Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Functions
protocols::relax Namespace Reference

Namespaces

 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  ClassicRelax
 A functor class which implements the classic Rosetta++ pose_relax protocol. More...
 
class  ClassicRelaxCreator
 
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  FastRelax
 
class  FastRelaxCreator
 
class  LocalRelax
 
class  LocalRelaxCreator
 
class  MiniRelax
 
class  RangeRelaxMover
 
class  RelaxProtocolBase
 
struct  RelaxScriptCommand
 
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
 
struct  SRelaxPose
 
struct  VariableSubstitutionPair
 
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::Realget_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)
 
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

using protocols::relax::AcceptToBestMoverCOP = typedef utility::pointer::shared_ptr< AcceptToBestMover const >
using protocols::relax::AcceptToBestMoverOP = typedef utility::pointer::shared_ptr< AcceptToBestMover >
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::shared_ptr< EnergyMapContainer const > protocols::relax::EnergyMapContainerCOP
typedef utility::pointer::shared_ptr< EnergyMapContainer > protocols::relax::EnergyMapContainerOP
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::weak_ptr< LocalRelax > protocols::relax::LocalRelaxAP
typedef utility::pointer::weak_ptr< LocalRelax const > protocols::relax::LocalRelaxCAP
typedef utility::pointer::shared_ptr< LocalRelax const > protocols::relax::LocalRelaxCOP
typedef utility::pointer::shared_ptr< LocalRelax > protocols::relax::LocalRelaxOP
typedef utility::pointer::shared_ptr< MiniRelax > protocols::relax::MiniRelaxOP
typedef utility::pointer::shared_ptr< RangeRelaxMover const > protocols::relax::RangeRelaxMoverCOP
typedef utility::pointer::shared_ptr< RangeRelaxMover > protocols::relax::RangeRelaxMoverOP
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< RelaxScriptFileContents const > protocols::relax::RelaxScriptFileContentsCOP
typedef utility::pointer::shared_ptr< RelaxScriptManager const > protocols::relax::RelaxScriptManagerCOP
typedef utility::pointer::shared_ptr< RelaxScriptManager > protocols::relax::RelaxScriptManagerOP
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

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 
)
void protocols::relax::add_coordinate_constraints_to_pose ( core::pose::Pose pose,
const core::pose::Pose constraint_target_pose,
protocols::loops::Loops exclude_regions 
)
void protocols::relax::add_virtual_residue_to_cterm ( core::pose::Pose pose)
void protocols::relax::coordinate_constrain_selection ( core::pose::Pose pose,
core::sequence::SequenceAlignment  aln,
core::Real  coord_sdev 
)
void protocols::relax::cyclize_pose ( core::pose::Pose pose)
void protocols::relax::delete_virtual_residues ( core::pose::Pose pose)
void protocols::relax::derive_sc_sc_restraints ( core::pose::Pose pose,
core::Real const  upper_dist_cutoff 
)
void protocols::relax::fill_in_filelines ( std::ifstream &  infile,
VariableSubstitutionPair const &  repeat_variable,
std::vector< std::string > &  filelines 
)
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 
)
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().

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::size().

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

RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd ( bool  NULL_if_no_flag)
RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd ( utility::options::OptionCollection const &  options,
bool  NULL_if_no_flag 
)
utility::vector1< core::Real > protocols::relax::get_per_residue_scores ( core::pose::Pose pose,
core::scoring::ScoreType  scoretype 
)
void protocols::relax::make_dna_rigid ( pose::Pose pose,
core::kinematics::MoveMap mm 
)
void protocols::relax::options_for_generate_relax_from_cmd ( utility::options::OptionKeyList &  opts)
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  )
void protocols::relax::relax_pose ( pose::Pose pose,
core::scoring::ScoreFunctionOP  scorefxn,
std::string const &  tag 
)
void protocols::relax::setup_for_dna ( core::scoring::ScoreFunction scorefxn)
void protocols::relax::setup_membrane_topology ( pose::Pose pose,
std::string  spanfile 
)
bool protocols::relax::string_has_suffix ( std::string const &  target,
std::string const &  suffix 
)
static basic::Tracer protocols::relax::TR ( "WorkUnit_BatchRelax"  )
static
static basic::Tracer protocols::relax::TR ( "protocols.simple_moves.RepeatProteinRelax"  )
static
static basic::Tracer protocols::relax::TR ( "LocalRelax"  )
static

Referenced by protocols::relax::membrane::add_mutant_to_vectors(), protocols::relax::AcceptToBestMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::RangeRelaxMover::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::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::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().