#include <ddGMover.hh>

Inheritance diagram for protocols::ddg::ddGMover:

Collaboration diagram for protocols::ddg::ddGMover:

Public Member Functions
	ddGMover ()

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

virtual	~ddGMover ()

void	neighbor_cutoff (double 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< double > wsc)

void	wt_unbound_score_components (ObjexxFCL::FArray2D< double > wusc)

void	mutant_score_components (ObjexxFCL::FArray2D< double > 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< double >	wt_score_components ()

ObjexxFCL::FArray2D< double >	wt_unbound_score_components ()

ObjexxFCL::FArray2D< double >	mutant_score_components ()

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

utility::vector1< double >	get_wt_min_score_components ()

utility::vector1< double >	get_wt_averaged_score_components ()

utility::vector1< double >	get_mutant_min_score_components ()

utility::vector1< double >	get_mutant_averaged_score_components ()

utility::vector1< double >	get_delta_energy_components ()

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

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

double	get_wt_averaged_totals ()

double	get_wt_min_totals ()

double	get_mutant_averaged_totals ()

double	get_mutant_min_totals ()

double	ddG ()

virtual void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	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 (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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
utility::vector1< int >	find_nbrs (core::pose::Pose &p, utility::vector1< int > &mutation_position, double radii)

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

bool	is_complete (ObjexxFCL::FArray2D< double > to_check)

double	sum (ddGs &scores_to_sum)

double	average (utility::vector1< double > &scores_to_average)

int	store_energies (ObjexxFCL::FArray2D< double > &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< double > &scores_to_average, utility::vector1< double > &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 (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 (pose::Pose &pose, core::scoring::ScoreFunctionOP s, core::pack::task::PackerTaskOP pt)

void	print_verbose_ddgs (utility::vector1< pose::Pose > mut, utility::vector1< 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< double >	wt_components_

ObjexxFCL::FArray2D< double >	wt_unbound_components_

ObjexxFCL::FArray2D< double >	mutant_components_

ObjexxFCL::FArray2D< double >	mutant_unbound_components_

utility::vector1< pose::Pose >	natives_

utility::vector1< pose::Pose >	mutants_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 52 of file ddGMover.hh.

Constructor & Destructor Documentation

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

Definition at line 117 of file ddGMover.cc.

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

Definition at line 150 of file ddGMover.cc.

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

virtual

Definition at line 188 of file ddGMover.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 1384 of file ddGMover.cc.

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(), 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(), store_energies(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR(), core::scoring::EMapVector::weighted_string_of(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::ddG_main().

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

private

Definition at line 244 of file ddGMover.cc.

References sum().

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

private

Definition at line 306 of file ddGMover.cc.

References 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().

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

private

Definition at line 374 of file ddGMover.cc.

References core::pack::pack_rotamers().

Referenced by apply(), and relax_wildtype_structure().

double protocols::ddg::ddGMover::ddG ( )

Definition at line 928 of file ddGMover.cc.

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().

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

Definition at line 617 of file ddGMover.cc.

References dbg_output_.

Referenced by protocols::ddG_main().

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

Definition at line 612 of file ddGMover.cc.

References dmp_pdb_.

Referenced by protocols::ddG_main().

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

private

Definition at line 192 of file ddGMover.cc.

References core::conformation::Residue::name1(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

utility::vector1< double > protocols::ddg::ddGMover::get_delta_energy_components ( )

Definition at line 827 of file ddGMover.cc.

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().

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

Definition at line 968 of file ddGMover.cc.

References min_cst_.

utility::vector1< double > protocols::ddg::ddGMover::get_mutant_averaged_score_components ( )

Definition at line 803 of file ddGMover.cc.

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().

double protocols::ddg::ddGMover::get_mutant_averaged_totals ( )

Definition at line 908 of file ddGMover.cc.

References get_mutant_averaged_score_components(), and sum().

Referenced by ddG().

utility::vector1< double > protocols::ddg::ddGMover::get_mutant_min_score_components ( )

Definition at line 770 of file ddGMover.cc.

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

Referenced by get_delta_energy_components(), and get_mutant_min_totals().

double protocols::ddg::ddGMover::get_mutant_min_totals ( )

Definition at line 918 of file ddGMover.cc.

References get_mutant_min_score_components(), and sum().

Referenced by apply(), and ddG().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 1554 of file ddGMover.cc.

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

Definition at line 983 of file ddGMover.cc.

References num_decoys_used_in_calculations_.

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

Definition at line 847 of file ddGMover.cc.

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

utility::vector1< double > protocols::ddg::ddGMover::get_wt_averaged_score_components ( )

Definition at line 749 of file ddGMover.cc.

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().

double protocols::ddg::ddGMover::get_wt_averaged_totals ( )

Definition at line 887 of file ddGMover.cc.

References get_wt_averaged_score_components(), and sum().

Referenced by ddG().

utility::vector1< double > protocols::ddg::ddGMover::get_wt_min_score_components ( )

Definition at line 716 of file ddGMover.cc.

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

Referenced by get_delta_energy_components(), and get_wt_min_totals().

double protocols::ddg::ddGMover::get_wt_min_totals ( )

Definition at line 897 of file ddGMover.cc.

References get_wt_min_score_components(), and sum().

Referenced by apply(), and ddG().

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

private

Definition at line 1373 of file ddGMover.cc.

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().

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

private

Experimental: add extra options controlling how the packer behaves

Definition at line 1259 of file ddGMover.cc.

Referenced by apply(), and relax_wildtype_structure().

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

Definition at line 1276 of file ddGMover.cc.

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

Referenced by apply().

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

private

Definition at line 221 of file ddGMover.cc.

Referenced by is_mutant_calc_complete(), and is_wt_calc_complete().

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

Definition at line 622 of file ddGMover.cc.

References interface_ddg_.

Referenced by protocols::ddG_main().

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

Definition at line 693 of file ddGMover.cc.

References interface_ddg_.

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

Definition at line 946 of file ddGMover.cc.

References is_complete(), and mutant_components_.

Referenced by protocols::ddG_main().

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

Definition at line 951 of file ddGMover.cc.

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

Referenced by apply().

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

Definition at line 941 of file ddGMover.cc.

References is_complete(), and wt_components_.

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

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

Definition at line 685 of file ddGMover.cc.

References min_cst_sfxn_.

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

private

Definition at line 480 of file ddGMover.cc.

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

Referenced by apply(), and relax_wildtype_structure().

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

Definition at line 637 of file ddGMover.cc.

References mutant_components_.

ObjexxFCL::FArray2D< double > protocols::ddg::ddGMover::mutant_score_components ( )

Definition at line 706 of file ddGMover.cc.

References mutant_components_.

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

Definition at line 868 of file ddGMover.cc.

References core::chemical::aa_unk, core::chemical::oneletter_code_from_aa(), core::pose::Pose::residue(), residues_to_mutate_, and core::pose::Pose::total_residue().

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

void protocols::ddg::ddGMover::neighbor_cutoff ( double cutoff)

Definition at line 586 of file ddGMover.cc.

References nbr_cutoff_.

Referenced by protocols::ddG_main().

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

Definition at line 670 of file ddGMover.cc.

References nbr_cutoff_.

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

private

Definition at line 1337 of file ddGMover.cc.

References core::conformation::Residue::name1(), nbr_cutoff_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by relax_wildtype_structure(), and setup_packer_task_for_mutations().

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

Definition at line 607 of file ddGMover.cc.

References num_iterations_.

Referenced by protocols::ddG_main().

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

Definition at line 690 of file ddGMover.cc.

References num_iterations_.

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

private

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.

Definition at line 988 of file ddGMover.cc.

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::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(), store_energies(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR(), core::scoring::EMapVector::weighted_string_of(), core::io::silent::SilentFileData::write_silent_struct(), wt_components_, and wt_unbound_components_.

Referenced by apply().

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

Definition at line 642 of file ddGMover.cc.

References residues_to_mutate_.

Referenced by protocols::ddG_main().

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

Definition at line 711 of file ddGMover.cc.

References residues_to_mutate_.

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

Definition at line 591 of file ddGMover.cc.

References restrict_to_nbrhood_.

Referenced by protocols::ddG_main().

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

Definition at line 675 of file ddGMover.cc.

References restrict_to_nbrhood_.

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

Definition at line 602 of file ddGMover.cc.

References scorefxn_.

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

Definition at line 680 of file ddGMover.cc.

References scorefxn_.

Referenced by minimize_with_constraints().

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

Definition at line 652 of file ddGMover.cc.

References mean_.

Referenced by protocols::ddG_main().

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

Definition at line 657 of file ddGMover.cc.

References min_, and num_decoys_used_in_calculations_.

Referenced by protocols::ddG_main().

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

Definition at line 647 of file ddGMover.cc.

References min_cst_.

Referenced by protocols::ddG_main().

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

Definition at line 596 of file ddGMover.cc.

References min_cst_sfxn_, and min_cst_sfxn_no_cst_weight_.

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

Definition at line 665 of file ddGMover.cc.

References num_decoys_used_in_calculations_.

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

private

Definition at line 422 of file ddGMover.cc.

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::total_residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by relax_wildtype_structure().

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.

Definition at line 1201 of file ddGMover.cc.

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::total_residue(), and protocols::TR().

Referenced by apply().

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

private

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

Definition at line 393 of file ddGMover.cc.

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

Referenced by relax_wildtype_structure().

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

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