#include <StepWiseMinimizer.hh>

Inheritance diagram for protocols::stepwise::modeler::StepWiseMinimizer:

[legend]

Public Member Functions
	StepWiseMinimizer (utility::vector1< core::pose::PoseOP > const &pose_list, working_parameters::StepWiseWorkingParametersCOP working_parameters, options::StepWiseModelerOptionsCOP options, core::scoring::ScoreFunctionCOP scorefxn)

	~StepWiseMinimizer () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

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

void	set_working_pack_res (utility::vector1< core::Size > const &setting)

utility::vector1< core::Size > const &	working_pack_res () const

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

core::Size const &	num_pose_minimize () const

utility::vector1< core::Size > const &	working_minimize_res () 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_side_chains_minimize (core::kinematics::MoveMap &mm, core::pose::Pose const &pose)

void	setup_minimizers ()

void	setup_scorefxns (core::pose::Pose const &pose)

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

void	do_full_minimizing (core::pose::Pose &pose)

void	do_clustering (core::pose::Pose &pose)

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

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

void	setup_all_moving_res (core::pose::Pose const &pose)

void	move_side_chain (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, core::Size const j)

void	output_empty_minimizer_silent_file () const

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

void	output_minimized_pose_list () const

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

utility::vector1< core::Size >	figure_out_working_minimize_res (core::pose::Pose const &pose)

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

options::StepWiseModelerOptionsCOP	options_

core::scoring::ScoreFunctionCOP	scorefxn_

core::scoring::ScoreFunctionOP	minimize_scorefxn_

core::scoring::ScoreFunctionOP	final_scorefxn_

core::Size	num_pose_minimize_

utility::vector1< core::Size > const	working_moving_res_

utility::vector1< core::Size >	working_fixed_res_

utility::vector1< core::Size >	working_calc_rms_res_

utility::vector1< core::Size >	working_pack_res_

utility::vector1< core::Size >	working_minimize_res_

core::optimization::CartesianMinimizerOP	cartesian_minimizer_

core::optimization::AtomTreeMinimizerOP	atom_tree_minimizer_

core::optimization::MinimizerOptionsOP	minimizer_options_

bool const	allow_virtual_o2prime_hydrogens_

protein::loop_close::StepWiseProteinCCD_CloserOP	protein_ccd_closer_

working_parameters::StepWiseWorkingParametersCOP	working_parameters_

core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map_

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

◆ StepWiseMinimizer()

protocols::stepwise::modeler::StepWiseMinimizer::StepWiseMinimizer	(	utility::vector1< core::pose::PoseOP > const &	pose_list,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters,
		options::StepWiseModelerOptionsCOP	options,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

References protocols::stepwise::modeler::protein::contains_protein(), figure_out_working_minimize_res(), num_pose_minimize_, options_, pose_list(), pose_list_, protocols::moves::Mover::set_native_pose(), and working_minimize_res_.

◆ ~StepWiseMinimizer()

protocols::stepwise::modeler::StepWiseMinimizer::~StepWiseMinimizer ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References check_pose_list(), do_clustering(), do_full_minimizing(), output_minimized_pose_list(), setup_minimizers(), and setup_scorefxns().

◆ check_pose_list()

bool protocols::stepwise::modeler::StepWiseMinimizer::check_pose_list ( core::pose::Pose const & pose )

private

References core::pose::Pose::clone(), options_, output_empty_minimizer_silent_file(), pose_list_, and protocols::TR().

Referenced by apply().

◆ close_chainbreaks()

void protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	mm
	)

private

References protocols::rna::movers::RNA_LoopCloser::apply(), do_minimize(), protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res(), protocols::stepwise::modeler::protein::just_protein(), protocols::stepwise::modeler::rna::just_rna(), protein_ccd_closer_, and working_moving_res_.

Referenced by do_full_minimizing().

◆ do_clustering()

void protocols::stepwise::modeler::StepWiseMinimizer::do_clustering ( core::pose::Pose & pose )

private

References protocols::stepwise::modeler::add_these(), protocols::stepwise::modeler::align::StepWiseClusterer::cluster(), protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd(), protocols::buns::energy, figure_out_working_minimize_res(), protocols::mean_field::min(), options_, protocols::stepwise::modeler::align::StepWiseClusterer::pose_list(), pose_list_, protocols::stepwise::modeler::align::StepWiseClusterer::set_calc_rms_res(), protocols::stepwise::modeler::align::StepWiseClusterer::set_max_decoys(), protocols::stepwise::modeler::align::StepWiseClusterer::set_pose_list(), core::simple_metrics::metrics::sum, protocols::TR(), protocols::hybridization::val, and working_minimize_res_.

Referenced by apply().

◆ do_full_minimizing()

void protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing ( core::pose::Pose & pose )

private

◆ do_minimize()

void protocols::stepwise::modeler::StepWiseMinimizer::do_minimize	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	mm
	)

private

References core::pose::rna::add_syn_anti_chi_constraints(), allow_virtual_o2prime_hydrogens_, protocols::recces::scratch::ThermalMinimizer::apply(), atom_tree_minimizer_, cartesian_minimizer_, core::pose::Pose::constraint_set(), protocols::magnesium::hydrate_magnesiums(), minimize_scorefxn_, minimizer_options_, protocols::stepwise::modeler::rna::o2prime_trials(), options_, protocols::stepwise::modeler::polar_hydrogens::pack_polar_hydrogens(), protocols::recces::scratch::ThermalMinimizer::set_kic_sampling(), protocols::recces::scratch::ThermalMinimizer::set_mm(), protocols::recces::scratch::ThermalMinimizer::set_n_cycle(), protocols::recces::scratch::ThermalMinimizer::set_output_min_pose(), protocols::recces::scratch::ThermalMinimizer::set_scorefxn(), protocols::recces::scratch::ThermalMinimizer::set_temp(), setup_vary_bond_geometry(), protocols::stepwise::modeler::THERMAL_SAMPLER, protocols::stepwise::modeler::TRADITIONAL_MINIMIZER, and working_pack_res_.

Referenced by close_chainbreaks(), and do_full_minimizing().

◆ figure_out_working_minimize_res()

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res ( core::pose::Pose const & pose )

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::extra_minimize_res(), core::pose::full_model_info::FullModelInfo::full_to_sub(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::pose::Pose::size(), working_fixed_res_, and working_minimize_res().

Referenced by do_clustering(), get_move_map_and_atom_level_domain_map(), and StepWiseMinimizer().

◆ get_move_map_and_atom_level_domain_map()

void protocols::stepwise::modeler::StepWiseMinimizer::get_move_map_and_atom_level_domain_map	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose
	)

private

References atom_level_domain_map_, protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), figure_out_working_minimize_res(), protocols::stepwise::modeler::freeze_waters(), options_, protocols::stepwise::modeler::output_movemap(), protocols::TR(), and working_minimize_res_.

Referenced by do_full_minimizing().

◆ get_name()

std::string protocols::stepwise::modeler::StepWiseMinimizer::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ initialize_parameters()

void protocols::stepwise::modeler::StepWiseMinimizer::initialize_parameters ( )

private

◆ let_neighboring_side_chains_minimize()

void protocols::stepwise::modeler::StepWiseMinimizer::let_neighboring_side_chains_minimize	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose
	)

private

References protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::stepwise::modeler::get_all_residues(), move_side_chain(), options_, working_moving_res_, and working_pack_res_.

Referenced by do_full_minimizing().

◆ move_side_chain()

void protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose,
		core::Size const	j
	)

private

References atom_level_domain_map_, core::chemical::rna::CHI, core::kinematics::MoveMap::get_chi(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::chemical::ResidueType::nchi(), options_, core::chemical::rings::q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_chi(), and core::chemical::VIRTUAL_RESIDUE_VARIANT.

Referenced by let_neighboring_side_chains_minimize().

◆ num_pose_minimize()

core::Size const& protocols::stepwise::modeler::StepWiseMinimizer::num_pose_minimize ( ) const

inline

References num_pose_minimize_.

◆ output_empty_minimizer_silent_file()

void protocols::stepwise::modeler::StepWiseMinimizer::output_empty_minimizer_silent_file ( ) const

private

References options_.

Referenced by check_pose_list().

◆ output_minimized_pose_list()

void protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list ( ) const

private

References protocols::stepwise::modeler::protein::contains_protein(), protocols::moves::Mover::get_native_pose(), options_, protocols::stepwise::modeler::rna::output_data(), protocols::stepwise::legacy::modeler::protein::output_pose_list(), protocols::stepwise::monte_carlo::output_to_silent_file(), pose_list_, working_calc_rms_res_, and working_parameters_.

Referenced by apply().

◆ pose_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseMinimizer::pose_list ( ) const

inline

References pose_list_.

Referenced by StepWiseMinimizer().

◆ set_scorefxn()

void protocols::stepwise::modeler::StepWiseMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

inline

References scorefxn_.

◆ set_working_pack_res()

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

inline

References working_pack_res_.

◆ setup_all_moving_res()

void protocols::stepwise::modeler::StepWiseMinimizer::setup_all_moving_res ( core::pose::Pose const & pose )

private

◆ setup_minimizers()

void protocols::stepwise::modeler::StepWiseMinimizer::setup_minimizers ( )

private

References atom_tree_minimizer_, cartesian_minimizer_, minimizer_options_, and options_.

Referenced by apply().

◆ setup_scorefxns()

void protocols::stepwise::modeler::StepWiseMinimizer::setup_scorefxns ( core::pose::Pose const & pose )

private

References final_scorefxn_, protocols::stepwise::modeler::get_minimize_scorefxn(), minimize_scorefxn_, options_, core::scoring::rna_chem_map, and scorefxn_.

Referenced by apply().

◆ setup_vary_bond_geometry()

void protocols::stepwise::modeler::StepWiseMinimizer::setup_vary_bond_geometry	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	mm
	)

private

References atom_level_domain_map_, core::scoring::bond_geometry, minimize_scorefxn_, options_, protocols::simple_moves::setup_vary_polar_hydrogen_geometry(), protocols::simple_moves::setup_vary_rna_bond_geometry(), and protocols::TR().

Referenced by do_minimize().

◆ working_minimize_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::StepWiseMinimizer::working_minimize_res ( ) const

inline

References working_minimize_res_.

Referenced by figure_out_working_minimize_res().

◆ working_pack_res()

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

inline

References working_pack_res_.

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

bool const protocols::stepwise::modeler::StepWiseMinimizer::allow_virtual_o2prime_hydrogens_

private

Referenced by do_minimize().

◆ atom_level_domain_map_

core::pose::toolbox::AtomLevelDomainMapOP protocols::stepwise::modeler::StepWiseMinimizer::atom_level_domain_map_

private

Referenced by get_move_map_and_atom_level_domain_map(), move_side_chain(), and setup_vary_bond_geometry().

◆ atom_tree_minimizer_

core::optimization::AtomTreeMinimizerOP protocols::stepwise::modeler::StepWiseMinimizer::atom_tree_minimizer_

private

Referenced by do_minimize(), and setup_minimizers().

◆ cartesian_minimizer_

core::optimization::CartesianMinimizerOP protocols::stepwise::modeler::StepWiseMinimizer::cartesian_minimizer_

private

Referenced by do_minimize(), and setup_minimizers().

◆ final_scorefxn_

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::StepWiseMinimizer::final_scorefxn_

private

Referenced by setup_scorefxns().

◆ minimize_scorefxn_

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::StepWiseMinimizer::minimize_scorefxn_

private

Referenced by do_full_minimizing(), do_minimize(), setup_scorefxns(), and setup_vary_bond_geometry().

◆ minimizer_options_

core::optimization::MinimizerOptionsOP protocols::stepwise::modeler::StepWiseMinimizer::minimizer_options_

private

Referenced by do_minimize(), and setup_minimizers().

◆ num_pose_minimize_

core::Size protocols::stepwise::modeler::StepWiseMinimizer::num_pose_minimize_

private

Referenced by do_full_minimizing(), num_pose_minimize(), and StepWiseMinimizer().

◆ options_

options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseMinimizer::options_

private

Referenced by check_pose_list(), do_clustering(), do_full_minimizing(), do_minimize(), get_move_map_and_atom_level_domain_map(), let_neighboring_side_chains_minimize(), move_side_chain(), output_empty_minimizer_silent_file(), output_minimized_pose_list(), setup_minimizers(), setup_scorefxns(), setup_vary_bond_geometry(), and StepWiseMinimizer().

◆ pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseMinimizer::pose_list_

private

Referenced by check_pose_list(), do_clustering(), do_full_minimizing(), output_minimized_pose_list(), pose_list(), and StepWiseMinimizer().

◆ protein_ccd_closer_

protein::loop_close::StepWiseProteinCCD_CloserOP protocols::stepwise::modeler::StepWiseMinimizer::protein_ccd_closer_

private

Referenced by close_chainbreaks().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseMinimizer::scorefxn_

private

Referenced by set_scorefxn(), and setup_scorefxns().

◆ working_calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_calc_rms_res_

private

Referenced by output_minimized_pose_list().

◆ working_fixed_res_

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_fixed_res_

private

Referenced by figure_out_working_minimize_res().

◆ working_minimize_res_

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_minimize_res_

private

Referenced by do_clustering(), get_move_map_and_atom_level_domain_map(), StepWiseMinimizer(), and working_minimize_res().

◆ working_moving_res_

utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseMinimizer::working_moving_res_

private

Referenced by close_chainbreaks(), and let_neighboring_side_chains_minimize().

◆ working_pack_res_

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_pack_res_

private

Referenced by do_full_minimizing(), do_minimize(), let_neighboring_side_chains_minimize(), set_working_pack_res(), and working_pack_res().

◆ working_parameters_

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseMinimizer::working_parameters_

private

Referenced by output_minimized_pose_list().

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

src/protocols/stepwise/modeler/StepWiseMinimizer.hh
src/protocols/stepwise/modeler/StepWiseMinimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseMinimizer()

◆ ~StepWiseMinimizer()

Member Function Documentation

◆ apply()

◆ check_pose_list()

◆ close_chainbreaks()

◆ do_clustering()

◆ do_full_minimizing()

◆ do_minimize()

◆ figure_out_working_minimize_res()

◆ get_move_map_and_atom_level_domain_map()

◆ get_name()

◆ initialize_parameters()

◆ let_neighboring_side_chains_minimize()

◆ move_side_chain()

◆ num_pose_minimize()

◆ output_empty_minimizer_silent_file()

◆ output_minimized_pose_list()

◆ pose_list()

◆ set_scorefxn()

◆ set_working_pack_res()

◆ setup_all_moving_res()

◆ setup_minimizers()

◆ setup_scorefxns()

◆ setup_vary_bond_geometry()

◆ working_minimize_res()

◆ working_pack_res()

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

◆ atom_level_domain_map_

◆ atom_tree_minimizer_

◆ cartesian_minimizer_

◆ final_scorefxn_

◆ minimize_scorefxn_

◆ minimizer_options_

◆ num_pose_minimize_

◆ options_

◆ pose_list_

◆ protein_ccd_closer_

◆ scorefxn_

◆ working_calc_rms_res_

◆ working_fixed_res_

◆ working_minimize_res_

◆ working_moving_res_

◆ working_pack_res_

◆ working_parameters_