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protocols::star Namespace Reference


class  Extender
class  StarAbinitio


using Probabilities = utility::vector1< core::Real >
< StarAbinitio
< StarAbinitio const > 


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 ("")
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...


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 ( ""  )
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

Referenced by generate_extended_pose().

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

Referenced by generate_extended_pose().

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

Referenced by generate_extended_pose().