#include <StarTreeBuilder.hh>

Inheritance diagram for protocols::nonlocal::StarTreeBuilder:

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

◆ StarTreeBuilder()

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

Member Function Documentation

◆ choose_anchor_position()

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().

◆ do_compute_jump_rmsd()

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().

◆ set_up()

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::HelixRotate::apply(), and protocols::nonlocal::SheetTranslate::apply().

◆ tear_down()

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

overridevirtual

Removes the virtual residue added to <pose> in calls to set_up()

Reimplemented from protocols::nonlocal::TreeBuilder.

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), do_compute_jump_rmsd(), PREFIX_FINAL, and virtual_res_.

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

Member Data Documentation

◆ PREFIX_FINAL

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

staticprotected

Referenced by tear_down().

◆ PREFIX_INITIAL

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

staticprotected

Referenced by set_up().

◆ virtual_res_

int protocols::nonlocal::StarTreeBuilder::virtual_res_

private

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