_takeoff_torsions()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_move_takeoff_torsions ( bool const value )

inline

References move_takeoff_torsions_.

◆ set_num_pose_minimize()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_num_pose_minimize ( core::Size const & setting )

inline

References num_pose_minimize_.

◆ set_rescore_only()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_rescore_only ( bool const & setting )

inline

References rescore_only_.

◆ set_scorefxn()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References fa_scorefxn_.

◆ set_use_coordinate_constraints()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_use_coordinate_constraints ( bool const & setting )

inline

References use_coordinate_constraints_.

◆ use_coordinate_constraints()

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::use_coordinate_constraints ( ) const

inline

References use_coordinate_constraints_.

Member Data Documentation

◆ calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::calc_rms_res_

private

Referenced by set_calc_rms_res().

◆ cartesian_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::cartesian_

private

Referenced by apply(), initialize_parameters(), and set_cartesian().

◆ fa_scorefxn_

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::fa_scorefxn_

private

Referenced by apply(), and set_scorefxn().

◆ fixed_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::fixed_res_

private

Referenced by apply(), and set_fixed_res().

◆ min_tolerance_

core::Real protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::min_tolerance_

private

Referenced by apply(), initialize_parameters(), and set_min_tolerance().

◆ min_type_

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::min_type_

private

Referenced by apply(), initialize_parameters(), set_cartesian(), and set_min_type().

◆ move_jumps_between_chains_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::move_jumps_between_chains_

private

Referenced by initialize_parameters(), and set_move_jumps_between_chains().

◆ move_takeoff_torsions_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::move_takeoff_torsions_

private

Referenced by apply(), initialize_parameters(), and set_move_takeoff_torsions().

◆ moving_residues_

utility::vector1< core::Size > const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::moving_residues_

private

Referenced by let_neighboring_chis_minimize().

◆ num_pose_minimize_

core::Size protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::num_pose_minimize_

private

Referenced by apply(), initialize_parameters(), num_pose_minimize(), and set_num_pose_minimize().

◆ pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_list_

private

Referenced by apply(), and pose_list().

◆ rescore_only_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::rescore_only_

private

Referenced by apply(), initialize_parameters(), and set_rescore_only().

◆ use_coordinate_constraints_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::use_coordinate_constraints_

private

Referenced by apply(), initialize_parameters(), set_use_coordinate_constraints(), and use_coordinate_constraints().

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

src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinMinimizer.hh
src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinMinimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseProteinMinimizer()

◆ ~StepWiseProteinMinimizer()

Member Function Documentation

◆ apply()

◆ get_name()

◆ initialize_parameters()

◆ let_neighboring_chis_minimize()

◆ num_pose_minimize()

◆ pose_has_chainbreak()

◆ pose_list()

◆ set_calc_rms_res()

◆ set_cartesian()

◆ set_fixed_res()

◆ set_min_tolerance()

◆ set_min_type()

◆ set_move_jumps_between_chains()

◆ set_move_takeoff_torsions()

◆ set_num_pose_minimize()

◆ set_rescore_only()

◆ set_scorefxn()

◆ set_use_coordinate_constraints()

◆ use_coordinate_constraints()

Member Data Documentation

◆ calc_rms_res_

◆ cartesian_

◆ fa_scorefxn_

◆ fixed_res_

◆ min_tolerance_

◆ min_type_

◆ move_jumps_between_chains_

◆ move_takeoff_torsions_

◆ moving_residues_

◆ num_pose_minimize_

◆ pose_list_

◆ rescore_only_

◆ use_coordinate_constraints_