Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::relax Namespace Reference

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::owning_ptr
< AtomCoordinateCstMover
AtomCoordinateCstMoverOP
 
typedef
utility::pointer::owning_ptr
< AtomCoordinateCstMover const > 
AtomCoordinateCstMoverCOP
 
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::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 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)
 

Variables

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 
)
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::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::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::scoring::constraints::ConstraintSet::add_constraint(), 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)
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 
)
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)

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 
)

Variable Documentation

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