protocols::fold_from_loops::utils::Nub Class Reference

#include <Nub.hh>

Inheritance diagram for protocols::fold_from_loops::utils::Nub:

Public Member Functions
	Nub ()
	Empty Constructor. More...
	~Nub () override
	Destructor. More...
void	apply (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &template_selection, utility::vector1< core::pose::PoseOP > const &template_pieces, utility::vector1< std::pair< core::Size, core::Size > > const &disulfides)
	Produces the unfolded pose. More...
void	transfer_unfolded_conformation (core::pose::Pose &pose)
void	refit_motif_sidechains (core::pose::Pose &pose)
core::pose::PoseOP	reference_pose () const
void	reference_pose (core::pose::PoseOP const &pose)
core::pose::PoseOP	unfolded_pose () const
core::fragment::FragSetOP	small_fragments () const
void	small_fragments (core::fragment::FragSetOP fragset)
core::fragment::FragSetOP	large_fragments () const
void	large_fragments (core::fragment::FragSetOP fragset)
core::id::SequenceMapping	template_to_unfolded_mapping () const
core::select::residue_selector::ResidueSelectorCOP	selector () const
void	selector (core::select::residue_selector::ResidueSelectorCOP const &selector)
core::select::residue_selector::ResidueSelectorCOP	binder_selector () const
void	binder_selector (core::select::residue_selector::ResidueSelectorCOP const &selector)
core::Size	default_flexibility () const
void	default_flexibility (core::Size pick)
bool	has_binder () const
bool	is_multisegment () const
core::Size	unfolded_jump () const
core::Size	design_size () const
utility::vector1< core::pose::PoseOP >	pieces () const
core::select::residue_selector::ResidueSubset	apply_selector (core::pose::Pose const &pose) const
core::select::residue_selector::ResidueRanges	apply_selector_as_ranges (core::pose::Pose const &pose) const
core::select::residue_selector::ResidueSubset	apply_binder_selector (core::pose::Pose const &pose) const
core::select::residue_selector::ResidueRanges	apply_binder_selector_as_ranges (core::pose::Pose const &pose) const
core::kinematics::MoveMapOP	movemap () const
core::select::movemap::MoveMapFactoryOP	movemapfactory () const
std::string	design_chain () const
utility::vector1< std::pair< core::Size, core::Size > >	disulfides () const
void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)

Static Public Member Functions
static void	provide_xml_definition (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaSimpleSubelementList &elements)
static std::string	object_name ()
static std::string	complex_object_name (std::string tag_name)
static std::string	segment_object_name ()
static core::select::residue_selector::ResidueSelectorCOP	default_selector ()
static std::string	motif_label ()
static std::string	flexible_label ()
static std::string	template_label ()
static std::string	hotspot_label ()
static std::string	coldspot_label ()
static std::string	context_label ()
static std::string	disulfide_label ()
static std::string	contact_label ()

Private Member Functions
void	get_nub_pieces (core::pose::Pose &pose)
	Extracts the regions of interest from the nub. More...
void	join_pieces (utility::vector1< core::pose::PoseOP > const &template_pieces)
	Attaches the template unfolded regions to the Nub to create the unfolded pose. More...
void	add_binders ()
	Add selecter binders if provided. More...
void	add_labels ()
	Add labels to the unfolded pose. More...
void	make_movemap ()
	Creates the movemap to submit to ab initio protocol. More...
void	assign_disulfides (utility::vector1< std::pair< core::Size, core::Size > > const &disulfides)
	Fixes and assigns disulfides to the unfolded pose. More...
void	fix_fragments ()
	Fixes fragments in case the insertion has changed the count of the residues of the template. More...
core::fragment::FragSetOP	fix_fragment (core::fragment::FragSetOP fragset)
	Fixes a FragSet. More...
core::Size	closest_binder (core::pose::Pose const &pose)
	Get closest binder residue to the FoldTree root. More...

Private Attributes
core::pose::PoseOP	reference_pose_
core::pose::PoseOP	unfolded_pose_
core::fragment::FragSetOP	small_
core::fragment::FragSetOP	large_
core::id::SequenceMapping	seqmap_
core::select::residue_selector::ResidueSelectorCOP	selector_
core::select::residue_selector::ResidueSelectorCOP	binder_selector_
core::select::residue_selector::ResidueSelectorCOP	insertion_selector_
core::Size	unfolded_jump_
bool	has_binder_
core::select::movemap::MoveMapFactoryOP	movemap_
utility::vector1< core::pose::PoseOP >	pieces_
utility::vector1< NubSegment >	piece_properties_
std::string	design_chain_
core::Size	design_size_
utility::vector1< std::pair< core::Size, core::Size > >	disulfides_
core::scoring::constraints::ConstraintSetOP	working_cst_
core::Size	default_flexibility_
core::Size	nub_disulfides_

Constructor & Destructor Documentation

Nub()

protocols::fold_from_loops::utils::Nub::Nub

(

)

Empty Constructor.

References movemap_.

~Nub()

protocols::fold_from_loops::utils::Nub::~Nub ( )

override

Destructor.

Member Function Documentation

add_binders()

void protocols::fold_from_loops::utils::Nub::add_binders ( )

private

Add selecter binders if provided.

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), binder_selector_, closest_binder(), core::pose::Pose::detached_copy(), protocols::simple_filters::dssp(), core::select::residue_selector::has_any_true_selection(), has_binder_, reference_pose_, core::pose::Pose::remove_constraints(), core::kinematics::FoldTree::reorder(), protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector(), core::pose::Pose::split_by_chain(), core::kinematics::FoldTree::split_existing_edge_at_residue(), protocols::fold_from_loops::utils::TR(), and unfolded_pose_.

Referenced by apply().

add_labels()

void protocols::fold_from_loops::utils::Nub::add_labels ( )

private

Add labels to the unfolded pose.

References protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), context_label(), design_chain_, has_binder_, insertion_selector_, protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::label(), motif_label(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::residue_selector(), template_label(), and unfolded_pose_.

Referenced by apply().

apply()

void protocols::fold_from_loops::utils::Nub::apply	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	template_selection,
		utility::vector1< core::pose::PoseOP > const &	template_pieces,
		utility::vector1< std::pair< core::Size, core::Size > > const &	disulfides
	)

Produces the unfolded pose.

References add_binders(), add_labels(), assign_disulfides(), core::pose::Pose::detached_copy(), disulfides(), protocols::simple_filters::dssp(), core::pose::Pose::empty(), fix_fragments(), get_nub_pieces(), insertion_selector_, join_pieces(), make_movemap(), protocols::fold_from_loops::utils::map_by_residue_subsets(), reference_pose_, seqmap_, protocols::fold_from_loops::utils::TR(), and unfolded_pose_.

apply_binder_selector()

core::select::residue_selector::ResidueSubset protocols::fold_from_loops::utils::Nub::apply_binder_selector

(

core::pose::Pose const &

pose

)

const

References binder_selector_.

apply_binder_selector_as_ranges()

core::select::residue_selector::ResidueRanges protocols::fold_from_loops::utils::Nub::apply_binder_selector_as_ranges

(

core::pose::Pose const &

pose

)

const

References binder_selector_.

apply_selector()

core::select::residue_selector::ResidueSubset protocols::fold_from_loops::utils::Nub::apply_selector

(

core::pose::Pose const &

pose

)

const

References selector_.

apply_selector_as_ranges()

core::select::residue_selector::ResidueRanges protocols::fold_from_loops::utils::Nub::apply_selector_as_ranges

(

core::pose::Pose const &

pose

)

const

References selector_.

assign_disulfides()

void protocols::fold_from_loops::utils::Nub::assign_disulfides ( utility::vector1< std::pair< core::Size, core::Size > > const &  disulfides )

private

Fixes and assigns disulfides to the unfolded pose.

References core::pose::add_variant_type_to_pose_residue(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), core::select::residue_selector::ResiduePDBInfoHasLabelSelector::apply(), core::chemical::DISULFIDE, disulfide_label(), disulfides(), disulfides_, nub_disulfides_, protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::residue_selector(), core::select::residue_selector::selection_positions(), seqmap_, core::select::residue_selector::ResiduePDBInfoHasLabelSelector::set_label(), core::id::to_string(), protocols::fold_from_loops::utils::TR(), unfolded_pose_, and protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::unlabel().

Referenced by apply().

binder_selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::binder_selector

(

)

const

References binder_selector_.

Referenced by parse_tag().

binder_selector() [2/2]

void protocols::fold_from_loops::utils::Nub::binder_selector

(

core::select::residue_selector::ResidueSelectorCOP const &

selector

)

References binder_selector_, and selector().

closest_binder()

core::Size protocols::fold_from_loops::utils::Nub::closest_binder ( core::pose::Pose const &  pose )

private

Get closest binder residue to the FoldTree root.

References core::kinematics::distance(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), and unfolded_pose_.

Referenced by add_binders().

coldspot_label()

std::string protocols::fold_from_loops::utils::Nub::coldspot_label ( )

static

Referenced by get_nub_pieces().

complex_object_name()

std::string protocols::fold_from_loops::utils::Nub::complex_object_name ( std::string  tag_name )

static

Referenced by provide_xml_definition().

contact_label()

std::string protocols::fold_from_loops::utils::Nub::contact_label ( )

static

context_label()

std::string protocols::fold_from_loops::utils::Nub::context_label ( )

static

Referenced by add_labels().

default_flexibility() [1/2]

core::Size protocols::fold_from_loops::utils::Nub::default_flexibility

(

)

const

References default_flexibility_.

default_flexibility() [2/2]

void protocols::fold_from_loops::utils::Nub::default_flexibility

(

core::Size

pick

)

References default_flexibility_.

default_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::default_selector ( )

static

design_chain()

std::string protocols::fold_from_loops::utils::Nub::design_chain

(

)

const

References design_chain_.

design_size()

core::Size protocols::fold_from_loops::utils::Nub::design_size

(

)

const

References design_size_.

disulfide_label()

std::string protocols::fold_from_loops::utils::Nub::disulfide_label ( )

static

Referenced by assign_disulfides().

disulfides()

utility::vector1< std::pair< core::Size, core::Size > > protocols::fold_from_loops::utils::Nub::disulfides

(

)

const

References disulfides_.

Referenced by apply(), and assign_disulfides().

fix_fragment()

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::fix_fragment ( core::fragment::FragSetOP  fragset )

private

Fixes a FragSet.

References core::fragment::FragData::pdbid(), seqmap_, and protocols::fold_from_loops::utils::TR().

Referenced by fix_fragments().

fix_fragments()

void protocols::fold_from_loops::utils::Nub::fix_fragments ( )

private

Fixes fragments in case the insertion has changed the count of the residues of the template.

References fix_fragment(), insertion_selector_, core::id::SequenceMapping::is_identity(), large_, seqmap_, small_, protocols::fold_from_loops::utils::TR(), and unfolded_pose_.

Referenced by apply().

flexible_label()

std::string protocols::fold_from_loops::utils::Nub::flexible_label ( )

static

Referenced by get_nub_pieces(), and make_movemap().

get_nub_pieces()

void protocols::fold_from_loops::utils::Nub::get_nub_pieces ( core::pose::Pose &  pose )

private

Extracts the regions of interest from the nub.

References core::select::residue_selector::ResidueIndexSelector::append_index(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply_without_merge(), protocols::fold_from_loops::utils::NubSegment::c_flex, coldspot_label(), core::pose::Pose::conformation(), default_flexibility_, design_chain_, core::conformation::disulfide_bonds(), flexible_label(), core::pose::get_chain_from_chain_id(), core::select::residue_selector::has_any_true_selection(), hotspot_label(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::label(), protocols::mean_field::min(), protocols::fold_from_loops::utils::NubSegment::n_flex, nub_disulfides_, protocols::fold_from_loops::utils::NubSegment::order, protocols::forge::methods::order(), core::pose::Pose::pdb_info(), piece_properties_, pieces_, protocols::sic_dock::range(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::residue_selector(), selector_, protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_residue_selector(), core::id::to_string(), and protocols::fold_from_loops::utils::TR().

Referenced by apply().

has_binder()

bool protocols::fold_from_loops::utils::Nub::has_binder

(

)

const

References has_binder_.

hotspot_label()

std::string protocols::fold_from_loops::utils::Nub::hotspot_label ( )

static

Referenced by get_nub_pieces().

is_multisegment()

bool protocols::fold_from_loops::utils::Nub::is_multisegment

(

)

const

References pieces_.

join_pieces()

void protocols::fold_from_loops::utils::Nub::join_pieces ( utility::vector1< core::pose::PoseOP > const &  template_pieces )

private

Attaches the template unfolded regions to the Nub to create the unfolded pose.

References core::pose::add_variant_type_to_pose_residue(), protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), core::pose::correctly_add_cutpoint_variants(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, design_chain_, design_size_, insertion_selector_, core::chemical::LOWER_TERMINUS_VARIANT, pieces_, core::pose::remove_variant_type_from_pose_residue(), core::select::residue_selector::ResidueRange::to_string(), core::id::to_string(), protocols::fold_from_loops::utils::TR(), unfolded_jump_, unfolded_pose_, and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by apply().

large_fragments() [1/2]

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::large_fragments

(

)

const

References large_.

large_fragments() [2/2]

void protocols::fold_from_loops::utils::Nub::large_fragments

(

core::fragment::FragSetOP

fragset

)

References large_.

make_movemap()

void protocols::fold_from_loops::utils::Nub::make_movemap ( )

private

Creates the movemap to submit to ab initio protocol.

References flexible_label(), core::select::movemap::mm_enable, movemap_, and template_label().

Referenced by apply().

motif_label()

std::string protocols::fold_from_loops::utils::Nub::motif_label ( )

static

Referenced by add_labels(), and refit_motif_sidechains().

movemap()

core::kinematics::MoveMapOP protocols::fold_from_loops::utils::Nub::movemap

(

)

const

References movemap_, and unfolded_pose_.

movemapfactory()

core::select::movemap::MoveMapFactoryOP protocols::fold_from_loops::utils::Nub::movemapfactory

(

)

const

References movemap_.

object_name()

std::string protocols::fold_from_loops::utils::Nub::object_name ( )

static

Referenced by parse_tag(), and provide_xml_definition().

parse_tag()

void protocols::fold_from_loops::utils::Nub::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

References binder_selector(), protocols::fold_from_loops::utils::NubSegment::c_flex, protocols::fold_from_loops::utils::NubSegment::coldspots, default_flexibility_, protocols::fold_from_loops::utils::NubSegment::n_flex, object_name(), protocols::fold_from_loops::utils::NubSegment::order, core::select::residue_selector::parse_residue_selector(), core::import_pose::PDB_file, piece_properties_, core::import_pose::pose_from_file(), reference_pose_, protocols::rosetta_scripts::saved_reference_pose(), segment_object_name(), selector(), and protocols::fold_from_loops::utils::TR().

pieces()

utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::utils::Nub::pieces

(

)

const

References pieces_.

provide_xml_definition()

void protocols::fold_from_loops::utils::Nub::provide_xml_definition ( utility::tag::XMLSchemaDefinition &  xsd, utility::tag::XMLSchemaSimpleSubelementList &  elements  )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), protocols::rosetta_scripts::attributes_for_saved_reference_pose_w_description(), complex_object_name(), object_name(), and segment_object_name().

Referenced by protocols::fold_from_loops::NubInitioMover::provide_xml_schema().

reference_pose() [1/2]

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::reference_pose

(

)

const

References reference_pose_.

reference_pose() [2/2]

void protocols::fold_from_loops::utils::Nub::reference_pose

(

core::pose::PoseOP const &

pose

)

References reference_pose_.

refit_motif_sidechains()

void protocols::fold_from_loops::utils::Nub::refit_motif_sidechains

(

core::pose::Pose &

pose

)

References design_chain_, has_binder_, motif_label(), core::pose::Pose::replace_residue(), selector(), and unfolded_pose_.

segment_object_name()

std::string protocols::fold_from_loops::utils::Nub::segment_object_name ( )

static

Referenced by parse_tag(), and provide_xml_definition().

selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::selector

(

)

const

References selector_.

Referenced by binder_selector(), parse_tag(), refit_motif_sidechains(), and selector().

selector() [2/2]

void protocols::fold_from_loops::utils::Nub::selector

(

core::select::residue_selector::ResidueSelectorCOP const &

selector

)

References selector(), and selector_.

small_fragments() [1/2]

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::small_fragments

(

)

const

References small_.

small_fragments() [2/2]

void protocols::fold_from_loops::utils::Nub::small_fragments

(

core::fragment::FragSetOP

fragset

)

References small_.

template_label()

std::string protocols::fold_from_loops::utils::Nub::template_label ( )

static

Referenced by add_labels(), and make_movemap().

template_to_unfolded_mapping()

core::id::SequenceMapping protocols::fold_from_loops::utils::Nub::template_to_unfolded_mapping

(

)

const

References seqmap_.

transfer_unfolded_conformation()

void protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation

(

core::pose::Pose &

pose

)

References core::pose::Pose::clear(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::conformation::Conformation::detect_disulfides(), disulfides_, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), core::pose::Pose::set_new_conformation(), core::pose::Pose::size(), protocols::fold_from_loops::utils::TR(), unfolded_pose_, and working_cst_.

unfolded_jump()

core::Size protocols::fold_from_loops::utils::Nub::unfolded_jump

(

)

const

References unfolded_jump_.

unfolded_pose()

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::unfolded_pose

(

)

const

References unfolded_pose_.

Member Data Documentation

binder_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::binder_selector_

private

Referenced by add_binders(), apply_binder_selector(), apply_binder_selector_as_ranges(), and binder_selector().

default_flexibility_

core::Size protocols::fold_from_loops::utils::Nub::default_flexibility_

private

Referenced by default_flexibility(), get_nub_pieces(), and parse_tag().

design_chain_

std::string protocols::fold_from_loops::utils::Nub::design_chain_

private

Referenced by add_labels(), design_chain(), get_nub_pieces(), join_pieces(), and refit_motif_sidechains().

design_size_

core::Size protocols::fold_from_loops::utils::Nub::design_size_

private

Referenced by design_size(), and join_pieces().

disulfides_

utility::vector1< std::pair< core::Size, core::Size > > protocols::fold_from_loops::utils::Nub::disulfides_

private

Referenced by assign_disulfides(), disulfides(), and transfer_unfolded_conformation().

has_binder_

bool protocols::fold_from_loops::utils::Nub::has_binder_

private

Referenced by add_binders(), add_labels(), has_binder(), and refit_motif_sidechains().

insertion_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::insertion_selector_

private

Referenced by add_labels(), apply(), fix_fragments(), and join_pieces().

large_

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::large_

private

Referenced by fix_fragments(), and large_fragments().

movemap_

core::select::movemap::MoveMapFactoryOP protocols::fold_from_loops::utils::Nub::movemap_

private

Referenced by make_movemap(), movemap(), movemapfactory(), and Nub().

nub_disulfides_

core::Size protocols::fold_from_loops::utils::Nub::nub_disulfides_

private

Referenced by assign_disulfides(), and get_nub_pieces().

piece_properties_

utility::vector1< NubSegment > protocols::fold_from_loops::utils::Nub::piece_properties_

private

Referenced by get_nub_pieces(), and parse_tag().

pieces_

utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::utils::Nub::pieces_

private

Referenced by get_nub_pieces(), is_multisegment(), join_pieces(), and pieces().

reference_pose_

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::reference_pose_

private

Referenced by add_binders(), apply(), parse_tag(), and reference_pose().

selector_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::selector_

private

Referenced by apply_selector(), apply_selector_as_ranges(), get_nub_pieces(), and selector().

seqmap_

core::id::SequenceMapping protocols::fold_from_loops::utils::Nub::seqmap_

private

Referenced by apply(), assign_disulfides(), fix_fragment(), fix_fragments(), and template_to_unfolded_mapping().

small_

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::small_

private

Referenced by fix_fragments(), and small_fragments().

unfolded_jump_

core::Size protocols::fold_from_loops::utils::Nub::unfolded_jump_

private

Referenced by join_pieces(), and unfolded_jump().

unfolded_pose_

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::unfolded_pose_

private

Referenced by add_binders(), add_labels(), apply(), assign_disulfides(), closest_binder(), fix_fragments(), join_pieces(), movemap(), refit_motif_sidechains(), transfer_unfolded_conformation(), and unfolded_pose().

working_cst_

core::scoring::constraints::ConstraintSetOP protocols::fold_from_loops::utils::Nub::working_cst_

private

Referenced by transfer_unfolded_conformation().

---

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

• src/protocols/fold_from_loops/utils/Nub.hh
• src/protocols/fold_from_loops/utils/Nub.cc