#include <RelaxProtocolBase.hh>

Inheritance diagram for protocols::relax::RelaxProtocolBase:

[legend]

Public Types
typedef moves::Mover	parent

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

Public Member Functions
	RelaxProtocolBase (core::scoring::ScoreFunctionOP)

	RelaxProtocolBase (std::string const &movername="RelaxProtocol")

	RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)

	~RelaxProtocolBase () override

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

void	set_defaults ()

void	set_default_minimization_settings ()

void	set_default_coordinate_settings ()

void	set_default_movemap ()

core::kinematics::MoveMapCOP	get_movemap () const

core::kinematics::MoveMapOP	get_movemap ()

const core::scoring::ScoreFunctionCOP	get_scorefxn () const

core::pack::task::TaskFactoryOP const &	get_task_factory () const

bool	cartesian () const

std::string	min_type () const

core::Size	max_iter () const

bool	dry_run () const

bool	constrain_relax_to_native_coords () const

bool	constrain_relax_to_start_coords () const

bool	constrain_coords () const

bool	coord_constrain_sidechains () const

bool	ramp_down_constraints () const

bool	constrain_relax_segments () const

bool	minimize_bond_lengths () const

bool	minimize_bond_angles () const

void	set_movemap (core::kinematics::MoveMapOP movemap)

void	set_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)

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

void	set_task_factory (core::pack::task::TaskFactoryOP task_factory)

void	cartesian (bool newval)
	Use cartesian (minimization step) More...

void	min_type (std::string min_type)

void	max_iter (core::Size max_iter)

void	dry_run (bool setting)

void	constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)

void	constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)

void	constrain_coords (bool constrain_coords)

void	coord_constrain_sidechains (bool coord_constrain_sidechains)

void	constrain_relax_segments (bool constrain_relax_segments)

void	ramp_down_constraints (bool ramp_down_constraints)

void	minimize_bond_lengths (bool minimize_bond_lengths)

void	minimize_bond_angles (bool minimize_bond_angles)

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

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	apply (Pose &)=0
	Main Method. 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...

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...

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. 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...

Static Public Member Functions
static void	register_options ()

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
core::scoring::ScoreFunctionOP	get_scorefxn ()

bool	fix_omega () const

int	minimize_bondlength_subset () const

int	minimize_bondangle_subset () const

bool	limit_aroma_chi2 () const

std::string	cst_files (core::Size const i) const

void	fix_omega (bool fix_omega)

void	minimize_bondangle_subset (int minimize_bondangle_subset)

void	minimize_bondlength_subset (int minimize_bondlength_subset)

void	initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)

void	set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)

void	output_debug_structure (core::pose::Pose &pose, std::string prefix)

void	add_cst_files (std::string const &cstfile)

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...

Private Attributes
bool	fix_omega_

bool	minimize_bond_lengths_

bool	minimize_bond_angles_

int	minimize_bondangle_subset_

int	minimize_bondlength_subset_

bool	constrain_relax_to_native_coords_

bool	constrain_relax_to_start_coords_

bool	constrain_coords_

bool	coord_constrain_sidechains_

bool	ramp_down_constraints_

bool	constrain_relax_segments_

utility::vector1< std::string >	cst_files_

std::string	min_type_

bool	cartesian_
	Do cartesian-space minimization? More...

core::Size	max_iter_
	maximum minimizer iterations More...

bool	limit_aroma_chi2_

core::kinematics::MoveMapOP	movemap_

core::select::movemap::MoveMapFactoryOP	movemap_factory_

core::scoring::ScoreFunctionOP	scorefxn_

core::pack::task::TaskFactoryOP	task_factory_
	task factory for packer ( used only FastRelax as of 11/05/2010 ) More...

bool	dry_run_
	Is this a dry run (i.e. do no cycles) More...

Member Typedef Documentation

◆ parent

typedef moves::Mover protocols::relax::RelaxProtocolBase::parent

Constructor & Destructor Documentation

◆ RelaxProtocolBase() [1/3]

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( core::scoring::ScoreFunctionOP score_in )

References set_defaults().

◆ RelaxProtocolBase() [2/3]

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( std::string const & movername = "RelaxProtocol" )

References set_defaults().

◆ RelaxProtocolBase() [3/3]

protocols::relax::RelaxProtocolBase::RelaxProtocolBase	(	std::string const &	movername,
		core::scoring::ScoreFunctionOP	score_in
	)

References set_defaults().

◆ ~RelaxProtocolBase()

protocols::relax::RelaxProtocolBase::~RelaxProtocolBase ( )

overridedefault

Member Function Documentation

◆ add_cst_files()

void protocols::relax::RelaxProtocolBase::add_cst_files ( std::string const & cstfile )

inlineprotected

References cst_files_.

Referenced by protocols::relax::FastRelax::parse_my_tag().

◆ apply_disulfides()

void protocols::relax::RelaxProtocolBase::apply_disulfides ( core::pose::Pose & pose )

References movemap_, protocols::antibody::design::repack, and core::pose::Pose::size().

Referenced by protocols::relax::ClassicRelax::apply(), and protocols::relax::MiniRelax::apply().

◆ cartesian() [1/2]

bool protocols::relax::RelaxProtocolBase::cartesian ( ) const

inline

References cartesian_.

Referenced by protocols::relax::CentroidRelax::apply(), protocols::relax::FastRelax::apply(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::check_nonideal_mintype(), protocols::evolution::NucleotideMutation::compute_folding_energies(), protocols::relax::FastRelax::do_minimize(), protocols::relax::FastRelax::parse_my_tag(), protocols::relax::RepeatProteinRelax::relax_pose(), and protocols::relax::CentroidRelax::set_cartesian().

◆ cartesian() [2/2]

void protocols::relax::RelaxProtocolBase::cartesian ( bool newval )

Use cartesian (minimization step)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.

References cartesian_.

◆ constrain_coords() [1/2]

bool protocols::relax::RelaxProtocolBase::constrain_coords ( ) const

inline

References constrain_coords_.

Referenced by protocols::relax::FastRelax::apply(), and constrain_coords().

◆ constrain_coords() [2/2]

void protocols::relax::RelaxProtocolBase::constrain_coords ( bool constrain_coords )

References constrain_coords(), and constrain_coords_.

◆ constrain_relax_segments() [1/2]

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments ( ) const

inline

References constrain_relax_segments_.

Referenced by constrain_relax_segments().

◆ constrain_relax_segments() [2/2]

void protocols::relax::RelaxProtocolBase::constrain_relax_segments ( bool constrain_relax_segments )

References constrain_relax_segments(), and constrain_relax_segments_.

◆ constrain_relax_to_native_coords() [1/2]

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( ) const

inline

References constrain_relax_to_native_coords_.

Referenced by constrain_relax_to_native_coords().

◆ constrain_relax_to_native_coords() [2/2]

void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( bool constrain_relax_to_native_coords )

References constrain_relax_to_native_coords(), and constrain_relax_to_native_coords_.

◆ constrain_relax_to_start_coords() [1/2]

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( ) const

inline

References constrain_relax_to_start_coords_.

Referenced by constrain_relax_to_start_coords().

◆ constrain_relax_to_start_coords() [2/2]

void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( bool constrain_relax_to_start_coords )

References constrain_relax_to_start_coords(), and constrain_relax_to_start_coords_.

◆ coord_constrain_sidechains() [1/2]

bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains ( ) const

inline

References coord_constrain_sidechains_.

Referenced by coord_constrain_sidechains().

◆ coord_constrain_sidechains() [2/2]

void protocols::relax::RelaxProtocolBase::coord_constrain_sidechains ( bool coord_constrain_sidechains )

References coord_constrain_sidechains(), and coord_constrain_sidechains_.

◆ cst_files()

std::string protocols::relax::RelaxProtocolBase::cst_files ( core::Size const i ) const

inlineprotected

References cst_files_.

Referenced by set_up_constraints().

◆ dry_run() [1/2]

bool protocols::relax::RelaxProtocolBase::dry_run ( ) const

inline

References dry_run_.

Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().

◆ dry_run() [2/2]

void protocols::relax::RelaxProtocolBase::dry_run ( bool setting )

References dry_run_.

◆ fix_omega() [1/2]

bool protocols::relax::RelaxProtocolBase::fix_omega ( ) const

inlineprotected

References fix_omega_.

◆ fix_omega() [2/2]

void protocols::relax::RelaxProtocolBase::fix_omega ( bool fix_omega )

inlineprotected

References fix_omega(), and fix_omega_.

Referenced by fix_omega().

◆ fresh_instance()

protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::clone().

◆ get_movemap() [1/2]

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::get_movemap ( )

References movemap_.

◆ get_movemap() [2/2]

core::kinematics::MoveMapCOP protocols::relax::RelaxProtocolBase::get_movemap ( ) const

References movemap_.

Referenced by protocols::denovo_design::movers::FastDesign::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::denovo_design::movers::FastDesign::create_default_task_factory(), protocols::relax::ClassicRelax::set_default_minimizer(), protocols::relax::ClassicRelax::set_default_moveset_phase1(), protocols::relax::ClassicRelax::set_default_moveset_phase2(), protocols::relax::ClassicRelax::set_default_moveset_phase3(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

◆ get_scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::get_scorefxn ( )

protected

References scorefxn_.

◆ get_scorefxn() [2/2]

const core::scoring::ScoreFunctionCOP protocols::relax::RelaxProtocolBase::get_scorefxn ( ) const

References scorefxn_.

◆ get_task_factory()

core::pack::task::TaskFactoryOP const & protocols::relax::RelaxProtocolBase::get_task_factory ( ) const

References task_factory_.

Referenced by protocols::denovo_design::movers::FastDesign::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::denovo_design::movers::FastDesign::create_default_task_factory(), and protocols::relax::FastRelax::setup_local_tf().

◆ initialize_movemap()

void protocols::relax::RelaxProtocolBase::initialize_movemap	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMap &	movemap
	)

protected

◆ limit_aroma_chi2()

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 ( ) const

inlineprotected

References limit_aroma_chi2_.

Referenced by protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::denovo_design::movers::FastDesign::create_default_task_factory(), and protocols::relax::FastRelax::setup_local_tf().

◆ max_iter() [1/2]

core::Size protocols::relax::RelaxProtocolBase::max_iter ( ) const

inline

References max_iter_.

Referenced by protocols::symmetric_docking::SymDockingHiRes::apply(), protocols::relax::FastRelax::do_minimize(), protocols::relax::FastRelax::inner_loop_ramp_repack_min_command(), and max_iter().

◆ max_iter() [2/2]

void protocols::relax::RelaxProtocolBase::max_iter ( core::Size max_iter )

References max_iter(), and max_iter_.

◆ min_type() [1/2]

std::string protocols::relax::RelaxProtocolBase::min_type ( ) const

inline

References min_type_.

Referenced by protocols::relax::CentroidRelax::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::relax::FastRelax::check_nonideal_mintype(), protocols::relax::FastRelax::do_minimize(), min_type(), protocols::relax::FastRelax::parse_my_tag(), protocols::relax::ClassicRelax::set_default(), and protocols::relax::CentroidRelax::set_min_type().

◆ min_type() [2/2]

void protocols::relax::RelaxProtocolBase::min_type ( std::string min_type )

References min_type(), and min_type_.

◆ minimize_bond_angles() [1/2]

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles ( ) const

inline

References minimize_bond_angles_.

Referenced by protocols::relax::FastRelax::check_nonideal_mintype(), and minimize_bond_angles().

◆ minimize_bond_angles() [2/2]

void protocols::relax::RelaxProtocolBase::minimize_bond_angles ( bool minimize_bond_angles )

References minimize_bond_angles(), and minimize_bond_angles_.

◆ minimize_bond_lengths() [1/2]

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( ) const

inline

References minimize_bond_lengths_.

Referenced by protocols::relax::FastRelax::check_nonideal_mintype(), and minimize_bond_lengths().

◆ minimize_bond_lengths() [2/2]

void protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( bool minimize_bond_lengths )

References minimize_bond_lengths(), and minimize_bond_lengths_.

◆ minimize_bondangle_subset() [1/2]

int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( ) const

inlineprotected

References minimize_bondangle_subset_.

◆ minimize_bondangle_subset() [2/2]

void protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( int minimize_bondangle_subset )

inlineprotected

References minimize_bondangle_subset(), and minimize_bondangle_subset_.

Referenced by minimize_bondangle_subset().

◆ minimize_bondlength_subset() [1/2]

int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( ) const

inlineprotected

References minimize_bondlength_subset_.

◆ minimize_bondlength_subset() [2/2]

void protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( int minimize_bondlength_subset )

inlineprotected

References minimize_bondlength_subset(), and minimize_bondlength_subset_.

Referenced by minimize_bondlength_subset().

◆ output_debug_structure()

void protocols::relax::RelaxProtocolBase::output_debug_structure	(	core::pose::Pose &	pose,
		std::string	prefix
	)

protected

References protocols::jd2::current_output_name(), protocols::moves::Mover::get_current_tag(), and core::io::silent::SilentFileData::write_silent_struct().

◆ provide_citation_info()

void protocols::relax::RelaxProtocolBase::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References scorefxn_, and task_factory_.

Referenced by protocols::relax::FastRelax::provide_citation_info().

◆ ramp_down_constraints() [1/2]

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints ( ) const

inline

References ramp_down_constraints_.

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::inner_loop_ramp_repack_min_command(), protocols::relax::FastRelax::parse_my_tag(), and ramp_down_constraints().

◆ ramp_down_constraints() [2/2]

void protocols::relax::RelaxProtocolBase::ramp_down_constraints ( bool ramp_down_constraints )

References ramp_down_constraints(), and ramp_down_constraints_.

◆ register_options()

void protocols::relax::RelaxProtocolBase::register_options ( )

static

Referenced by protocols::relax::ClassicRelax::register_options().

◆ set_default_coordinate_settings()

void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings ( )

References constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, constrain_relax_to_start_coords_, coord_constrain_sidechains_, limit_aroma_chi2_, and ramp_down_constraints_.

Referenced by set_defaults().

◆ set_default_minimization_settings()

void protocols::relax::RelaxProtocolBase::set_default_minimization_settings ( )

References cartesian_, fix_omega_, max_iter_, min_type_, minimize_bond_angles_, minimize_bond_lengths_, minimize_bondangle_subset_, and minimize_bondlength_subset_.

Referenced by set_defaults().

◆ set_default_movemap()

void protocols::relax::RelaxProtocolBase::set_default_movemap ( )

References movemap_.

Referenced by protocols::relax::ClassicRelax::set_default(), and set_defaults().

◆ set_defaults()

void protocols::relax::RelaxProtocolBase::set_defaults ( )

References dry_run_, set_default_coordinate_settings(), set_default_minimization_settings(), and set_default_movemap().

Referenced by RelaxProtocolBase().

◆ set_movemap()

void protocols::relax::RelaxProtocolBase::set_movemap ( core::kinematics::MoveMapOP movemap )

References movemap_.

Referenced by protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::relax::CentroidRelax::CentroidRelax(), protocols::relax::ClassicRelax::ClassicRelax(), protocols::evolution::NucleotideMutation::compute_folding_energies(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains(), protocols::relax::FastRelax::parse_my_tag(), protocols::relax::RepeatProteinRelax::relax_pose(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

◆ set_movemap_factory()

void protocols::relax::RelaxProtocolBase::set_movemap_factory ( core::select::movemap::MoveMapFactoryOP mm_factory )

References movemap_factory_.

Referenced by protocols::relax::FastRelax::parse_my_tag().

◆ set_scorefxn()

void protocols::relax::RelaxProtocolBase::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

References scorefxn_.

Referenced by protocols::relax::FastRelax::parse_my_tag(), protocols::relax::ClassicRelax::set_default(), and protocols::relax::CentroidRelax::set_score_function().

◆ set_task_factory()

void protocols::relax::RelaxProtocolBase::set_task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory_.

Referenced by protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::FastRelax::parse_my_tag(), and protocols::denovo_design::movers::FastDesign::set_up_default_task_factory().

◆ set_up_constraints()

void protocols::relax::RelaxProtocolBase::set_up_constraints	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	local_movemap
	)

protected

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), protocols::relax::AtomCoordinateCstMover::ambiguous_hnq(), protocols::relax::AtomCoordinateCstMover::apply(), core::scoring::atom_pair_constraint, protocols::relax::AtomCoordinateCstMover::bounded(), core::io::pdb::build_pose_from_pdb_as_is(), constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, core::pose::Pose::constraint_set(), coord_constrain_sidechains_, core::scoring::coordinate_constraint, cst_files(), cst_files_, protocols::relax::AtomCoordinateCstMover::cst_sd(), protocols::relax::AtomCoordinateCstMover::cst_sidechain(), protocols::relax::AtomCoordinateCstMover::cst_width(), protocols::relax::cyclize_pose(), protocols::relax::derive_sc_sc_restraints(), protocols::abinitio::filename(), core::pose::Pose::fold_tree(), get_scorefxn(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::kinematics::MoveMap::set_jump(), protocols::relax::AtomCoordinateCstMover::set_loop_segments(), and protocols::relax::AtomCoordinateCstMover::set_refstruct().

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

Member Data Documentation

◆ cartesian_

bool protocols::relax::RelaxProtocolBase::cartesian_

private

Do cartesian-space minimization?

Referenced by cartesian(), and set_default_minimization_settings().

◆ constrain_coords_

bool protocols::relax::RelaxProtocolBase::constrain_coords_

private

Referenced by constrain_coords(), set_default_coordinate_settings(), and set_up_constraints().

◆ constrain_relax_segments_

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_

private

Referenced by constrain_relax_segments(), set_default_coordinate_settings(), and set_up_constraints().

◆ constrain_relax_to_native_coords_

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_

private

Referenced by constrain_relax_to_native_coords(), set_default_coordinate_settings(), and set_up_constraints().

◆ constrain_relax_to_start_coords_

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_

private

Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().

◆ coord_constrain_sidechains_

bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_

private

Referenced by coord_constrain_sidechains(), set_default_coordinate_settings(), and set_up_constraints().

◆ cst_files_

utility::vector1< std::string > protocols::relax::RelaxProtocolBase::cst_files_

private

Referenced by add_cst_files(), cst_files(), and set_up_constraints().

◆ dry_run_

bool protocols::relax::RelaxProtocolBase::dry_run_

private

Is this a dry run (i.e. do no cycles)

Referenced by dry_run(), and set_defaults().

◆ fix_omega_

bool protocols::relax::RelaxProtocolBase::fix_omega_

private

Referenced by fix_omega(), initialize_movemap(), and set_default_minimization_settings().

◆ limit_aroma_chi2_

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_

private

Referenced by limit_aroma_chi2(), and set_default_coordinate_settings().

◆ max_iter_

core::Size protocols::relax::RelaxProtocolBase::max_iter_

private

maximum minimizer iterations

Referenced by max_iter(), and set_default_minimization_settings().

◆ min_type_

std::string protocols::relax::RelaxProtocolBase::min_type_

private

Referenced by min_type(), and set_default_minimization_settings().

◆ minimize_bond_angles_

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles_

private

Referenced by initialize_movemap(), minimize_bond_angles(), and set_default_minimization_settings().

◆ minimize_bond_lengths_

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths_

private

Referenced by initialize_movemap(), minimize_bond_lengths(), and set_default_minimization_settings().

◆ minimize_bondangle_subset_

int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset_

private

Referenced by initialize_movemap(), minimize_bondangle_subset(), and set_default_minimization_settings().

◆ minimize_bondlength_subset_

int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset_

private

Referenced by initialize_movemap(), minimize_bondlength_subset(), and set_default_minimization_settings().

◆ movemap_

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::movemap_

private

Referenced by apply_disulfides(), get_movemap(), set_default_movemap(), and set_movemap().

◆ movemap_factory_

core::select::movemap::MoveMapFactoryOP protocols::relax::RelaxProtocolBase::movemap_factory_

private

Referenced by initialize_movemap(), and set_movemap_factory().

◆ ramp_down_constraints_

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_

private

Referenced by ramp_down_constraints(), and set_default_coordinate_settings().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::scorefxn_

private

Referenced by get_scorefxn(), provide_citation_info(), and set_scorefxn().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::relax::RelaxProtocolBase::task_factory_

private

task factory for packer ( used only FastRelax as of 11/05/2010 )

Referenced by get_task_factory(), provide_citation_info(), and set_task_factory().

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

src/protocols/relax/RelaxProtocolBase.hh
src/protocols/relax/RelaxProtocolBase.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ RelaxProtocolBase() [1/3]

◆ RelaxProtocolBase() [2/3]

◆ RelaxProtocolBase() [3/3]

◆ ~RelaxProtocolBase()

Member Function Documentation

◆ add_cst_files()

◆ apply_disulfides()

◆ cartesian() [1/2]

◆ cartesian() [2/2]

◆ constrain_coords() [1/2]

◆ constrain_coords() [2/2]

◆ constrain_relax_segments() [1/2]

◆ constrain_relax_segments() [2/2]

◆ constrain_relax_to_native_coords() [1/2]

◆ constrain_relax_to_native_coords() [2/2]

◆ constrain_relax_to_start_coords() [1/2]

◆ constrain_relax_to_start_coords() [2/2]

◆ coord_constrain_sidechains() [1/2]

◆ coord_constrain_sidechains() [2/2]

◆ cst_files()

◆ dry_run() [1/2]

◆ dry_run() [2/2]

◆ fix_omega() [1/2]

◆ fix_omega() [2/2]

◆ fresh_instance()

◆ get_movemap() [1/2]

◆ get_movemap() [2/2]

◆ get_scorefxn() [1/2]

◆ get_scorefxn() [2/2]

◆ get_task_factory()

◆ initialize_movemap()

◆ limit_aroma_chi2()

◆ max_iter() [1/2]

◆ max_iter() [2/2]

◆ min_type() [1/2]

◆ min_type() [2/2]

◆ minimize_bond_angles() [1/2]

◆ minimize_bond_angles() [2/2]

◆ minimize_bond_lengths() [1/2]

◆ minimize_bond_lengths() [2/2]

◆ minimize_bondangle_subset() [1/2]

◆ minimize_bondangle_subset() [2/2]

◆ minimize_bondlength_subset() [1/2]

◆ minimize_bondlength_subset() [2/2]

◆ output_debug_structure()

◆ provide_citation_info()

◆ ramp_down_constraints() [1/2]

◆ ramp_down_constraints() [2/2]

◆ register_options()

◆ set_default_coordinate_settings()

◆ set_default_minimization_settings()

◆ set_default_movemap()

◆ set_defaults()

◆ set_movemap()

◆ set_movemap_factory()

◆ set_scorefxn()

◆ set_task_factory()

◆ set_up_constraints()

Member Data Documentation

◆ cartesian_

◆ constrain_coords_

◆ constrain_relax_segments_

◆ constrain_relax_to_native_coords_

◆ constrain_relax_to_start_coords_

◆ coord_constrain_sidechains_

◆ cst_files_

◆ dry_run_

◆ fix_omega_

◆ limit_aroma_chi2_

◆ max_iter_

◆ min_type_

◆ minimize_bond_angles_