Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization. More...

#include <CentroidRelax.hh>

Inheritance diagram for protocols::relax::CentroidRelax:

Classes
struct	parameters
	Container for ramp settings. More...

Public Member Functions
	CentroidRelax ()

	CentroidRelax (core::kinematics::MoveMapOP mm)

	CentroidRelax (core::kinematics::MoveMapOP mm, core::scoring::ScoreFunctionOP cen_scorefxn_in)

	~CentroidRelax () override

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

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	set_defaults ()

void	set_rounds (core::Size rounds)

void	set_use_increased_vdw_radii (bool use)
	use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio) More...

void	set_use_rama2b (bool use)
	Sets to use Rama2b instead of Rama - default True. More...

void	set_ramp_rama (bool use)
	Ramp Rama according to centroid relax parameters. More...

void	set_ramp_vdw (bool use)
	Ramp VDW according to centroid relax parameters. More...

void	set_score_function (core::scoring::ScoreFunctionOP cen_score)
	Sets main scorefunction used for centroid minimization. More...

void	set_fa_score_function (core::scoring::ScoreFunctionOP fa_score)
	Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol. More...

void	set_min_type (std::string min)
	Sets the minimizer type. More...

void	set_cartesian (bool cart)
	Sets to use the cartesian minimizer. More...

void	do_final_repack (bool repack_sc)
	If a fullatom pose is passed, should we repack sidechains according to movemap? More...

void	apply (core::pose::Pose &pose) override
	Applies the protocol, See notes. 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

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...

Private Member Functions
void	read_default_parameters ()
	Load the default parameters from the default file. More...

void	setup_class_movemap_and_constraints (Pose &pose)
	used internally to setup extra stuff for movemap. More...

void	setup_increased_vdw_radii ()
	increase VDW radii for backbone to help geometry and decrease rmsd More...

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

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 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...

Detailed Description

Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization.

Minimize a centroid representation of a pose. Ramp VDW/Rama or both.

May tweak structure by up to ~2.5 A without constraints. Use custom constraints or coordinate constraints through relax options for best results. Using starting coordinate constraints, structure is tweaked by ~.3/.4 A Use increased VDW radii option for bb to improve bb-geometry when not using constraints

Constructor & Destructor Documentation

protocols::relax::CentroidRelax::CentroidRelax ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), protocols::hybridization::score, set_defaults(), and set_score_function().

protocols::relax::CentroidRelax::CentroidRelax ( core::kinematics::MoveMapOP mm )

References core::scoring::ScoreFunctionFactory::create_score_function(), protocols::hybridization::score, set_defaults(), protocols::relax::RelaxProtocolBase::set_movemap(), and set_score_function().

protocols::relax::CentroidRelax::CentroidRelax	(	core::kinematics::MoveMapOP	mm,
		core::scoring::ScoreFunctionOP	cen_scorefxn_in
	)

References set_defaults(), protocols::relax::RelaxProtocolBase::set_movemap(), and set_score_function().

protocols::relax::CentroidRelax::~CentroidRelax ( )

overridedefault

Member Function Documentation

void protocols::relax::CentroidRelax::apply ( core::pose::Pose & pose )

overridevirtual

Applies the protocol, See notes.

Setting ramp_rama and ramp_vdw to false switches to the BASIC protocol which is rounds of the centroid minmover

Implements protocols::moves::Mover.

References protocols::relax::RelaxProtocolBase::cartesian(), cen_scorefxn_, core::pack::task::TaskFactory::create_packer_task(), def_parameters, fa_scorefxn_, core::pose::Pose::is_centroid(), protocols::relax::CentroidRelax::parameters::min_params, protocols::relax::RelaxProtocolBase::min_type(), movemap_, core::scoring::rama, core::scoring::rama2b, protocols::relax::CentroidRelax::parameters::rama_params, rama_type_, ramp_rama_, ramp_vdw_, repack_sc_, rounds_, set_ramp_rama(), set_ramp_vdw(), setup_class_movemap_and_constraints(), setup_increased_vdw_radii(), core::pose::Pose::size(), protocols::relax::TR(), use_increased_vdw_radii_, core::scoring::vdw, and protocols::relax::CentroidRelax::parameters::vdw_params.

protocols::moves::MoverOP protocols::relax::CentroidRelax::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. 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.

Reimplemented from protocols::moves::Mover.

void protocols::relax::CentroidRelax::do_final_repack ( bool repack_sc )

If a fullatom pose is passed, should we repack sidechains according to movemap?

References repack_sc_.

Referenced by set_defaults().

string protocols::relax::CentroidRelax::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::relax::CentroidRelax::read_default_parameters ( )

private

Load the default parameters from the default file.

References protocols::relax::CentroidRelax::parameters::cst_params, def_parameters, protocols::mean_field::min(), protocols::relax::CentroidRelax::parameters::min_params, protocols::relax::CentroidRelax::parameters::rama_params, and protocols::relax::CentroidRelax::parameters::vdw_params.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_cartesian ( bool cart )

Sets to use the cartesian minimizer.

References protocols::relax::RelaxProtocolBase::cartesian(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::hybridization::score, set_min_type(), and set_score_function().

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_defaults ( )

References do_final_repack(), core::scoring::get_score_function(), read_default_parameters(), set_cartesian(), set_fa_score_function(), set_ramp_rama(), set_ramp_vdw(), set_rounds(), set_use_increased_vdw_radii(), and set_use_rama2b().

Referenced by CentroidRelax().

void protocols::relax::CentroidRelax::set_fa_score_function ( core::scoring::ScoreFunctionOP fa_score )

Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol.

References fa_scorefxn_, and protocols::hybridization::score.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_min_type ( std::string min )

Sets the minimizer type.

References protocols::relax::RelaxProtocolBase::min_type().

Referenced by set_cartesian().

void protocols::relax::CentroidRelax::set_ramp_rama ( bool use )

Ramp Rama according to centroid relax parameters.

References ramp_rama_.

Referenced by apply(), and set_defaults().

void protocols::relax::CentroidRelax::set_ramp_vdw ( bool use )

Ramp VDW according to centroid relax parameters.

References ramp_vdw_.

Referenced by apply(), and set_defaults().

void protocols::relax::CentroidRelax::set_rounds ( core::Size rounds )

References rounds_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_score_function ( core::scoring::ScoreFunctionOP cen_score )

Sets main scorefunction used for centroid minimization.

References cen_scorefxn_, core::scoring::chainbreak, protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::hybridization::score, and protocols::relax::RelaxProtocolBase::set_scorefxn().

Referenced by CentroidRelax(), and set_cartesian().

void protocols::relax::CentroidRelax::set_use_increased_vdw_radii ( bool use )

use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio)

References use_increased_vdw_radii_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_use_rama2b ( bool use )

Sets to use Rama2b instead of Rama - default True.

References cen_scorefxn_, core::scoring::rama, core::scoring::rama2b, and rama_type_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::setup_class_movemap_and_constraints ( Pose & pose )

private

used internally to setup extra stuff for movemap.

References cen_scorefxn_, protocols::relax::RelaxProtocolBase::get_movemap(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::symmetry::is_symmetric(), protocols::relax::make_dna_rigid(), core::pose::symmetry::make_symmetric_movemap(), movemap_, protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::RelaxProtocolBase::set_up_constraints(), and protocols::relax::TR().

Referenced by apply().

void protocols::relax::CentroidRelax::setup_increased_vdw_radii ( )

private

increase VDW radii for backbone to help geometry and decrease rmsd

References core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name(), cen_scorefxn_, and protocols::relax::TR().

Referenced by apply().

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::relax::CentroidRelax::cen_scorefxn_

private

Referenced by apply(), set_score_function(), set_use_rama2b(), setup_class_movemap_and_constraints(), and setup_increased_vdw_radii().

parameters protocols::relax::CentroidRelax::def_parameters

private

Referenced by apply(), and read_default_parameters().

core::scoring::ScoreFunctionOP protocols::relax::CentroidRelax::fa_scorefxn_

private

Referenced by apply(), and set_fa_score_function().

core::kinematics::MoveMapOP protocols::relax::CentroidRelax::movemap_

private

Referenced by apply(), and setup_class_movemap_and_constraints().

core::scoring::ScoreType protocols::relax::CentroidRelax::rama_type_

private

Referenced by apply(), and set_use_rama2b().

bool protocols::relax::CentroidRelax::ramp_rama_

private

Referenced by apply(), and set_ramp_rama().

bool protocols::relax::CentroidRelax::ramp_vdw_

private

Referenced by apply(), and set_ramp_vdw().

bool protocols::relax::CentroidRelax::repack_sc_

private

Referenced by apply(), and do_final_repack().

core::Size protocols::relax::CentroidRelax::rounds_

private

Referenced by apply(), and set_rounds().

bool protocols::relax::CentroidRelax::use_increased_vdw_radii_

private

Referenced by apply(), and set_use_increased_vdw_radii().

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

src/protocols/relax/CentroidRelax.hh
src/protocols/relax/CentroidRelax.cc

Private Attributes
bool	use_increased_vdw_radii_

bool	ramp_rama_

bool	ramp_vdw_

core::Size	rounds_

bool	repack_sc_

core::scoring::ScoreFunctionOP	cen_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

core::kinematics::MoveMapOP	movemap_

core::scoring::ScoreType	rama_type_

parameters	def_parameters

Classes

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation