Classes
class	ClassicRelaxCreator
class	ClassicRelax
	A functor class which implements the classic Rosetta++ pose_relax protocol. More...
struct	SRelaxPose
struct	RelaxScriptCommand
class	FastRelax
class	FastRelaxCreator
class	MiniRelax
class	RelaxProtocolBase
class	WorkUnit_BatchRelax
class	WorkUnit_BatchRelax_and_PostRescore
Typedefs
typedef utility::pointer::owning_ptr < FastRelax >	FastRelaxOP
typedef utility::pointer::owning_ptr < FastRelax const >	FastRelaxCOP
typedef utility::pointer::access_ptr < FastRelax >	FastRelaxAP
typedef utility::pointer::access_ptr < FastRelax const >	FastRelaxCAP
typedef utility::pointer::owning_ptr < MiniRelax >	MiniRelaxOP
typedef utility::pointer::owning_ptr < RelaxProtocolBase >	RelaxProtocolBaseOP
typedef utility::pointer::owning_ptr < RelaxProtocolBase const >	RelaxProtocolBaseCOP
typedef utility::pointer::access_ptr < RelaxProtocolBase >	RelaxProtocolBaseAP
typedef utility::pointer::access_ptr < RelaxProtocolBase const >	RelaxProtocolBaseCAP
typedef utility::pointer::owning_ptr < WorkUnit_BatchRelax >	WorkUnit_BatchRelaxOP
typedef utility::pointer::owning_ptr < WorkUnit_BatchRelax const >	WorkUnit_BatchRelaxCOP
Functions
void	coordinate_constrain_selection (core::pose::Pose &pose, core::sequence::SequenceAlignment aln, core::Real coord_sdev)
core::scoring::constraints::ConstraintSetOP	generate_bb_coordinate_constraints (core::pose::Pose &pose, utility::vector1< core::Real > const &coord_sdevs)
	Generate a set of coordinate constraints to backbone atoms using the given standard deviations, with one sd per-reside. If no constraint should be applied to a given residue, give a -1 for the value of the sdev.
void	delete_virtual_residues (core::pose::Pose &pose)
utility::vector1< core::Real >	get_per_residue_scores (core::pose::Pose &pose, core::scoring::ScoreType scoretype)
void	add_virtual_residue_to_cterm (core::pose::Pose &pose)
void	derive_sc_sc_restraints (core::pose::Pose &pose, core::Real const upper_dist_cutoff)
void	add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)
bool	rama_list_pred (const std::pair< core::Size, core::Real > &left, const std::pair< core::Size, core::Real > &right)
void	fix_worst_bad_ramas (core::pose::Pose &original_pose, core::Size how_many, core::Real skip_prob, core::Real limit_RMS, core::Real limit_rama)
int	Relax_main (bool)
RelaxProtocolBaseOP	generate_relax_from_cmd (bool NULL_if_no_flag)
void	setup_membrane_topology (pose::Pose &pose, std::string spanfile)
void	relax_pose (pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag)
static basic::Tracer	TR ("WorkUnit_BatchRelax")

Typedef Documentation

Function Documentation

void protocols::relax::add_coordinate_constraints_to_pose	(	core::pose::Pose &	pose,
		const core::pose::Pose &	constraint_target_pose,
		protocols::loops::Loops &	exclude_regions
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), protocols::loops::Loops::invert(), core::chemical::ResidueTypeSet::name_map(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().

Referenced by fix_worst_bad_ramas().

void protocols::relax::add_virtual_residue_to_cterm ( core::pose::Pose & pose )

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), make_table_of_pilot_apps::name, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), and core::pose::Pose::total_residue().

void protocols::relax::coordinate_constrain_selection	(	core::pose::Pose &	pose,
		core::sequence::SequenceAlignment	aln,
		core::Real	coord_sdev
	)

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), generate_bb_coordinate_constraints(), make_table_of_pilot_apps::name, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::sequence::SequenceAlignment::sequence_mapping(), core::sequence::SequenceAlignment::size(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::relax::MiniRelax::apply().

void protocols::relax::delete_virtual_residues ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::relax::MiniRelax::apply(), and protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps().

void protocols::relax::derive_sc_sc_restraints	(	core::pose::Pose &	pose,
		core::Real const	upper_dist_cutoff
	)

References core::pose::Pose::add_constraint(), core::kinematics::distance(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), tr(), and core::conformation::Residue::xyz().

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

void protocols::relax::fix_worst_bad_ramas	(	core::pose::Pose &	original_pose,
		core::Size	how_many,
		core::Real	skip_prob,
		core::Real	limit_RMS,
		core::Real	limit_rama
	)

core::scoring::constraints::ConstraintSetOP protocols::relax::generate_bb_coordinate_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > const &	coord_sdevs
	)

Generate a set of coordinate constraints to backbone atoms using the given standard deviations, with one sd per-reside. If no constraint should be applied to a given residue, give a -1 for the value of the sdev.

References core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd ( bool NULL_if_no_flag )

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::getScoreFunction(), script, and tr().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::wum::MPI_Relax::register_work_units(), Relax_main(), relax_pose(), and protocols::abinitio::AbrelaxMover::set_defaults().

utility::vector1< core::Real > protocols::relax::get_per_residue_scores	(	core::pose::Pose &	pose,
		core::scoring::ScoreType	scoretype
	)

References core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), and core::pose::Pose::total_residue().

Referenced by protocols::relax::MiniRelax::apply().

bool protocols::relax::rama_list_pred	(	const std::pair< core::Size, core::Real > &	left,
		const std::pair< core::Size, core::Real > &	right
	)

Referenced by fix_worst_bad_ramas().

int protocols::relax::Relax_main ( bool )

References generate_relax_from_cmd(), core::scoring::constraints::get_cst_fa_file_option(), protocols::jd2::JobDistributor::get_instance(), core::import_pose::pose_from_pdb(), protocols::jd2::set_native_in_mover(), and protocols::simple_moves::SuperimposeMover::set_reference_pose().

void protocols::relax::relax_pose	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::string const &	tag
	)

References generate_relax_from_cmd().

Referenced by protocols::symmetric_docking::SymDockProtocol::apply(), protocols::wum::MPI_Relax::register_work_units(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::vip::VIP_Mover::relax_favorable_poses().

void protocols::relax::setup_membrane_topology	(	pose::Pose &	pose,
		std::string	spanfile
	)

References core::pose::Pose::data(), core::scoring::MembraneTopology::initialize(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

static basic::Tracer protocols::relax::TR ( "WorkUnit_BatchRelax" ) [static]

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation