protocols::denovo_design::components::RemodelLoopMoverPoseFolder Class Reference

Folds residues in a pose using RemodelLoopMover. More...

#include <RemodelLoopMoverPoseFolder.hh>

Inheritance diagram for protocols::denovo_design::components::RemodelLoopMoverPoseFolder:

Public Types
typedef protocols::denovo_design::components::PoseFolder	PoseFolder
typedef protocols::denovo_design::components::PoseFolderOP	PoseFolderOP

Public Member Functions
	RemodelLoopMoverPoseFolder ()
	~RemodelLoopMoverPoseFolder () override
PoseFolderOP	clone () const override
void	apply (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &movable, protocols::loops::Loops const &loops) const override
	performs folding More...
void	set_scorefxn (core::scoring::ScoreFunction const &sfxn)
void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn)
Public Member Functions inherited from protocols::denovo_design::components::PoseFolder
	PoseFolder (std::string const &type)
	Default constructor. More...
	~PoseFolder () override
	Destructor. More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
std::string const &	type () const

Static Public Member Functions
static std::string	class_name ()
static core::scoring::ScoreFunctionOP	default_score_function ()

Protected Member Functions
void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override

Private Member Functions
void	remove_cutpoints (StructureData &sd, protocols::loops::Loops const &loops) const
protocols::moves::MoverOP	create_remodel_loop_mover (core::pose::Pose const &pose, StructureData const &sd, core::select::residue_selector::ResidueSubset const &movable, protocols::loops::Loops const &loops) const
core::kinematics::MoveMapOP	create_false_movemap (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &movable) const
core::scoring::ScoreFunctionOP	create_scorefxn (core::pose::Pose const &pose) const

Private Attributes
core::scoring::ScoreFunctionCOP	scorefxn_

Detailed Description

Folds residues in a pose using RemodelLoopMover.

Member Typedef Documentation

PoseFolder

typedef protocols::denovo_design::components::PoseFolder protocols::denovo_design::components::RemodelLoopMoverPoseFolder::PoseFolder

PoseFolderOP

typedef protocols::denovo_design::components::PoseFolderOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::PoseFolderOP

Constructor & Destructor Documentation

RemodelLoopMoverPoseFolder()

protocols::denovo_design::components::RemodelLoopMoverPoseFolder::RemodelLoopMoverPoseFolder

(

)

~RemodelLoopMoverPoseFolder()

protocols::denovo_design::components::RemodelLoopMoverPoseFolder::~RemodelLoopMoverPoseFolder ( )

overridedefault

Member Function Documentation

apply()

void protocols::denovo_design::components::RemodelLoopMoverPoseFolder::apply ( core::pose::Pose &  pose, core::select::residue_selector::ResidueSubset const &  movable, protocols::loops::Loops const &  loops  ) const

overridevirtual

performs folding

Parameters

pose	- The pose to be folded, with all residues added. The pose should be prepared with any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose should be adjusted, and no residues should be added or removed.
movable	- Subset of residues for which new backbone conformations will be sampled. Residues specified as 'True' in movable must also be present in one or more Loops in order to be folded. Movable's size must match pose.size()
loops	- Loops to be folded. Cutpoints specified here must be match the cutpoints found in the pose. Residues not within any loop should not be folded. Residues contained in a loop but not in the movable set should not be folded.

Exceptions

EXCN_Fold

if anything goes wrong in folding. Derived classes should throw this.

Implements protocols::denovo_design::components::PoseFolder.

References create_remodel_loop_mover(), core::pose::Pose::fold_tree(), protocols::moves::MS_SUCCESS, remove_cutpoints(), protocols::TR(), and protocols::denovo_design::components::PoseFolder::type().

class_name()

std::string protocols::denovo_design::components::RemodelLoopMoverPoseFolder::class_name ( )

static

Referenced by protocols::denovo_design::movers::FoldArchitectMover::parse_folder().

clone()

RemodelLoopMoverPoseFolder::PoseFolderOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::clone ( ) const

overridevirtual

Implements protocols::denovo_design::components::PoseFolder.

create_false_movemap()

core::kinematics::MoveMapOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap ( core::pose::Pose const &  pose, core::select::residue_selector::ResidueSubset const &  movable  ) const

private

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), and protocols::TR().

Referenced by create_remodel_loop_mover().

create_remodel_loop_mover()

protocols::moves::MoverOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover ( core::pose::Pose const &  pose, StructureData const &  sd, core::select::residue_selector::ResidueSubset const &  movable, protocols::loops::Loops const &  loops  ) const

private

References protocols::denovo_design::components::StructureData::abego(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), create_false_movemap(), create_scorefxn(), protocols::denovo_design::components::Picker::pick_and_cache_fragments(), and protocols::denovo_design::components::StructureData::ss().

Referenced by apply().

create_scorefxn()

core::scoring::ScoreFunctionOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_scorefxn ( core::pose::Pose const &  pose ) const

private

References default_score_function(), and scorefxn_.

Referenced by create_remodel_loop_mover().

default_score_function()

core::scoring::ScoreFunctionOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::default_score_function ( )

static

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::rg, and core::scoring::vdw.

Referenced by create_scorefxn().

parse_tag()

void protocols::denovo_design::components::RemodelLoopMoverPoseFolder::parse_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overrideprotectedvirtual

Implements protocols::denovo_design::components::PoseFolder.

References core::scoring::parse_score_function(), and set_scorefxn().

remove_cutpoints()

void protocols::denovo_design::components::RemodelLoopMoverPoseFolder::remove_cutpoints ( StructureData &  sd, protocols::loops::Loops const &  loops  ) const

private

References protocols::denovo_design::components::StructureData::segment_name(), protocols::denovo_design::components::StructureData::set_cutpoint(), and protocols::TR().

Referenced by apply().

set_scorefxn() [1/2]

void protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn

(

core::scoring::ScoreFunction const &

sfxn

)

References core::scoring::ScoreFunction::clone().

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), and parse_tag().

set_scorefxn() [2/2]

void protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn

(

core::scoring::ScoreFunctionCOP

sfxn

)

References scorefxn_.

Member Data Documentation

scorefxn_

core::scoring::ScoreFunctionCOP protocols::denovo_design::components::RemodelLoopMoverPoseFolder::scorefxn_

private

Referenced by create_scorefxn(), and set_scorefxn().

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

• src/protocols/denovo_design/components/RemodelLoopMoverPoseFolder.hh
• src/protocols/denovo_design/components/RemodelLoopMoverPoseFolder.cc