protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

Inheritance diagram for protocols::relax::RelaxProtocolBase:

Collaboration diagram for protocols::relax::RelaxProtocolBase:

List of all members.

Public Types
typedef moves::Mover	parent
Public Member Functions
	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).
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_mainchain_bond_lengths (bool setting)
void	minimize_mainchain_bond_angles (bool setting)
bool	minimize_bond_lengths () const
bool	minimize_bond_angles () const
bool	minimize_mainchain_bond_lengths () const
bool	minimize_mainchain_bond_angles () 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)
Static Public Member Functions
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.
Protected Member Functions
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
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?
bool	limit_aroma_chi2_

---

Member Typedef Documentation

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

Reimplemented in protocols::relax::ClassicRelax, and protocols::relax::MiniRelax.

---

Constructor & Destructor Documentation

protocols::relax::RelaxProtocolBase::RelaxProtocolBase

(

core::scoring::ScoreFunctionOP

score_in

)

References set_defaults().

protocols::relax::RelaxProtocolBase::RelaxProtocolBase

(

std::string const &

movername = "RelaxProtocol"

)

References set_defaults().

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

References set_defaults().

protocols::relax::RelaxProtocolBase::~RelaxProtocolBase

(

)

---

Member Function Documentation

void protocols::relax::RelaxProtocolBase::apply_disulfides

(

core::pose::Pose &

pose

)

References core::scoring::ScoreFunctionFactory::create_score_function(), and core::pose::Pose::total_residue().

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

void protocols::relax::RelaxProtocolBase::cartesian

(

bool

newval

)

[inline]

References cartesian_.

bool protocols::relax::RelaxProtocolBase::cartesian

(

)

const [inline]

References cartesian_.

Referenced by protocols::relax::FastRelax::parse_my_tag(), and set_default_minimization_settings().

bool protocols::relax::RelaxProtocolBase::constrain_coords

(

)

const [inline]

References constrain_coords_.

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

void protocols::relax::RelaxProtocolBase::constrain_coords

(

bool

constrain_coords

)

[inline]

References constrain_coords(), and constrain_coords_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments

(

)

const [inline]

References constrain_relax_segments_.

Referenced by constrain_relax_segments(), and set_default_coordinate_settings().

void protocols::relax::RelaxProtocolBase::constrain_relax_segments

(

bool

constrain_relax_segments

)

[inline]

References constrain_relax_segments(), and constrain_relax_segments_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords

(

)

const [inline]

References constrain_relax_to_native_coords_.

Referenced by constrain_relax_to_native_coords(), and set_default_coordinate_settings().

void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords

(

bool

constrain_relax_to_native_coords

)

[inline]

References constrain_relax_to_native_coords(), and constrain_relax_to_native_coords_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords

(

)

const [inline]

References constrain_relax_to_start_coords_.

Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().

void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords

(

bool

constrain_relax_to_start_coords

)

[inline]

References constrain_relax_to_start_coords(), and constrain_relax_to_start_coords_.

bool protocols::relax::RelaxProtocolBase::dry_run

(

)

const [inline]

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

bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints

(

)

const [inline]

References explicit_ramp_constraints_.

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

virtual protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::fresh_instance

(

)

const [inline, virtual]

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).

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().

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

(

)

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::set_default_minimizer(), protocols::relax::ClassicRelax::set_default_moveset_phase1(), protocols::relax::ClassicRelax::set_default_moveset_phase2(), and protocols::relax::ClassicRelax::set_default_moveset_phase3().

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

(

)

const

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

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

(

)

[protected]

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

(

)

const

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

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

References core::id::D, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), core::kinematics::MoveMap::set(), core::id::THETA, and core::pose::Pose::total_residue().

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

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2

(

)

const [inline]

References limit_aroma_chi2_.

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

void protocols::relax::RelaxProtocolBase::minimize_bond_angles

(

bool

setting

)

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles

(

)

const

Referenced by set_default_minimization_settings().

void protocols::relax::RelaxProtocolBase::minimize_bond_lengths

(

bool

setting

)

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths

(

)

const

Referenced by set_default_minimization_settings().

void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles

(

bool

setting

)

bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles

(

)

const

Referenced by set_default_minimization_settings().

void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths

(

bool

setting

)

bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths

(

)

const

Referenced by set_default_minimization_settings().

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

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

void protocols::relax::RelaxProtocolBase::ramp_down_constraints

(

bool

ramp_down_constraints

)

[inline]

References explicit_ramp_constraints_, ramp_down_constraints(), and ramp_down_constraints_.

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints

(

)

const [inline]

References ramp_down_constraints_.

Referenced by protocols::relax::FastRelax::FastRelax(), and ramp_down_constraints().

void protocols::relax::RelaxProtocolBase::register_options

(

)

[static]

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.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::relax::ClassicRelax.

void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings

(

)

References constrain_coords_, constrain_relax_segments(), constrain_relax_segments_, constrain_relax_to_native_coords(), constrain_relax_to_native_coords_, constrain_relax_to_start_coords(), constrain_relax_to_start_coords_, coord_constrain_sidechains_, explicit_ramp_constraints_, limit_aroma_chi2(), limit_aroma_chi2_, and ramp_down_constraints_.

Referenced by set_defaults().

void protocols::relax::RelaxProtocolBase::set_default_minimization_settings

(

)

References cartesian(), cartesian_, min_type_, minimize_bond_angles(), minimize_bond_lengths(), minimize_mainchain_bond_angles(), and minimize_mainchain_bond_lengths().

Referenced by set_defaults().

void protocols::relax::RelaxProtocolBase::set_default_movemap

(

)

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

void protocols::relax::RelaxProtocolBase::set_dry_run

(

bool

setting

)

[inline]

void protocols::relax::RelaxProtocolBase::set_min_type

(

std::string

min_type

)

References min_type_.

Referenced by protocols::comparative_modeling::hybridize::HybridizeProtocol::apply().

void protocols::relax::RelaxProtocolBase::set_movemap

(

core::kinematics::MoveMapOP

movemap

)

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::ClassicRelax(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), and protocols::relax::FastRelax::parse_my_tag().

void protocols::relax::RelaxProtocolBase::set_scorefxn

(

core::scoring::ScoreFunctionOP

score

)

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

void protocols::relax::RelaxProtocolBase::set_task_factory

(

core::pack::task::TaskFactoryOP

taskf

)

Referenced by protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), and protocols::relax::FastRelax::parse_my_tag().

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::Pose::add_constraint(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, core::scoring::calpha_superimpose_pose(), constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, coord_constrain_sidechains_, core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), protocols::relax::derive_sc_sc_restraints(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), get_scorefxn(), core::chemical::ResidueTypeSet::name_map(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::num_jump(), ramp_down_constraints_, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::kinematics::MoveMap::set_jump(), and core::pose::Pose::total_residue().

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

---

Member Data Documentation

bool protocols::relax::RelaxProtocolBase::cartesian_ [protected]

Do cartesian-space minimization?

Referenced by cartesian(), protocols::relax::FastRelax::do_minimize(), and set_default_minimization_settings().

bool protocols::relax::RelaxProtocolBase::constrain_coords_ [protected]

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

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_ [protected]

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

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_ [protected]

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

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_ [protected]

Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().

bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_ [protected]

Referenced by set_default_coordinate_settings(), and set_up_constraints().

bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints_ [protected]

Referenced by explicit_ramp_constraints(), ramp_down_constraints(), and set_default_coordinate_settings().

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_ [protected]

Referenced by limit_aroma_chi2(), and set_default_coordinate_settings().

std::string protocols::relax::RelaxProtocolBase::min_type_ [protected]

Referenced by protocols::relax::FastRelax::do_minimize(), protocols::relax::ClassicRelax::set_default(), set_default_minimization_settings(), and set_min_type().

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_ [protected]

Referenced by protocols::relax::ClassicRelax::apply(), ramp_down_constraints(), set_default_coordinate_settings(), and set_up_constraints().

---

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

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