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protocols::medal Namespace Reference

Classes

class  MedalExchangeMover
 
class  MedalMover
 

Typedefs

typedef
utility::pointer::shared_ptr
< MedalFreeMover > 
MedalFreeMoverOP
 
typedef
utility::pointer::shared_ptr
< MedalFreeMover const > 
MedalFreeMoverCOP
 
using Trigger = std::function< void(const core::pose::Pose &)>
 
typedef
utility::pointer::shared_ptr
< MedalMover
MedalMoverOP
 
typedef
utility::pointer::shared_ptr
< MedalMover const > 
MedalMoverCOP
 
using Probabilities = utility::vector1< core::Real >
 

Functions

static basic::Tracer TR ("protocols.medal.MedalExchangeMover")
 
protocols::loops::LoopsCOP combine_loops (LoopsCOP aligned, LoopsCOP unaligned)
 Combines both sets of loops, sorting the result in increasing order of start position More...
 
void setup_coordinate_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
 Create coordinate constraints restraining aligned residues to their initial positions More...
 
void setup_atom_pair_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
 Retain user-specified distance restraints that operate on pairs of aligned residues More...
 
void setup_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
 
void check_required_common ()
 Standard options More...
 
void check_required_cm ()
 Comparative modeling options More...
 
void * graphics_main (protocols::moves::MoverOP mover)
 
void * Medal_main (void *)
 Entry point for Medal protocol. More...
 
void * MedalExchange_main (void *)
 Entry point for MedalExchange protocol. More...
 
static basic::Tracer TR ("protocols.medal.MedalMover")
 
void on_pose_accept (const core::pose::Pose &pose)
 
void end_bias_probabilities (const core::Size num_residues, Probabilities *p)
 Lower sampling probability near termini. More...
 
void alignment_probabilities (core::Size const num_residues, const core::sequence::SequenceAlignment &alignment, Probabilities *p)
 Computes per-residue alignment probabilities. To minimize assumptions about the fold tree, the number of residues in the pose is an explicit input. More...
 
void chunk_probabilities (const protocols::loops::Loops &chunks, Probabilities *p)
 Computes per-residue chunk probabilities. A linear voting scheme is used to bias sampling toward larger chunks. More...
 
void cutpoint_probabilities (core::Size const num_residues, const core::kinematics::FoldTree &tree, Probabilities *p)
 Computes per-residue cutpoint probabilities. Sampling is biased toward residues proximal to a cutpoint. More...
 
void invalidate_residues_spanning_cuts (const core::kinematics::FoldTree &tree, const core::Size fragment_len, Probabilities *probs)
 Zeroes out the probability of residues for which fragment insertion would cross cutpoint boundaries. More...
 
void as_set (protocols::loops::LoopsCOP loops, boost::unordered_set< core::Size > *s)
 Populates a hash table with the residues contained in loops. More...
 
void to_centroid (core::pose::Pose *pose)
 

Variables

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

Typedef Documentation

typedef utility::pointer::shared_ptr<MedalFreeMover const> protocols::medal::MedalFreeMoverCOP
typedef utility::pointer::shared_ptr<MedalFreeMover> protocols::medal::MedalFreeMoverOP
typedef utility::pointer::shared_ptr<MedalMover const> protocols::medal::MedalMoverCOP
typedef utility::pointer::shared_ptr<MedalMover> protocols::medal::MedalMoverOP
typedef utility::vector1< core::Real > protocols::medal::Probabilities
using protocols::medal::Trigger = typedef std::function<void (const core::pose::Pose &)>

Function Documentation

void protocols::medal::alignment_probabilities ( const core::Size  num_residues,
const core::sequence::SequenceAlignment alignment,
Probabilities *  p 
)

Computes per-residue alignment probabilities. To minimize assumptions about the fold tree, the number of residues in the pose is an explicit input.

References core::id::SequenceMapping::push_back(), and core::sequence::SequenceAlignment::sequence_mapping().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

void protocols::medal::as_set ( protocols::loops::LoopsCOP  loops,
boost::unordered_set< core::Size > *  s 
)

Populates a hash table with the residues contained in loops.

Referenced by setup_atom_pair_constraints().

void protocols::medal::check_required_cm ( )

Comparative modeling options

References core::scoring::alignment, and ERROR_PREFIX.

Referenced by Medal_main(), and MedalExchange_main().

void protocols::medal::check_required_common ( )

Standard options

References ERROR_PREFIX.

Referenced by Medal_main(), and MedalExchange_main().

void protocols::medal::chunk_probabilities ( const protocols::loops::Loops chunks,
Probabilities *  p 
)

Computes per-residue chunk probabilities. A linear voting scheme is used to bias sampling toward larger chunks.

Linear voting based on chunk length Assumes <chunks> are in ascending order

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

protocols::loops::LoopsCOP protocols::medal::combine_loops ( LoopsCOP  aligned,
LoopsCOP  unaligned 
)

Combines both sets of loops, sorting the result in increasing order of start position

Referenced by protocols::medal::MedalExchangeMover::apply().

void protocols::medal::cutpoint_probabilities ( const core::Size  num_residues,
const core::kinematics::FoldTree tree,
Probabilities *  p 
)
void protocols::medal::end_bias_probabilities ( const core::Size  num_residues,
Probabilities *  p 
)

Lower sampling probability near termini.

Biases sampling away from termini.

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

void* protocols::medal::graphics_main ( protocols::moves::MoverOP  mover)
void protocols::medal::invalidate_residues_spanning_cuts ( const core::kinematics::FoldTree tree,
const core::Size  fragment_len,
Probabilities *  probs 
)

Zeroes out the probability of residues for which fragment insertion would cross cutpoint boundaries.

Given a fold tree and fragment library, zero out residues whose modification would span a cutpoint boundary

References core::kinematics::FoldTree::cutpoint(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities(), protocols::star::compute_per_residue_probabilities(), and protocols::medal::MedalExchangeMover::setup_sampling_probs().

void * protocols::medal::Medal_main ( void *  )

Entry point for Medal protocol.

References check_required_cm(), check_required_common(), and graphics_main().

void * protocols::medal::MedalExchange_main ( void *  )

Entry point for MedalExchange protocol.

References check_required_cm(), check_required_common(), and graphics_main().

void protocols::medal::on_pose_accept ( const core::pose::Pose pose)
void protocols::medal::setup_atom_pair_constraints ( const Pose pose,
LoopsCOP  aligned,
ConstraintSetOP  constraints 
)

Retain user-specified distance restraints that operate on pairs of aligned residues

References as_set(), core::scoring::atom_pair_constraint, and core::pack::dunbrack::c.

Referenced by setup_constraints().

void protocols::medal::setup_constraints ( const Pose pose,
LoopsCOP  aligned,
ConstraintSetOP  constraints 
)
void protocols::medal::setup_coordinate_constraints ( const Pose pose,
LoopsCOP  aligned,
ConstraintSetOP  constraints 
)
void protocols::medal::to_centroid ( core::pose::Pose pose)
static basic::Tracer protocols::medal::TR ( "protocols.medal.MedalExchangeMover"  )
static
static basic::Tracer protocols::medal::TR ( "protocols.medal.MedalMover"  )
static

Variable Documentation

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