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protocols::star Namespace Reference

Classes

class  Extender
 
class  StarAbinitio
 

Typedefs

using Probabilities = utility::vector1< core::Real >
 
typedef
utility::pointer::shared_ptr
< StarAbinitio
StarAbinitioOP
 
typedef
utility::pointer::shared_ptr
< StarAbinitio const > 
StarAbinitioCOP
 

Functions

void generate_extended_pose (Pose *extended_pose, const std::string &sequence)
 
void copy_residues (const Pose &src, core::Size start, core::Size stop, Pose *dst)
 
static basic::Tracer TR ("protocols.star.StarAbinitio")
 
void compute_per_residue_probabilities (core::Size num_residues, core::Size fragment_len, const FoldTree &tree, Probabilities *probs)
 
void update_sequence_separation (core::Size distance, Pose *pose)
 
void setup_constraints (const Loops &aligned, Pose *pose)
 
void tear_down_constraints (Pose *pose)
 
ScoreFunctionOP setup_score (const std::string &weights, Real cb)
 
void configure_rmc (MoverOP mover, ScoreFunctionOP score, core::Size num_cycles, Real temperature, bool recover_low, RationalMonteCarlo *rmc)
 
void check_required ()
 
void * graphics_main (protocols::moves::MoverOP mover)
 
void * StarAbinitio_main (void *)
 Entry point for StarAbinitio protocol. More...
 
void emit_intermediate (const core::pose::Pose &pose, const std::string &silent_filename)
 Writes pose to disk with the specified filename if -abinitio:debug is enabled. More...
 
void simple_fold_tree (core::pose::Pose &pose)
 Restores simple kinematics to pose. More...
 
void to_centroid (core::pose::Pose &pose)
 Converts pose to centroid residue type set. More...
 

Variables

static const Real EXT_PHI = -150
 
static const Real EXT_PSI = +150
 
static const Real EXT_OMG = +180
 
const std::string ERROR_PREFIX = "Failed to specify required option "
 

Typedef Documentation

using protocols::star::Probabilities = typedef utility::vector1<core::Real>
typedef utility::pointer::shared_ptr<StarAbinitio const> protocols::star::StarAbinitioCOP
typedef utility::pointer::shared_ptr<StarAbinitio> protocols::star::StarAbinitioOP

Function Documentation

void protocols::star::check_required ( )
void protocols::star::compute_per_residue_probabilities ( core::Size  num_residues,
core::Size  fragment_len,
const FoldTree &  tree,
Probabilities *  probs 
)
void protocols::star::configure_rmc ( MoverOP  mover,
ScoreFunctionOP  score,
core::Size  num_cycles,
Real  temperature,
bool  recover_low,
RationalMonteCarlo *  rmc 
)
void protocols::star::copy_residues ( const Pose src,
core::Size  start,
core::Size  stop,
Pose dst 
)
void protocols::star::emit_intermediate ( const core::pose::Pose pose,
const std::string &  silent_filename 
)

Writes pose to disk with the specified filename if -abinitio:debug is enabled.

References core::pack::interaction_graph::debug, and protocols::kinmatch::str().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::generate_extended_pose ( Pose extended_pose,
const std::string &  sequence 
)
void* protocols::star::graphics_main ( protocols::moves::MoverOP  mover)
void protocols::star::setup_constraints ( const Loops &  aligned,
Pose pose 
)
ScoreFunctionOP protocols::star::setup_score ( const std::string &  weights,
Real  cb 
)

Instantiates a score function by name and sets constraint terms to the value specified by the options system (-constraints:cst_weight)

References core::scoring::atom_pair_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::linear_chainbreak, and protocols::hybridization::score.

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::simple_fold_tree ( core::pose::Pose pose)
void * protocols::star::StarAbinitio_main ( void *  )

Entry point for StarAbinitio protocol.

References check_required(), and graphics_main().

void protocols::star::tear_down_constraints ( Pose pose)
void protocols::star::to_centroid ( core::pose::Pose pose)
static basic::Tracer protocols::star::TR ( "protocols.star.StarAbinitio"  )
static
void protocols::star::update_sequence_separation ( core::Size  distance,
Pose pose 
)

Regulates the application of constraints during folding based on distance between residues in the fold tree. The MonteCarlo object should be reset after calling this function.

References core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), and TR().

Referenced by setup_constraints().

Variable Documentation

const std::string protocols::star::ERROR_PREFIX = "Failed to specify required option "

Referenced by check_required().

const Real protocols::star::EXT_OMG = +180
static

Referenced by generate_extended_pose().

const Real protocols::star::EXT_PHI = -150
static

Referenced by generate_extended_pose().

const Real protocols::star::EXT_PSI = +150
static

Referenced by generate_extended_pose().