protocols::relax Namespace Reference

Namespaces
	membrane

Classes
class	AtomCoordinateCstMover
class	AtomCoordinateCstMoverCreator
class	CentroidRelax
	Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization. More...
class	ClassicRelax
	A functor class which implements the classic Rosetta++ pose_relax protocol. More...
class	ClassicRelaxCreator
class	FastRelax
class	FastRelaxCreator
class	MiniRelax
class	RelaxProtocolBase
struct	RelaxScriptCommand
struct	SRelaxPose
class	WorkUnit_BatchRelax
class	WorkUnit_BatchRelax_and_PostRescore

Typedefs
typedef utility::pointer::shared_ptr < AtomCoordinateCstMover >	AtomCoordinateCstMoverOP
typedef utility::pointer::shared_ptr < AtomCoordinateCstMover const >	AtomCoordinateCstMoverCOP
typedef utility::pointer::shared_ptr < CentroidRelax >	CentroidRelaxOP
typedef utility::pointer::shared_ptr < CentroidRelax const >	CentroidRelaxCOP
typedef utility::pointer::weak_ptr < CentroidRelax >	CentroidRelaxAP
typedef utility::pointer::weak_ptr < CentroidRelax const >	CentroidRelaxCAP
typedef utility::pointer::shared_ptr < FastRelax >	FastRelaxOP
typedef utility::pointer::shared_ptr < FastRelax const >	FastRelaxCOP
typedef utility::pointer::weak_ptr < FastRelax >	FastRelaxAP
typedef utility::pointer::weak_ptr < FastRelax const >	FastRelaxCAP
typedef utility::pointer::shared_ptr < MiniRelax >	MiniRelaxOP
typedef utility::pointer::shared_ptr < RelaxProtocolBase >	RelaxProtocolBaseOP
typedef utility::pointer::shared_ptr < RelaxProtocolBase const >	RelaxProtocolBaseCOP
typedef utility::pointer::weak_ptr < RelaxProtocolBase >	RelaxProtocolBaseAP
typedef utility::pointer::weak_ptr < RelaxProtocolBase const >	RelaxProtocolBaseCAP
typedef utility::pointer::shared_ptr < WorkUnit_BatchRelax >	WorkUnit_BatchRelaxOP
typedef utility::pointer::shared_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. More...
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 (core::pose::Pose &pose, std::string spanfile)
	(pba) read in membrane topology More...
void	make_dna_rigid (core::pose::Pose &pose, core::kinematics::MoveMap &mm)
	Make DNA Rigid in movemap if found in pose. More...
void	setup_for_dna (core::scoring::ScoreFunction &scorefxn)
	Set energy method options for DNA-DNA. Any other optimization for DNA relax should go here. More...
void	relax_pose (pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag)
static thread_local basic::Tracer	TR ("WorkUnit_BatchRelax")

Typedef Documentation

typedef utility::pointer::shared_ptr< AtomCoordinateCstMover const > protocols::relax::AtomCoordinateCstMoverCOP

typedef utility::pointer::shared_ptr< AtomCoordinateCstMover > protocols::relax::AtomCoordinateCstMoverOP

typedef utility::pointer::weak_ptr< CentroidRelax > protocols::relax::CentroidRelaxAP

typedef utility::pointer::weak_ptr< CentroidRelax const > protocols::relax::CentroidRelaxCAP

typedef utility::pointer::shared_ptr< CentroidRelax const > protocols::relax::CentroidRelaxCOP

typedef utility::pointer::shared_ptr< CentroidRelax > protocols::relax::CentroidRelaxOP

typedef utility::pointer::weak_ptr< FastRelax > protocols::relax::FastRelaxAP

typedef utility::pointer::weak_ptr< FastRelax const > protocols::relax::FastRelaxCAP

typedef utility::pointer::shared_ptr< FastRelax const > protocols::relax::FastRelaxCOP

typedef utility::pointer::shared_ptr< FastRelax > protocols::relax::FastRelaxOP

typedef utility::pointer::shared_ptr< MiniRelax > protocols::relax::MiniRelaxOP

typedef utility::pointer::weak_ptr< RelaxProtocolBase > protocols::relax::RelaxProtocolBaseAP

typedef utility::pointer::weak_ptr< RelaxProtocolBase const > protocols::relax::RelaxProtocolBaseCAP

typedef utility::pointer::shared_ptr< RelaxProtocolBase const > protocols::relax::RelaxProtocolBaseCOP

typedef utility::pointer::shared_ptr< RelaxProtocolBase > protocols::relax::RelaxProtocolBaseOP

typedef utility::pointer::shared_ptr< WorkUnit_BatchRelax const > protocols::relax::WorkUnit_BatchRelaxCOP

typedef utility::pointer::shared_ptr< WorkUnit_BatchRelax > protocols::relax::WorkUnit_BatchRelaxOP

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(), core::pose::Pose::total_residue(), and utility_exit.

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(), core::chemical::ResidueTypeSet::name_map(), 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(), core::chemical::ResidueTypeSet::name_map(), 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::chemical::ResidueType::name(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::relax::MiniRelax::apply(), protocols::relax::FastRelax::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(), distance(), numeric::xyzVector< class >::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
	)

References a(), add_coordinate_constraints_to_pose(), BB, core::scoring::CA_rmsd(), coordinate_constraint, omega, options, rama, rama_list_pred(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::total_residue(), TR(), and numeric::random::uniform().

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

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::get_score_function(), option, TR(), and user.

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::relax::membrane::MPFastRelaxMover::MPFastRelaxMover(), protocols::frag_picker::FragmentCandidate::output_silent(), Relax_main(), relax_pose(), protocols::rotamer_recovery::RRProtocolRelax::run(), 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().

void protocols::relax::make_dna_rigid	(	pose::Pose &	pose,
		core::kinematics::MoveMap &	mm
	)

Make DNA Rigid in movemap if found in pose.

References core::conformation::Residue::is_DNA(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::Pose::total_residue(), and TR().

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

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(), core::scoring::constraints::get_cst_file_option(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::go(), option, core::import_pose::pose_from_pdb(), protocols::jd2::set_native_in_mover(), and user.

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::frag_picker::FragmentCandidate::output_silent(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::vip::VIP_Mover::relax_favorable_poses().

void protocols::relax::setup_for_dna

(

core::scoring::ScoreFunction &

scorefxn

)

Set energy method options for DNA-DNA. Any other optimization for DNA relax should go here.

References options.

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

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

(pba) read in membrane topology

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

static thread_local basic::Tracer protocols::relax::TR ( "WorkUnit_BatchRelax"  )

static

Referenced by protocols::relax::AtomCoordinateCstMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::relax::FastRelax::cmd_accept_to_best(), fix_worst_bad_ramas(), protocols::relax::WorkUnit_BatchRelax::post_process(), protocols::relax::WorkUnit_BatchRelax::pre_process(), protocols::relax::FastRelax::read_script_file(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::relax::ClassicRelax::set_default(), protocols::relax::FastRelax::set_script_from_lines(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::relax::ClassicRelax::set_tolerance(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), protocols::relax::CentroidRelax::setup_increased_vdw_radii(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), and protocols::relax::membrane::MPFastRelaxMover::show_protocol().