#include <FastDesign.hh>

Inheritance diagram for protocols::denovo_design::movers::FastDesign:

Public Member Functions
	FastDesign ()
	default constructor More...

	FastDesign (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
	Constructor with some options. More...

	FastDesign (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
	Constructor with some options. More...

	~FastDesign () override
	virtual constructor to allow derivation More...

void	set_up_default_task_factory ()
	Create the default task factory. Must be called before design can occur. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the FastDesignTags. More...

protocols::moves::MoverOP	fresh_instance () const override
	Return the name of this mover. More...

protocols::moves::MoverOP	clone () const override
	return a copy of this class in an owning pointer More...

void	apply (core::pose::Pose &pose) override
	Apply the FastDesign. Overloaded apply function from mover base class. More...

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

void	add_constraint_generator (protocols::constraint_generator::ConstraintGeneratorCOP generator)
	Adds a constraint generator. Currently only used if ramp_down_constraints is set. If constraint generators are present, each time the constraint weights are changed, the constraint generators will be used to selectively remove constraint-generated constraints and add new ones. More...

void	clear_constraint_generators ()
	Clears the list of constraint generators. More...

void	set_clear_designable_residues (bool const clear_res)
	If set, residues that are designable will be mutated to alanine before design. More...

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

Public Member Functions inherited from protocols::relax::FastRelax
	FastRelax (core::Size standard_repeats=0)
	Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
	Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
	Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file)
	Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile. More...

void	set_script_to_batchrelax_default (core::Size standard_repeats=0)
	Override the stored script with the default script for batchrelax Ignores '-default_repeat' value. More...

void	set_script_from_lines (std::vector< std::string > const &filelines)
	replace schedule by providing lines of commands explicitly More...

void	set_force_nonideal (bool val)
	Force us to batchrelax with nonideal geometry (using additional memory) More...

void	dualspace (bool val)
	Use the dualspace (Dihedral + Cartesian) relax protocol (Default false) More...

bool	dualspace ()

core::Size	default_repeats () const
	Return the number of repeats. More...

void	set_movemap_disables_packing_of_fixed_chi_positions (bool const setting)
	Set whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...

bool	movemap_disables_packing_of_fixed_chi_positions () const
	Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...

	~FastRelax () override
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the FastRelaxTags. More...

void	set_to_default ()
	Initializes class using option system. This is called by the constructors. More...

protocols::moves::MoverOP	clone () const override
	return a fresh instance of this class in an owning pointer More...

void	apply (core::pose::Pose &pose) override
	Apply the FastRelax. Overloaded apply function from mover base class. More...

void	batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=nullptr, core::Real decay_rate=0.5)
	Batch Relax, a new even faster way to relax entire batches of structures. More...

void	set_enable_design (bool const val)
	sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.) More...

std::string	get_name () const override
	Return the name of this mover. More...

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

Public Member Functions inherited from protocols::relax::RelaxProtocolBase
	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	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 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

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 std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::relax::FastRelax
static std::string	mover_name ()
	Return the name of this mover. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_fast_relax (utility::tag::XMLSchemaDefinition &)

Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
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
void	set_constraint_weight (core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight, core::pose::Pose &pose) const override
	sets constraint weights – used with constraint ramping More...

Protected Member Functions inherited from protocols::relax::FastRelax
void	cmd_accept_to_best (const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count)

void	do_minimize (core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)

void	do_md (core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)

std::string	determine_default_relax_script ()
	default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_ More...

core::pack::task::TaskFactoryOP	setup_local_tf (core::pose::Pose const &pose, core::kinematics::MoveMapOP const &local_movemap)
	helper function for apply(). Helps setup the task factory More...

Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
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 Member Functions
core::pack::task::TaskFactoryOP	create_default_task_factory () const

Private Attributes
bool	clear_designable_residues_
	Should we clear designable residues (sets them to ALA so that they can be rebuilt) More...

core::Size	run_count_

protocols::constraint_generator::ConstraintGeneratorCOPs	cgs_

Additional Inherited Members
Public Types inherited from protocols::relax::RelaxProtocolBase
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

Constructor & Destructor Documentation

protocols::denovo_design::movers::FastDesign::FastDesign ( )

default constructor

FastDesign main code:

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::FastDesign	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		core::Size	standard_repeats = `0`
	)

Constructor with some options.

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::FastDesign	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		std::string const &	script_file
	)

Constructor with some options.

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::~FastDesign ( )

overridedefault

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Member Function Documentation

void protocols::denovo_design::movers::FastDesign::add_constraint_generator ( protocols::constraint_generator::ConstraintGeneratorCOP generator )

Adds a constraint generator. Currently only used if ramp_down_constraints is set. If constraint generators are present, each time the constraint weights are changed, the constraint generators will be used to selectively remove constraint-generated constraints and add new ones.

References cgs_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FastDesign::apply ( core::pose::Pose & pose )

overridevirtual

Apply the FastDesign. Overloaded apply function from mover base class.

Implements protocols::moves::Mover.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_ala, core::chemical::aa_dal, core::chemical::aa_dpr, core::chemical::aa_pro, protocols::simple_moves::MutateResidue::apply(), clear_designable_residues_, clone(), protocols::relax::RelaxProtocolBase::get_movemap(), protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::relax::RelaxProtocolBase::get_task_factory(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueTypeBase::is_d_aa(), core::chemical::ResidueTypeBase::is_l_aa(), core::conformation::Residue::is_protein(), protocols::moves::Mover::reset_status(), core::pose::Pose::residue(), run_count_, core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::type().

void protocols::denovo_design::movers::FastDesign::clear_constraint_generators ( )

Clears the list of constraint generators.

References cgs_.

protocols::moves::MoverOP protocols::denovo_design::movers::FastDesign::clone ( ) const

overridevirtual

return a copy of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

Referenced by apply().

core::pack::task::TaskFactoryOP protocols::denovo_design::movers::FastDesign::create_default_task_factory ( ) const

private

References core::id::CHI, protocols::relax::RelaxProtocolBase::get_movemap(), protocols::relax::RelaxProtocolBase::get_task_factory(), protocols::relax::RelaxProtocolBase::limit_aroma_chi2(), core::kinematics::MoveMap::movemap_torsion_id_begin(), core::kinematics::MoveMap::movemap_torsion_id_end(), and protocols::TR().

Referenced by set_up_default_task_factory().

protocols::moves::MoverOP protocols::denovo_design::movers::FastDesign::fresh_instance ( ) const

overridevirtual

Return the name of this mover.

return an blank version of ourselves

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

std::string protocols::denovo_design::movers::FastDesign::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

std::string protocols::denovo_design::movers::FastDesign::mover_name ( )

static

Referenced by get_name(), protocols::denovo_design::movers::FastDesignCreator::keyname(), and provide_xml_schema().

void protocols::denovo_design::movers::FastDesign::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Parses the FastDesignTags.

Reimplemented from protocols::moves::Mover.

References add_constraint_generator(), clear_designable_residues_, set_clear_designable_residues(), and set_up_default_task_factory().

void protocols::denovo_design::movers::FastDesign::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

void protocols::denovo_design::movers::FastDesign::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name().

Referenced by protocols::denovo_design::movers::FastDesignCreator::provide_xml_schema().

void protocols::denovo_design::movers::FastDesign::set_clear_designable_residues ( bool const clear_res )

inline

If set, residues that are designable will be mutated to alanine before design.

References clear_designable_residues_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FastDesign::set_constraint_weight	(	core::scoring::ScoreFunctionOP	local_scorefxn,
		core::scoring::EnergyMap const &	full_weights,
		core::Real const	weight,
		core::pose::Pose &	pose
	)		const