protocols::relax Namespace Reference

Classes
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
class	FastRelax
class	FastRelaxCreator
class	MiniRelax
class	RelaxProtocolBase
class	WorkUnit_BatchRelax
class	WorkUnit_BatchRelax_and_PostRescore

Typedefs
typedef utility::pointer::owning_ptr < CentroidRelax >	CentroidRelaxOP
typedef utility::pointer::owning_ptr < CentroidRelax const >	CentroidRelaxCOP
typedef utility::pointer::access_ptr < CentroidRelax >	CentroidRelaxAP
typedef utility::pointer::access_ptr < CentroidRelax const >	CentroidRelaxCAP
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. 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	relax_pose (pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag)
static basic::Tracer	TR ("WorkUnit_BatchRelax")

Typedef Documentation

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

Definition at line 33 of file CentroidRelax.fwd.hh.

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

Definition at line 34 of file CentroidRelax.fwd.hh.

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

Definition at line 31 of file CentroidRelax.fwd.hh.

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

Definition at line 27 of file CentroidRelax.fwd.hh.

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

Definition at line 34 of file FastRelax.fwd.hh.

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

Definition at line 35 of file FastRelax.fwd.hh.

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

Definition at line 32 of file FastRelax.fwd.hh.

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

Definition at line 28 of file FastRelax.fwd.hh.

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

Definition at line 24 of file MiniRelax.fwd.hh.

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

Definition at line 34 of file RelaxProtocolBase.fwd.hh.

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

Definition at line 35 of file RelaxProtocolBase.fwd.hh.

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

Definition at line 32 of file RelaxProtocolBase.fwd.hh.

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

Definition at line 28 of file RelaxProtocolBase.fwd.hh.

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

Definition at line 29 of file WorkUnit_BatchRelax.hh.

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

Definition at line 27 of file WorkUnit_BatchRelax.hh.

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
	)

Definition at line 55 of file Ramady.cc.

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)

Definition at line 166 of file cst_util.cc.

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
	)

Definition at line 48 of file cst_util.cc.

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)

Definition at line 136 of file cst_util.cc.

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(), 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
	)

Definition at line 181 of file cst_util.cc.

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
	)

Definition at line 115 of file Ramady.cc.

References core::chemical::aa_pro, add_coordinate_constraints_to_pose(), core::id::BB, core::scoring::CA_rmsd(), core::scoring::coordinate_constraint, core::scoring::omega, core::id::omega_torsion(), core::id::phi_torsion(), core::scoring::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::scoring::ScoreFunction::set_weight(), core::pose::Pose::total_residue(), and TR().

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.

Definition at line 105 of file cst_util.cc.

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)

Definition at line 71 of file util.cc.

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 core::TR().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::frag_picker::FragmentCandidate::output_silent(), 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
	)

Definition at line 149 of file cst_util.cc.

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.

Definition at line 126 of file util.cc.

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 core::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
	)

Definition at line 110 of file Ramady.cc.

Referenced by fix_worst_bad_ramas().

int protocols::relax::Relax_main

(

bool

)

Definition at line 73 of file relax_main.cc.

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::pose_from_pdb(), and protocols::jd2::set_native_in_mover().

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

Definition at line 138 of file util.cc.

References generate_relax_from_cmd().

Referenced by protocols::symmetric_docking::SymDockProtocol::apply(), protocols::frag_picker::FragmentCandidate::output_silent(), 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
	)

(pba) read in membrane topology

Definition at line 118 of file util.cc.

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

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), fix_worst_bad_ramas(), protocols::relax::FastRelax::makeDnaRigid(), 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_to_batchrelax_default(), protocols::relax::ClassicRelax::set_tolerance(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), and protocols::relax::CentroidRelax::setup_increased_vdw_radii().