protocols::relax Namespace Reference

Namespaces
	loop
	membrane

Classes
class	AcceptToBestMover
class	AcceptToBestMoverCreator
class	AtomCoordinateCstMover
class	AtomCoordinateCstMoverCreator
class	CentroidRelax
	Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization. More...
class	ClassicRelaxCreator
class	ClassicRelax
	A functor class which implements the classic Rosetta++ pose_relax protocol. More...
struct	SRelaxPose
struct	RelaxScriptCommand
struct	VariableSubstitutionPair
class	FastRelax
class	FastRelaxCreator
class	LocalRelax
class	LocalRelaxCreator
class	MiniRelax
class	RangeRelaxMover
class	RelaxProtocolBase
struct	DatabaseRelaxScript
	Represents a single line of database/sampling/relax_scripts/index.dat. More...
class	EnergyMapContainer
	A class for storing energy maps, since they're not created by owning pointer by default. More...
class	RelaxScriptFileContents
	A simple wrapper class to store a vector of file contents. More...
class	RelaxScriptManager
	A singleton class for managing relax scripts, to ensure that they are loaded once and only once from disk. More...
class	RepeatProteinRelax
class	RepeatProteinRelaxCreator
class	WorkUnit_BatchRelax
class	WorkUnit_BatchRelax_and_PostRescore

Typedefs
using	AcceptToBestMoverOP = utility::pointer::shared_ptr< AcceptToBestMover >
using	AcceptToBestMoverCOP = utility::pointer::shared_ptr< AcceptToBestMover const >
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< LocalRelax >	LocalRelaxOP
typedef utility::pointer::shared_ptr< LocalRelax const >	LocalRelaxCOP
typedef utility::pointer::weak_ptr< LocalRelax >	LocalRelaxAP
typedef utility::pointer::weak_ptr< LocalRelax const >	LocalRelaxCAP
typedef utility::pointer::shared_ptr< MiniRelax >	MiniRelaxOP
typedef utility::pointer::shared_ptr< RangeRelaxMover >	RangeRelaxMoverOP
typedef utility::pointer::shared_ptr< RangeRelaxMover const >	RangeRelaxMoverCOP
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< EnergyMapContainer >	EnergyMapContainerOP
typedef utility::pointer::shared_ptr< EnergyMapContainer const >	EnergyMapContainerCOP
typedef utility::pointer::shared_ptr< RelaxScriptManager >	RelaxScriptManagerOP
typedef utility::pointer::shared_ptr< RelaxScriptManager const >	RelaxScriptManagerCOP
typedef utility::pointer::shared_ptr< RelaxScriptFileContents >	RelaxScriptFileContentsOP
typedef utility::pointer::shared_ptr< RelaxScriptFileContents const >	RelaxScriptFileContentsCOP
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	fill_in_filelines (std::ifstream &infile, VariableSubstitutionPair const &repeat_variable, std::vector< std::string > &filelines)
bool	string_has_suffix (std::string const &target, std::string const &suffix)
static basic::Tracer	TR ("LocalRelax")
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)
static basic::Tracer	TR ("protocols.simple_moves.RepeatProteinRelax")
RelaxProtocolBaseOP	generate_relax_from_cmd (bool NULL_if_no_cmd=false)
	Create a relax mover reading from the global options collection. More...
RelaxProtocolBaseOP	generate_relax_from_cmd (utility::options::OptionCollection const &options, bool NULL_if_no_flag=false)
void	options_for_generate_relax_from_cmd (utility::options::OptionKeyList &opts)
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)
void	fixH (core::pose::Pose &pose)
	Rebuild all polymer bond-dependent atoms in the pose. More...
void	cyclize_pose (core::pose::Pose &pose)
	Add terminal peptide bond and cyclic constraints to pose. More...
core::scoring::constraints::ConstraintCOPs	add_coordinate_constraint_func_atoms (core::pose::Pose const &pose, core::Size const resnum, core::conformation::Residue const &rsd_i, core::scoring::func::HarmonicFuncOP coord_cst_func, core::id::AtomID const &anchor_atom)
static basic::Tracer	TR ("WorkUnit_BatchRelax")

Typedef Documentation

AcceptToBestMoverCOP

using protocols::relax::AcceptToBestMoverCOP = typedef utility::pointer::shared_ptr< AcceptToBestMover const >

AcceptToBestMoverOP

using protocols::relax::AcceptToBestMoverOP = typedef utility::pointer::shared_ptr< AcceptToBestMover >

AtomCoordinateCstMoverCOP

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

AtomCoordinateCstMoverOP

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

CentroidRelaxAP

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

CentroidRelaxCAP

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

CentroidRelaxCOP

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

CentroidRelaxOP

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

EnergyMapContainerCOP

typedef utility::pointer::shared_ptr< EnergyMapContainer const > protocols::relax::EnergyMapContainerCOP

EnergyMapContainerOP

typedef utility::pointer::shared_ptr< EnergyMapContainer > protocols::relax::EnergyMapContainerOP

FastRelaxAP

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

FastRelaxCAP

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

FastRelaxCOP

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

FastRelaxOP

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

LocalRelaxAP

typedef utility::pointer::weak_ptr< LocalRelax > protocols::relax::LocalRelaxAP

LocalRelaxCAP

typedef utility::pointer::weak_ptr< LocalRelax const > protocols::relax::LocalRelaxCAP

LocalRelaxCOP

typedef utility::pointer::shared_ptr< LocalRelax const > protocols::relax::LocalRelaxCOP

LocalRelaxOP

typedef utility::pointer::shared_ptr< LocalRelax > protocols::relax::LocalRelaxOP

MiniRelaxOP

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

RangeRelaxMoverCOP

typedef utility::pointer::shared_ptr< RangeRelaxMover const > protocols::relax::RangeRelaxMoverCOP

RangeRelaxMoverOP

typedef utility::pointer::shared_ptr< RangeRelaxMover > protocols::relax::RangeRelaxMoverOP

RelaxProtocolBaseAP

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

RelaxProtocolBaseCAP

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

RelaxProtocolBaseCOP

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

RelaxProtocolBaseOP

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

RelaxScriptFileContentsCOP

typedef utility::pointer::shared_ptr< RelaxScriptFileContents const > protocols::relax::RelaxScriptFileContentsCOP

RelaxScriptFileContentsOP

typedef utility::pointer::shared_ptr< RelaxScriptFileContents > protocols::relax::RelaxScriptFileContentsOP

RelaxScriptManagerCOP

typedef utility::pointer::shared_ptr< RelaxScriptManager const > protocols::relax::RelaxScriptManagerCOP

RelaxScriptManagerOP

typedef utility::pointer::shared_ptr< RelaxScriptManager > protocols::relax::RelaxScriptManagerOP

WorkUnit_BatchRelaxCOP

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

WorkUnit_BatchRelaxOP

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

Function Documentation

add_coordinate_constraint_func_atoms()

core::scoring::constraints::ConstraintCOPs protocols::relax::add_coordinate_constraint_func_atoms	(	core::pose::Pose const &	pose,
		core::Size const	resnum,
		core::conformation::Residue const &	rsd_i,
		core::scoring::func::HarmonicFuncOP	coord_cst_func,
		core::id::AtomID const &	anchor_atom
	)

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::ResidueType::atom_index(), core::conformation::Residue::name(), core::pose::Pose::residue(), TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups().

add_coordinate_constraints_to_pose()

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(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::last_backbone_atom(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::pose::virtual_type_for_pose(), and core::conformation::Residue::xyz().

Referenced by fix_worst_bad_ramas().

add_virtual_residue_to_cterm()

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::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::virtual_type_for_pose().

coordinate_constrain_selection()

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::conformation::Residue::name(), core::id::SequenceMapping::push_back(), core::pose::Pose::residue(), core::sequence::SequenceAlignment::sequence_mapping(), core::pose::Pose::size(), core::sequence::SequenceAlignment::size(), tr(), and core::pose::virtual_type_for_pose().

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

cyclize_pose()

void protocols::relax::cyclize_pose

(

core::pose::Pose &

pose

)

Add terminal peptide bond and cyclic constraints to pose.

Author

Gaurav Bhardwaj, Baker laboratory

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu) – moved from protocols/forge/methods/util.hh/cc

References core::pose::Pose::add_constraint(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), fixH(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::chemical::element::N, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Conformation::update_polymeric_connection().

Referenced by protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::abinitio::AbrelaxApplication::relax(), protocols::relax::RelaxProtocolBase::set_up_constraints(), and protocols::abinitio::AbrelaxApplication::setup_fold().

delete_virtual_residues()

void protocols::relax::delete_virtual_residues

(

core::pose::Pose &

pose

)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::MiniRelax::apply(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(), and protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly().

derive_sc_sc_restraints()

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::size(), tr(), and core::conformation::Residue::xyz().

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

fill_in_filelines()

void protocols::relax::fill_in_filelines	(	std::ifstream &	infile,
		VariableSubstitutionPair const &	repeat_variable,
		std::vector< std::string > &	filelines
	)

References protocols::relax::VariableSubstitutionPair::string_being_added, and protocols::relax::VariableSubstitutionPair::string_being_replaced.

fix_worst_bad_ramas()

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 core::pose::motif::a(), core::conformation::Residue::aa(), core::chemical::aa_pro, add_coordinate_constraints_to_pose(), core::id::BB, core::scoring::CA_rmsd(), core::scoring::coordinate_constraint, core::pose::Pose::energies(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::omega(), core::scoring::omega, core::id::omega_torsion(), core::scoring::Energies::onebody_energies(), core::pose::Pose::phi(), core::id::phi_torsion(), core::pose::Pose::psi(), core::scoring::rama, rama_list_pred(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::optimization::AtomTreeMinimizer::run(), 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::scoring::ScoreFunction::set_weight(), core::pose::Pose::size(), and TR().

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

fixH()

void protocols::relax::fixH

(

core::pose::Pose &

pose

)

Rebuild all polymer bond-dependent atoms in the pose.

Rewritten from an earlier, uglier function that manually placed H atom in non-pro.

Author

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::conformation(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only(), and core::pose::Pose::size().

Referenced by cyclize_pose().

generate_bb_coordinate_constraints()

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::conformation::Residue::last_backbone_atom(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

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

generate_relax_from_cmd() [1/2]

RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd

(

bool

NULL_if_no_flag

)

Create a relax mover reading from the global options collection.

References generate_relax_from_cmd().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::frag_picker::FragmentCandidate::output_silent(), Relax_main(), protocols::rotamer_recovery::RRProtocolRelax::run(), and protocols::abinitio::AbrelaxMover::set_defaults().

generate_relax_from_cmd() [2/2]

RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd	(	utility::options::OptionCollection const &	options,
		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(), and TR().

Referenced by generate_relax_from_cmd(), and relax_pose().

get_per_residue_scores()

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::size().

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

make_dna_rigid()

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::size(), and TR().

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

options_for_generate_relax_from_cmd()

void protocols::relax::options_for_generate_relax_from_cmd

(

utility::options::OptionKeyList &

opts

)

rama_list_pred()

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

References core::sequence::left.

Referenced by fix_worst_bad_ramas().

Relax_main()

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(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::jd2::set_native_in_mover().

relax_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::relax::RepeatProteinRelax::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::vip::VIP_Mover::relax_favorable_poses().

setup_for_dna()

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 core::scoring::ScoreFunction::energy_method_options(), core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA(), and core::scoring::ScoreFunction::set_energy_method_options().

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

setup_membrane_topology()

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

(pba) read in membrane topology

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

string_has_suffix()

bool protocols::relax::string_has_suffix	(	std::string const &	target,
		std::string const &	suffix
	)

TR() [1/3]

static basic::Tracer protocols::relax::TR ( "LocalRelax"  )

static

Referenced by protocols::relax::membrane::add_mutant_to_vectors(), protocols::relax::AcceptToBestMover::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::relax::membrane::check_mutants_ok(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::relax::RelaxScriptManager::create_relax_script_instance(), protocols::relax::RelaxScriptManager::determine_closest_scorefunction(), protocols::relax::RangeRelaxMover::finalize_setup(), fix_worst_bad_ramas(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), protocols::relax::RangeRelaxMover::get_window_repack_residues(), protocols::relax::RangeRelaxMover::idealize_pose(), protocols::relax::RangeRelaxMover::init_from_cmd(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::relax::RelaxScriptManager::initialize_relax_scripts_in_database(), protocols::relax::FastRelax::inner_loop_accept_to_best_command(), protocols::relax::FastRelax::inner_loop_reset_reference_command(), protocols::relax::LocalRelax::optimization_loop(), protocols::relax::FastRelax::parse_my_tag(), protocols::relax::WorkUnit_BatchRelax::post_process(), protocols::relax::WorkUnit_BatchRelax::pre_process(), protocols::relax::RangeRelaxMover::print_score(), protocols::relax::FastRelax::read_script_file(), protocols::relax::RepeatProteinRelax::relax_pose(), protocols::relax::RangeRelaxMover::repack_all(), protocols::relax::RangeRelaxMover::repack_sequence_window(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::relax::RelaxScriptManager::script_file_path(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::relax::ClassicRelax::set_default(), protocols::relax::FastRelax::set_script_from_lines(), protocols::relax::ClassicRelax::set_tolerance(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), protocols::relax::CentroidRelax::setup_increased_vdw_radii(), protocols::relax::FastRelax::setup_local_tf(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), and protocols::relax::membrane::MPFastRelaxMover::show_protocol().

TR() [2/3]

static basic::Tracer protocols::relax::TR ( "protocols.simple_moves.RepeatProteinRelax"  )

static

TR() [3/3]

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

static