Classes | Typedefs | Functions | Variables
protocols::star Namespace Reference


class  Extender
class  StarAbinitio


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


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

◆ Probabilities

using protocols::star::Probabilities = typedef utility::vector1<core::Real>

◆ StarAbinitioCOP

typedef utility::pointer::shared_ptr<StarAbinitio const> protocols::star::StarAbinitioCOP

◆ StarAbinitioOP

typedef utility::pointer::shared_ptr<StarAbinitio> protocols::star::StarAbinitioOP

Function Documentation

◆ check_required()

void protocols::star::check_required ( )

◆ compute_per_residue_probabilities()

void protocols::star::compute_per_residue_probabilities ( core::Size  num_residues,
core::Size  fragment_len,
const FoldTree tree,
Probabilities probs 

◆ configure_rmc()

void protocols::star::configure_rmc ( MoverOP  mover,
ScoreFunctionOP  score,
core::Size  num_cycles,
Real  temperature,
bool  recover_low,
RationalMonteCarlo rmc 

◆ copy_residues()

void protocols::star::copy_residues ( const Pose src,
core::Size  start,
core::Size  stop,
Pose dst 

◆ emit_intermediate()

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().

◆ generate_extended_pose()

void protocols::star::generate_extended_pose ( Pose extended_pose,
const std::string &  sequence 

◆ graphics_main()

void* protocols::star::graphics_main ( protocols::moves::MoverOP  mover)

◆ setup_constraints()

void protocols::star::setup_constraints ( const Loops aligned,
Pose pose 

◆ setup_score()

ScoreFunctionOP protocols::star::setup_score ( const std::string &  weights,
Real  cb 

@detail 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().

◆ simple_fold_tree()

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

◆ StarAbinitio_main()

void * protocols::star::StarAbinitio_main ( void *  )

Entry point for StarAbinitio protocol.

References check_required(), and graphics_main().

◆ tear_down_constraints()

void protocols::star::tear_down_constraints ( Pose pose)

◆ to_centroid()

void protocols::star::to_centroid ( core::pose::Pose pose)

◆ TR()

static basic::Tracer protocols::star::TR ( ""  )

◆ update_sequence_separation()

void protocols::star::update_sequence_separation ( core::Size  distance,
Pose pose 

@detail 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::kinematics::distance(), 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().