#include <ddGMover.hh>

Inheritance diagram for protocols::ddg::ddGMover:

[legend]

Public Member Functions
	ddGMover ()

	ddGMover (core::scoring::ScoreFunctionOP s, core::scoring::ScoreFunctionOP m, utility::vector1< core::chemical::AA > const &res_to_mutate)

	~ddGMover () override

void	neighbor_cutoff (core::Real cutoff)

void	restrict_to_nbrs (bool truefalse)

void	score_function (core::scoring::ScoreFunctionOP s)

void	set_minimization_score_function (core::scoring::ScoreFunctionOP s)

void	num_iterations (int num)

void	dump_pdbs (bool truefalse)

void	debug_output (bool truefalse)

void	is_interface_ddg (bool truefalse)

void	wt_score_components (ObjexxFCL::FArray2D< core::Real > wsc)

void	wt_unbound_score_components (ObjexxFCL::FArray2D< core::Real > wusc)

void	mutant_score_components (ObjexxFCL::FArray2D< core::Real > msc)

void	residues_to_mutate (utility::vector1< core::chemical::AA > residues)

void	set_min_cst (bool truefalse)

void	set_mean (bool truefalse)

void	set_min (bool truefalse)

void	set_num_decoys_used_in_calculations (core::Real num_lowe_used)

core::Real	neighbor_cutoff ()

bool	restrict_to_nbrs ()

core::scoring::ScoreFunctionOP	score_function ()

core::scoring::ScoreFunctionOP	minimization_score_function ()

int	num_iterations ()

bool	is_interface_ddg ()

ObjexxFCL::FArray2D< core::Real >	wt_score_components ()

ObjexxFCL::FArray2D< core::Real >	wt_unbound_score_components ()

ObjexxFCL::FArray2D< core::Real >	mutant_score_components ()

utility::vector1< core::chemical::AA >	residues_to_mutate ()

utility::vector1< core::Real >	get_wt_min_score_components ()

utility::vector1< core::Real >	get_wt_averaged_score_components ()

utility::vector1< core::Real >	get_mutant_min_score_components ()

utility::vector1< core::Real >	get_mutant_averaged_score_components ()

utility::vector1< core::Real >	get_delta_energy_components ()

void	get_scorefunction_header (core::scoring::ScoreFunctionOP sfxn, utility::vector1< std::string > &components)

std::string	mutation_label (core::pose::Pose const &pose) const

core::Real	get_wt_averaged_totals ()

core::Real	get_wt_min_totals ()

core::Real	get_mutant_averaged_totals ()

core::Real	get_mutant_min_totals ()

core::Real	ddG ()

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...

bool	is_wt_calc_complete ()

bool	is_mutant_calc_complete ()

bool	is_properly_initialized (core::pose::Pose &pose)

bool	get_min_cst ()

bool	use_mean ()

bool	use_min ()

core::Real	get_num_decoys_used_in_calculations ()

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
utility::vector1< int >	find_nbrs (core::pose::Pose &p, utility::vector1< int > &mutation_position, core::Real radii)

void	setup_packertask (core::pack::task::PackerTaskOP pt, core::pose::Pose &p)

bool	is_complete (ObjexxFCL::FArray2D< core::Real > to_check)

core::Real	sum (ddGs &scores_to_sum)

core::Real	average (utility::vector1< core::Real > &scores_to_average)

int	store_energies (ObjexxFCL::FArray2D< core::Real > &two_d_e_arrays, core::scoring::ScoreFunction &s, core::pose::Pose &p, int next_index, int size_to_expect)

int	average_score_components (ObjexxFCL::FArray2D< core::Real > &scores_to_average, utility::vector1< core::Real > &averaged_scores)

void	calculate_interface_unbound_energy (core::pose::Pose &p, core::scoring::ScoreFunctionOP s, core::pack::task::PackerTaskOP pt)

void	setup_rotamer_constraints (core::pose::Pose &p, core::scoring::ScoreFunction &s, utility::vector1< int > &mutation_position, bool all_but_mutation_site, utility::vector1< char > &constraints_at_pos)

void	setup_repack_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, bool all_but_mut_site, utility::vector1< char > &constraints_at_pos)
	sets up only rotamer constraints available during repacking More...

void	setup_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, float const cst_tol, bool all_but_mut_site, utility::vector1< char > &constraints_at_pos)

void	minimize_with_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionOP s, core::pack::task::PackerTaskOP pt)

void	print_verbose_ddgs (utility::vector1< core::pose::Pose > mut, utility::vector1< core::pose::Pose > wt, core::scoring::ScoreFunctionOP sfxn, bool mean, bool min, std::string filename)

void	relax_wildtype_structure (core::pose::Pose &pose, protocols::scoring::Interface &protein_interface, std::string const &wt_traj, bool output_silent)
	APL's attempts at refactoring this code. More...

void	setup_packer_task_for_mutations (core::pose::Pose const &pose, protocols::scoring::Interface const &protein_interface, utility::vector1< int > const &mutations, core::pack::task::PackerTaskOP packer_task)
	Initialize a packer task to reflect the residues that should be repacked based on the structure of the wildtype pose. More...

void	initialize_task_level_behavior (core::pack::task::PackerTaskOP packer_task)

bool	is_any_pdb_empty (core::pose::Pose const &pose, std::string const &mutant_traj, bool const output_silent) const

utility::vector1< bool >	neighborhood_of_mutations (core::pose::Pose const &pose, utility::vector1< int > const &mutations) const

void	initialize_rotamer_behavior_for_residue_level_task (core::pack::task::ResidueLevelTask &rltask) const

Private Attributes
core::Real	num_decoys_used_in_calculations_

bool	mean_

bool	min_

bool	min_cst_

core::Real	nbr_cutoff_

bool	restrict_to_nbrhood_

bool	interface_ddg_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	min_cst_sfxn_

core::scoring::ScoreFunctionOP	min_cst_sfxn_no_cst_weight_
	minimize the score with this score function More...

core::scoring::constraints::ConstraintSetOP	cst_set_
	report the score with this score function More...

core::scoring::constraints::ConstraintSetOP	min_cst_set_wt_

utility::vector1< char >	min_cst_wt_types_

core::scoring::constraints::ConstraintSetOP	min_cst_set_mut_

utility::vector1< char >	min_cst_mut_types_

core::scoring::constraints::ConstraintSetOP	repack_cst_set_wt_

utility::vector1< char >	repack_wt_types_

core::scoring::constraints::ConstraintSetOP	repack_cst_set_mut_

utility::vector1< char >	repack_mut_types_

utility::vector1< core::chemical::AA >	residues_to_mutate_

int	num_iterations_

bool	dmp_pdb_

bool	dbg_output_

ObjexxFCL::FArray2D< core::Real >	wt_components_

ObjexxFCL::FArray2D< core::Real >	wt_unbound_components_

ObjexxFCL::FArray2D< core::Real >	mutant_components_

ObjexxFCL::FArray2D< core::Real >	mutant_unbound_components_

utility::vector1< core::pose::Pose >	natives_

utility::vector1< core::pose::Pose >	mutants_

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

◆ ddGMover() [1/2]

protocols::ddg::ddGMover::ddGMover ( )

◆ ddGMover() [2/2]

protocols::ddg::ddGMover::ddGMover	(	core::scoring::ScoreFunctionOP	s,
		core::scoring::ScoreFunctionOP	m,
		utility::vector1< core::chemical::AA > const &	res_to_mutate
	)

◆ ~ddGMover()

protocols::ddg::ddGMover::~ddGMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::ddg::ddGMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::chemical::aa_unk, calculate_interface_unbound_energy(), core::pose::Pose::chain(), core::pose::Pose::constraint_set(), dbg_output_, dmp_pdb_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), get_mutant_min_totals(), get_wt_min_totals(), initialize_task_level_behavior(), interface_ddg_, is_any_pdb_empty(), is_properly_initialized(), min_cst_, min_cst_set_mut_, min_cst_sfxn_, min_cst_sfxn_no_cst_weight_, minimize_with_constraints(), mutant_components_, mutant_unbound_components_, mutants_, mutation_label(), num_iterations_, core::pack::pack_rotamers_loop(), core::chemical::rings::q, relax_wildtype_structure(), core::pose::Pose::remove_constraints(), repack_cst_set_mut_, residues_to_mutate_, restrict_to_nbrhood_, scorefxn_, core::io::silent::SilentFileData::set_filename(), setup_packer_task_for_mutations(), core::pose::Pose::size(), store_energies(), core::scoring::Energies::total_energies(), protocols::TR(), core::scoring::EMapVector::weighted_string_of(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::ddG_main().

◆ average()

core::Real protocols::ddg::ddGMover::average ( utility::vector1< core::Real > & scores_to_average )

private

References sum().

◆ average_score_components()

int protocols::ddg::ddGMover::average_score_components	(	ObjexxFCL::FArray2D< core::Real > &	scores_to_average,
		utility::vector1< core::Real > &	averaged_scores
	)

private

References protocols::mean_field::min(), protocols::ddg::min_index(), num_decoys_used_in_calculations_, num_iterations_, and core::scoring::total_score.

Referenced by get_mutant_averaged_score_components(), and get_wt_averaged_score_components().

◆ calculate_interface_unbound_energy()

void protocols::ddg::ddGMover::calculate_interface_unbound_energy	(	core::pose::Pose &	p,
		core::scoring::ScoreFunctionOP	s,
		core::pack::task::PackerTaskOP	pt
	)

private

References core::pack::pack_rotamers().

Referenced by apply(), and relax_wildtype_structure().

◆ ddG()

core::Real protocols::ddg::ddGMover::ddG ( )

References get_mutant_averaged_totals(), get_mutant_min_totals(), get_wt_averaged_totals(), get_wt_min_totals(), mean_, and min_.

Referenced by protocols::ddG_main().

◆ debug_output()

void protocols::ddg::ddGMover::debug_output ( bool truefalse )

References dbg_output_.

Referenced by protocols::ddG_main().

◆ dump_pdbs()

void protocols::ddg::ddGMover::dump_pdbs ( bool truefalse )

References dmp_pdb_.

Referenced by protocols::ddG_main().

◆ find_nbrs()

utility::vector1< int > protocols::ddg::ddGMover::find_nbrs	(	core::pose::Pose &	p,
		utility::vector1< int > &	mutation_position,
		core::Real	radii
	)

private

References core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

◆ get_delta_energy_components()

utility::vector1< core::Real > protocols::ddg::ddGMover::get_delta_energy_components ( )

References get_mutant_averaged_score_components(), get_mutant_min_score_components(), get_wt_averaged_score_components(), get_wt_min_score_components(), mean_, and min_.

Referenced by protocols::ddG_main().

◆ get_min_cst()

bool protocols::ddg::ddGMover::get_min_cst ( )

References min_cst_.

◆ get_mutant_averaged_score_components()

utility::vector1< core::Real > protocols::ddg::ddGMover::get_mutant_averaged_score_components ( )

References average_score_components(), interface_ddg_, mutant_components_, and mutant_unbound_components_.

Referenced by protocols::ddG_main(), get_delta_energy_components(), and get_mutant_averaged_totals().

◆ get_mutant_averaged_totals()

core::Real protocols::ddg::ddGMover::get_mutant_averaged_totals ( )

References get_mutant_averaged_score_components(), and sum().

Referenced by ddG().

◆ get_mutant_min_score_components()

utility::vector1< core::Real > protocols::ddg::ddGMover::get_mutant_min_score_components ( )

References protocols::ddg::min_index(), mutant_components_, and core::scoring::total_score.

Referenced by get_delta_energy_components(), and get_mutant_min_totals().

◆ get_mutant_min_totals()

core::Real protocols::ddg::ddGMover::get_mutant_min_totals ( )

References get_mutant_min_score_components(), and sum().

Referenced by apply(), and ddG().

◆ get_name()

std::string protocols::ddg::ddGMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_num_decoys_used_in_calculations()

core::Real protocols::ddg::ddGMover::get_num_decoys_used_in_calculations ( )

References num_decoys_used_in_calculations_.

◆ get_scorefunction_header()

void protocols::ddg::ddGMover::get_scorefunction_header	(	core::scoring::ScoreFunctionOP	sfxn,
		utility::vector1< std::string > &	components
	)

References core::sequence::end, core::scoring::name_from_score_type(), and core::scoring::score_type_from_name().

◆ get_wt_averaged_score_components()

utility::vector1< core::Real > protocols::ddg::ddGMover::get_wt_averaged_score_components ( )

References average_score_components(), interface_ddg_, wt_components_, and wt_unbound_components_.

Referenced by protocols::ddG_main(), get_delta_energy_components(), and get_wt_averaged_totals().

◆ get_wt_averaged_totals()

core::Real protocols::ddg::ddGMover::get_wt_averaged_totals ( )

References get_wt_averaged_score_components(), and sum().

Referenced by ddG().

◆ get_wt_min_score_components()

utility::vector1< core::Real > protocols::ddg::ddGMover::get_wt_min_score_components ( )

References protocols::ddg::min_index(), core::scoring::total_score, and wt_components_.

Referenced by get_delta_energy_components(), and get_wt_min_totals().

◆ get_wt_min_totals()

core::Real protocols::ddg::ddGMover::get_wt_min_totals ( )

References get_wt_min_score_components(), and sum().

Referenced by apply(), and ddG().

◆ initialize_rotamer_behavior_for_residue_level_task()

void protocols::ddg::ddGMover::initialize_rotamer_behavior_for_residue_level_task ( core::pack::task::ResidueLevelTask & rltask ) const

private

References core::pack::task::ResidueLevelTask::or_ex1(), core::pack::task::ResidueLevelTask::or_ex2(), and core::pack::task::ResidueLevelTask::or_include_current().

Referenced by relax_wildtype_structure(), and setup_packer_task_for_mutations().

◆ initialize_task_level_behavior()

void protocols::ddg::ddGMover::initialize_task_level_behavior ( core::pack::task::PackerTaskOP packer_task )

private

Experimental: add extra options controlling how the packer behaves

Referenced by apply(), and relax_wildtype_structure().

◆ is_any_pdb_empty()

bool protocols::ddg::ddGMover::is_any_pdb_empty	(	core::pose::Pose const &	pose,
		std::string const &	mutant_traj,
		bool const	output_silent
	)		const

private

determine if we need to do any work, or if we have checkpoints saving us from some work

References dmp_pdb_, mutation_label(), num_iterations_, core::chemical::rings::q, core::io::silent::SilentFileData::read_file(), core::io::silent::SilentFileData::read_tags_fast(), and restrict_to_nbrhood_.

Referenced by apply().

◆ is_complete()

bool protocols::ddg::ddGMover::is_complete ( ObjexxFCL::FArray2D< core::Real > to_check )

private

Referenced by is_mutant_calc_complete(), and is_wt_calc_complete().

◆ is_interface_ddg() [1/2]

bool protocols::ddg::ddGMover::is_interface_ddg ( )

References interface_ddg_.

◆ is_interface_ddg() [2/2]

void protocols::ddg::ddGMover::is_interface_ddg ( bool truefalse )

References interface_ddg_.

Referenced by protocols::ddG_main().

◆ is_mutant_calc_complete()

bool protocols::ddg::ddGMover::is_mutant_calc_complete ( )

References is_complete(), and mutant_components_.

Referenced by protocols::ddG_main().

◆ is_properly_initialized()

bool protocols::ddg::ddGMover::is_properly_initialized ( core::pose::Pose & pose )

References residues_to_mutate_, and core::pose::Pose::size().

Referenced by apply().

◆ is_wt_calc_complete()

bool protocols::ddg::ddGMover::is_wt_calc_complete ( )

References is_complete(), and wt_components_.

Referenced by protocols::ddG_main(), and relax_wildtype_structure().

◆ minimization_score_function()

core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::minimization_score_function ( )

References min_cst_sfxn_.

◆ minimize_with_constraints()

void protocols::ddg::ddGMover::minimize_with_constraints	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	s,
		core::pack::task::PackerTaskOP	pt
	)

private

References core::scoring::fa_rep, core::optimization::MinimizerOptions::max_iter(), core::optimization::MinimizerOptions::nblist_auto_update(), core::pack::pack_rotamers(), core::optimization::AtomTreeMinimizer::run(), score_function(), core::kinematics::MoveMap::set_bb(), and core::kinematics::MoveMap::set_chi().

Referenced by apply(), and relax_wildtype_structure().

◆ mutant_score_components() [1/2]

ObjexxFCL::FArray2D< core::Real > protocols::ddg::ddGMover::mutant_score_components ( )

References mutant_components_.

◆ mutant_score_components() [2/2]

void protocols::ddg::ddGMover::mutant_score_components ( ObjexxFCL::FArray2D< core::Real > msc )

References mutant_components_.

◆ mutation_label()

std::string protocols::ddg::ddGMover::mutation_label ( core::pose::Pose const & pose ) const

References core::chemical::aa_unk, core::chemical::oneletter_code_from_aa(), core::chemical::rings::q, core::pose::Pose::residue(), residues_to_mutate_, and core::pose::Pose::size().

Referenced by apply(), protocols::ddG_main(), is_any_pdb_empty(), and relax_wildtype_structure().

◆ neighbor_cutoff() [1/2]

Real protocols::ddg::ddGMover::neighbor_cutoff ( )

References nbr_cutoff_.

◆ neighbor_cutoff() [2/2]

void protocols::ddg::ddGMover::neighbor_cutoff ( core::Real cutoff )

References nbr_cutoff_.

Referenced by protocols::ddG_main().

◆ neighborhood_of_mutations()

utility::vector1< bool > protocols::ddg::ddGMover::neighborhood_of_mutations	(	core::pose::Pose const &	pose,
		utility::vector1< int > const &	mutations
	)		const

private

References core::conformation::Residue::nbr_atom(), nbr_cutoff_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by relax_wildtype_structure(), and setup_packer_task_for_mutations().

◆ num_iterations() [1/2]

int protocols::ddg::ddGMover::num_iterations ( )

References num_iterations_.

◆ num_iterations() [2/2]

void protocols::ddg::ddGMover::num_iterations ( int num )

References num_iterations_.

Referenced by protocols::ddG_main().

◆ print_verbose_ddgs()

void protocols::ddg::ddGMover::print_verbose_ddgs	(	utility::vector1< core::pose::Pose >	mut,
		utility::vector1< core::pose::Pose >	wt,
		core::scoring::ScoreFunctionOP	sfxn,
		bool	mean,
		bool	min,
		std::string	filename
	)

private

◆ relax_wildtype_structure()

void protocols::ddg::ddGMover::relax_wildtype_structure	(	core::pose::Pose &	pose,
		protocols::scoring::Interface &	protein_interface,
		std::string const &	wt_traj,
		bool	output_silent
	)

private

APL's attempts at refactoring this code.

Apply the protocol to the wild type species.

References core::chemical::aa_unk, protocols::scoring::Interface::calculate(), calculate_interface_unbound_energy(), core::pose::Pose::chain(), core::pose::Pose::constraint_set(), dbg_output_, protocols::scoring::Interface::distance(), dmp_pdb_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), initialize_rotamer_behavior_for_residue_level_task(), initialize_task_level_behavior(), interface_ddg_, protocols::scoring::Interface::is_interface(), is_wt_calc_complete(), min_cst_, min_cst_mut_types_, min_cst_set_mut_, min_cst_set_wt_, min_cst_sfxn_, min_cst_sfxn_no_cst_weight_, min_cst_wt_types_, minimize_with_constraints(), mutation_label(), natives_, neighborhood_of_mutations(), num_iterations_, core::pack::pack_rotamers_loop(), core::chemical::rings::q, core::pose::Pose::remove_constraints(), repack_cst_set_mut_, repack_cst_set_wt_, repack_mut_types_, repack_wt_types_, residues_to_mutate_, restrict_to_nbrhood_, scorefxn_, core::io::silent::SilentFileData::set_filename(), setup_constraints(), setup_repack_constraints(), core::pose::Pose::size(), store_energies(), core::scoring::Energies::total_energies(), protocols::TR(), core::scoring::EMapVector::weighted_string_of(), core::io::silent::SilentFileData::write_silent_struct(), wt_components_, and wt_unbound_components_.

Referenced by apply().

◆ residues_to_mutate() [1/2]

utility::vector1< core::chemical::AA > protocols::ddg::ddGMover::residues_to_mutate ( )

References residues_to_mutate_.

◆ residues_to_mutate() [2/2]

void protocols::ddg::ddGMover::residues_to_mutate ( utility::vector1< core::chemical::AA > residues )

References residues_to_mutate_.

Referenced by protocols::ddG_main().

◆ restrict_to_nbrs() [1/2]

bool protocols::ddg::ddGMover::restrict_to_nbrs ( )

References restrict_to_nbrhood_.

◆ restrict_to_nbrs() [2/2]

void protocols::ddg::ddGMover::restrict_to_nbrs ( bool truefalse )

References restrict_to_nbrhood_.

Referenced by protocols::ddG_main().

◆ score_function() [1/2]

core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::score_function ( )

References scorefxn_.

Referenced by minimize_with_constraints().

◆ score_function() [2/2]

void protocols::ddg::ddGMover::score_function ( core::scoring::ScoreFunctionOP s )

References scorefxn_.

◆ set_mean()

void protocols::ddg::ddGMover::set_mean ( bool truefalse )

References mean_.

Referenced by protocols::ddG_main().

◆ set_min()

void protocols::ddg::ddGMover::set_min ( bool truefalse )

References min_, and num_decoys_used_in_calculations_.

Referenced by protocols::ddG_main().

◆ set_min_cst()

void protocols::ddg::ddGMover::set_min_cst ( bool truefalse )

References min_cst_.

Referenced by protocols::ddG_main().

◆ set_minimization_score_function()

void protocols::ddg::ddGMover::set_minimization_score_function ( core::scoring::ScoreFunctionOP s )

References min_cst_sfxn_, and min_cst_sfxn_no_cst_weight_.

◆ set_num_decoys_used_in_calculations()

void protocols::ddg::ddGMover::set_num_decoys_used_in_calculations ( core::Real num_lowe_used )

References num_decoys_used_in_calculations_.

◆ setup_constraints()

void protocols::ddg::ddGMover::setup_constraints	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		float const	cst_tol,
		bool	all_but_mut_site,
		utility::vector1< char > &	constraints_at_pos
	)

private

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::scoring::constraints::ConstraintIO::read_constraints(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by relax_wildtype_structure().

◆ setup_packer_task_for_mutations()

void protocols::ddg::ddGMover::setup_packer_task_for_mutations	(	core::pose::Pose const &	pose,
		protocols::scoring::Interface const &	protein_interface,
		utility::vector1< int > const &	mutations,
		core::pack::task::PackerTaskOP	packer_task
	)

private

Initialize a packer task to reflect the residues that should be repacked based on the structure of the wildtype pose.

References core::chemical::aa_unk, initialize_rotamer_behavior_for_residue_level_task(), interface_ddg_, protocols::scoring::Interface::is_interface(), neighborhood_of_mutations(), residues_to_mutate_, restrict_to_nbrhood_, core::pose::Pose::size(), and protocols::TR().

Referenced by apply().

◆ setup_packertask()

void protocols::ddg::ddGMover::setup_packertask	(	core::pack::task::PackerTaskOP	pt,
		core::pose::Pose &	p
	)

private

◆ setup_repack_constraints()

void protocols::ddg::ddGMover::setup_repack_constraints	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		bool	all_but_mut_site,
		utility::vector1< char > &	constraints_at_pos
	)

private

sets up only rotamer constraints available during repacking

References core::chemical::aa_unk, core::scoring::atom_pair_constraint, core::pose::Pose::remove_constraints(), and residues_to_mutate_.

Referenced by relax_wildtype_structure().

◆ setup_rotamer_constraints()

void protocols::ddg::ddGMover::setup_rotamer_constraints	(	core::pose::Pose &	p,
		core::scoring::ScoreFunction &	s,
		utility::vector1< int > &	mutation_position,
		bool	all_but_mutation_site,
		utility::vector1< char > &	constraints_at_pos
	)

private

◆ store_energies()

int protocols::ddg::ddGMover::store_energies	(	ObjexxFCL::FArray2D< core::Real > &	two_d_e_arrays,
		core::scoring::ScoreFunction &	s,
		core::pose::Pose &	p,
		int	next_index,
		int	size_to_expect
	)