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

#include <CentroidRelax.hh>

Inheritance diagram for protocols::relax::CentroidRelax:

Collaboration diagram for protocols::relax::CentroidRelax:

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

Public Member Functions
	CentroidRelax ()

	CentroidRelax (MoveMapOP mm)

	CentroidRelax (MoveMapOP mm, ScoreFunctionOP cen_scorefxn_in)

virtual	~CentroidRelax ()

virtual string	get_name () const
	Each derived class must specify its name. The class name. More...

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

void	set_defaults ()

void	set_rounds (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 (ScoreFunctionOP cen_score)
	Sets main scorefunction used for centroid minimization. More...

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

void	set_min_type (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...

virtual void	apply (Pose &pose)
	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 ()

virtual protocols::moves::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_defaults ()

void	set_default_minimization_settings ()

void	set_default_coordinate_settings ()

void	set_default_movemap ()

void	minimize_bond_lengths (bool setting)

void	minimize_bond_angles (bool setting)

void	minimize_bondlength_subset (int setting)

void	minimize_bondangle_subset (int setting)

bool	minimize_bond_lengths () const

bool	minimize_bond_angles () const

int	minimize_bondlength_subset () const

int	minimize_bondangle_subset () const

bool	constrain_relax_to_native_coords () const

bool	constrain_relax_to_start_coords () const

bool	constrain_coords () const

bool	explicit_ramp_constraints () const

bool	ramp_down_constraints () const

bool	constrain_relax_segments () const

bool	limit_aroma_chi2 () const

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	ramp_down_constraints (bool ramp_down_constraints)

void	constrain_relax_segments (bool constrain_relax_segments)

void	cartesian (bool newval)

bool	cartesian () const

core::kinematics::MoveMapOP	get_movemap ()

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

void	set_min_type (std::string min_type)

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

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

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

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

void	set_dry_run (bool setting)

bool	dry_run () const

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

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void	register_options ()

Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
void	initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)

core::scoring::ScoreFunctionOP	get_scorefxn ()

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

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

Protected Attributes inherited from protocols::relax::RelaxProtocolBase
bool	constrain_relax_to_native_coords_

bool	constrain_relax_to_start_coords_

bool	constrain_coords_

bool	coord_constrain_sidechains_

bool	explicit_ramp_constraints_

bool	ramp_down_constraints_

bool	constrain_relax_segments_

std::string	min_type_

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

bool	limit_aroma_chi2_

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

Definition at line 56 of file CentroidRelax.hh.

Constructor & Destructor Documentation

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

Definition at line 69 of file CentroidRelax.cc.

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

Referenced by clone().

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

Definition at line 79 of file CentroidRelax.cc.

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

protocols::relax::CentroidRelax::CentroidRelax	(	MoveMapOP	mm,
		ScoreFunctionOP	cen_scorefxn_in
	)

Definition at line 89 of file CentroidRelax.cc.

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

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

virtual

Definition at line 99 of file CentroidRelax.cc.

Member Function Documentation

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

virtual

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.

Definition at line 253 of file CentroidRelax.cc.

References protocols::relax::RelaxProtocolBase::cartesian_, cen_scorefxn_, core::pack::task::TaskFactory::create_packer_task(), def_parameters, fa_scorefxn_, core::pose::Pose::is_centroid(), core::pose::symmetry::is_symmetric(), 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::total_residue(), 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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 102 of file CentroidRelax.cc.

References CentroidRelax().

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

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

Definition at line 248 of file CentroidRelax.cc.

References repack_sc_.

Referenced by set_defaults().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 107 of file CentroidRelax.cc.

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

private

Load the default parameters from the default file.

Definition at line 228 of file CentroidRelax.cc.

References protocols::relax::CentroidRelax::parameters::cst_params, def_parameters, 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.

Definition at line 207 of file CentroidRelax.cc.

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

Referenced by set_defaults().

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

Definition at line 126 of file CentroidRelax.cc.

References do_final_repack(), core::scoring::getScoreFunction(), 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 ( ScoreFunctionOP fa_score)

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

Definition at line 121 of file CentroidRelax.cc.

References fa_scorefxn_.

Referenced by set_defaults().

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

Sets the minimizer type.

Definition at line 223 of file CentroidRelax.cc.

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.

Definition at line 173 of file CentroidRelax.cc.

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.

Definition at line 202 of file CentroidRelax.cc.

References ramp_vdw_.

Referenced by apply(), and set_defaults().

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

Definition at line 141 of file CentroidRelax.cc.

References rounds_.

Referenced by set_defaults().

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

Sets main scorefunction used for centroid minimization.

Definition at line 112 of file CentroidRelax.cc.

References cen_scorefxn_, core::scoring::chainbreak, protocols::relax::RelaxProtocolBase::get_scorefxn(), 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)

Definition at line 146 of file CentroidRelax.cc.

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.

Definition at line 151 of file CentroidRelax.cc.

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.

Definition at line 177 of file CentroidRelax.cc.

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

Definition at line 193 of file CentroidRelax.cc.

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

Referenced by apply().

Member Data Documentation

bool protocols::relax::CentroidRelax::cartesian_mode_

private

Definition at line 121 of file CentroidRelax.hh.

ScoreFunctionOP protocols::relax::CentroidRelax::cen_scorefxn_

private

Definition at line 123 of file CentroidRelax.hh.

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

Definition at line 136 of file CentroidRelax.hh.

Referenced by apply(), and read_default_parameters().

ScoreFunctionOP protocols::relax::CentroidRelax::fa_scorefxn_

private

Definition at line 124 of file CentroidRelax.hh.

Referenced by apply(), and set_fa_score_function().

MoveMapOP protocols::relax::CentroidRelax::movemap_

private

Definition at line 125 of file CentroidRelax.hh.

Referenced by apply(), and setup_class_movemap_and_constraints().

ScoreType protocols::relax::CentroidRelax::rama_type_

private

Definition at line 126 of file CentroidRelax.hh.

Referenced by apply(), and set_use_rama2b().

bool protocols::relax::CentroidRelax::ramp_rama_

private

Definition at line 118 of file CentroidRelax.hh.

Referenced by apply(), and set_ramp_rama().

bool protocols::relax::CentroidRelax::ramp_vdw_

private

Definition at line 119 of file CentroidRelax.hh.

Referenced by apply(), and set_ramp_vdw().

bool protocols::relax::CentroidRelax::repack_sc_

private

Definition at line 122 of file CentroidRelax.hh.

Referenced by apply(), and do_final_repack().

Size protocols::relax::CentroidRelax::rounds_

private

Definition at line 120 of file CentroidRelax.hh.

Referenced by apply(), and set_rounds().

bool protocols::relax::CentroidRelax::use_increased_vdw_radii_

private

Definition at line 117 of file CentroidRelax.hh.

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_

Size	rounds_

bool	cartesian_mode_

bool	repack_sc_

ScoreFunctionOP	cen_scorefxn_

ScoreFunctionOP	fa_scorefxn_

MoveMapOP	movemap_

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