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Public Member Functions | Protected Member Functions | Static Protected Attributes | Private Attributes | List of all members
protocols::nonlocal::StarTreeBuilder Class Reference

#include <StarTreeBuilder.hh>

Inheritance diagram for protocols::nonlocal::StarTreeBuilder:
Inheritance graph
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Public Member Functions

 StarTreeBuilder ()
 
void set_up (const protocols::loops::Loops &chunks, core::pose::Pose *pose) override
 Constructs a star fold tree by placing a virtual residue at <chunks> center of mass and adding jumps from it to a stochastically chosen anchor residue in each chunk. Cutpoints are added on chunk boundaries. More...
 
void tear_down (core::pose::Pose *pose) override
 Removes the virtual residue added to <pose> in calls to set_up() More...
 

Protected Member Functions

core::Size choose_anchor_position (const protocols::loops::Loop &chunk) const
 Stochastically selects an anchor position. More...
 
void do_compute_jump_rmsd (core::pose::Pose *model, const std::string &prefix="") const
 When native is available, computes rmsd of jump residues, storing the results as comments in silent file output. If specified, prefix string will precede the result in the silent file output. More...
 

Static Protected Attributes

static const std::string PREFIX_INITIAL = "initial"
 
static const std::string PREFIX_FINAL = "final"
 

Private Attributes

int virtual_res_
 Index of the virtual residue we added to the pose in set_up() More...
 

Constructor & Destructor Documentation

protocols::nonlocal::StarTreeBuilder::StarTreeBuilder ( )

Member Function Documentation

core::Size protocols::nonlocal::StarTreeBuilder::choose_anchor_position ( const protocols::loops::Loop chunk) const
protected

Stochastically selects an anchor position.

mu- midpoint of the chunk sigma- linear function of chunk length

References protocols::loops::Loop::length(), core::conformation::membrane::normal, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by set_up().

void protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd ( core::pose::Pose model,
const std::string &  prefix = "" 
) const
protected

When native is available, computes rmsd of jump residues, storing the results as comments in silent file output. If specified, prefix string will precede the result in the silent file output.

References core::pose::add_comment(), core::scoring::compute_jump_rmsd(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::kinmatch::str().

Referenced by set_up(), and tear_down().

void protocols::nonlocal::StarTreeBuilder::set_up ( const protocols::loops::Loops chunks,
core::pose::Pose pose 
)
overridevirtual

Constructs a star fold tree by placing a virtual residue at <chunks> center of mass and adding jumps from it to a stochastically chosen anchor residue in each chunk. Cutpoints are added on chunk boundaries.

Note: assumes <chunks> are sorted in increasing order of start position.

Important: chunks must be sorted in increasing order of start position. The simplest way to achieve this is a call to Loops::sequential_order().

Additionally, every residue in pose must belong to one and only one chunk.

Implements protocols::nonlocal::TreeBuilder.

References core::pose::addVirtualResAsRoot(), core::conformation::membrane::center, protocols::loops::Loops::center_of_mass(), choose_anchor_position(), protocols::loops::cut_point, do_compute_jump_rmsd(), core::pose::Pose::fold_tree(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::loops::Loops::num_loop(), PREFIX_INITIAL, core::pose::Pose::size(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and virtual_res_.

Referenced by protocols::medal::MedalMover::apply(), protocols::nonlocal::SheetTranslate::apply(), and protocols::nonlocal::HelixRotate::apply().

void protocols::nonlocal::StarTreeBuilder::tear_down ( core::pose::Pose pose)
overridevirtual

Member Data Documentation

const std::string protocols::nonlocal::StarTreeBuilder::PREFIX_FINAL = "final"
staticprotected

Referenced by tear_down().

const std::string protocols::nonlocal::StarTreeBuilder::PREFIX_INITIAL = "initial"
staticprotected

Referenced by set_up().

int protocols::nonlocal::StarTreeBuilder::virtual_res_
private

Index of the virtual residue we added to the pose in set_up()

Referenced by set_up(), and tear_down().


The documentation for this class was generated from the following files: