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

#include <Nub.hh>

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

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

Empty Constructor.

References movemap_.

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

Destructor.

Member Function Documentation

void protocols::fold_from_loops::utils::Nub::add_binders ( )
private
void protocols::fold_from_loops::utils::Nub::add_labels ( )
private
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 
)
core::select::residue_selector::ResidueSubset protocols::fold_from_loops::utils::Nub::apply_binder_selector ( core::pose::Pose const &  pose) const

References binder_selector_.

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_.

core::select::residue_selector::ResidueSubset protocols::fold_from_loops::utils::Nub::apply_selector ( core::pose::Pose const &  pose) const

References selector_.

core::select::residue_selector::ResidueRanges protocols::fold_from_loops::utils::Nub::apply_selector_as_ranges ( core::pose::Pose const &  pose) const

References selector_.

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

References binder_selector_.

Referenced by parse_tag().

void protocols::fold_from_loops::utils::Nub::binder_selector ( core::select::residue_selector::ResidueSelectorCOP const &  selector)

References binder_selector_, and selector().

core::Size protocols::fold_from_loops::utils::Nub::closest_binder ( core::pose::Pose const &  pose)
private
std::string protocols::fold_from_loops::utils::Nub::coldspot_label ( )
static

Referenced by get_nub_pieces().

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

Referenced by provide_xml_definition().

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

Referenced by add_labels().

core::Size protocols::fold_from_loops::utils::Nub::default_flexibility ( ) const

References default_flexibility_.

void protocols::fold_from_loops::utils::Nub::default_flexibility ( core::Size  pick)

References default_flexibility_.

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::default_selector ( )
static
std::string protocols::fold_from_loops::utils::Nub::design_chain ( ) const

References design_chain_.

core::Size protocols::fold_from_loops::utils::Nub::design_size ( ) const

References design_size_.

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

Referenced by assign_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().

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

Fixes a FragSet.

References core::fragment::FragData::pdbid(), and seqmap_.

Referenced by 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_, and unfolded_pose_.

Referenced by apply().

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

Referenced by get_nub_pieces(), and make_movemap().

void protocols::fold_from_loops::utils::Nub::get_nub_pieces ( core::pose::Pose pose)
private
bool protocols::fold_from_loops::utils::Nub::has_binder ( ) const

References has_binder_.

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

Referenced by get_nub_pieces().

bool protocols::fold_from_loops::utils::Nub::is_multisegment ( ) const

References pieces_.

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

References large_.

void protocols::fold_from_loops::utils::Nub::large_fragments ( core::fragment::FragSetOP  fragset)

References large_.

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().

std::string protocols::fold_from_loops::utils::Nub::motif_label ( )
static
core::kinematics::MoveMapOP protocols::fold_from_loops::utils::Nub::movemap ( ) const

References movemap_, and unfolded_pose_.

core::select::movemap::MoveMapFactoryOP protocols::fold_from_loops::utils::Nub::movemapfactory ( ) const
std::string protocols::fold_from_loops::utils::Nub::object_name ( )
static
void protocols::fold_from_loops::utils::Nub::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::utils::Nub::pieces ( ) const

References pieces_.

void protocols::fold_from_loops::utils::Nub::provide_xml_definition ( utility::tag::XMLSchemaDefinition &  xsd,
utility::tag::XMLSchemaSimpleSubelementList &  elements 
)
static
core::pose::PoseOP protocols::fold_from_loops::utils::Nub::reference_pose ( ) const

References reference_pose_.

void protocols::fold_from_loops::utils::Nub::reference_pose ( core::pose::PoseOP const &  pose)

References reference_pose_.

void protocols::fold_from_loops::utils::Nub::refit_motif_sidechains ( core::pose::Pose pose)
std::string protocols::fold_from_loops::utils::Nub::segment_object_name ( )
static
core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::selector ( ) const
void protocols::fold_from_loops::utils::Nub::selector ( core::select::residue_selector::ResidueSelectorCOP const &  selector)

References selector(), and selector_.

core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::small_fragments ( ) const

References small_.

void protocols::fold_from_loops::utils::Nub::small_fragments ( core::fragment::FragSetOP  fragset)

References small_.

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

Referenced by add_labels(), and make_movemap().

core::id::SequenceMapping protocols::fold_from_loops::utils::Nub::template_to_unfolded_mapping ( ) const

References seqmap_.

void protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation ( core::pose::Pose pose)
core::Size protocols::fold_from_loops::utils::Nub::unfolded_jump ( ) const

References unfolded_jump_.

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::unfolded_pose ( ) const

References unfolded_pose_.

Member Data Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::binder_selector_
private
core::Size protocols::fold_from_loops::utils::Nub::default_flexibility_
private
std::string protocols::fold_from_loops::utils::Nub::design_chain_
private
core::Size protocols::fold_from_loops::utils::Nub::design_size_
private

Referenced by design_size(), and join_pieces().

utility::vector1< std::pair< core::Size, core::Size > > protocols::fold_from_loops::utils::Nub::disulfides_
private
bool protocols::fold_from_loops::utils::Nub::has_binder_
private
core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::insertion_selector_
private
core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::large_
private

Referenced by fix_fragments(), and large_fragments().

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

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

core::Size protocols::fold_from_loops::utils::Nub::nub_disulfides_
private
utility::vector1< NubSegment > protocols::fold_from_loops::utils::Nub::piece_properties_
private

Referenced by get_nub_pieces(), and parse_tag().

utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::utils::Nub::pieces_
private
core::pose::PoseOP protocols::fold_from_loops::utils::Nub::reference_pose_
private
core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::utils::Nub::selector_
private
core::id::SequenceMapping protocols::fold_from_loops::utils::Nub::seqmap_
private
core::fragment::FragSetOP protocols::fold_from_loops::utils::Nub::small_
private

Referenced by fix_fragments(), and small_fragments().

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

Referenced by join_pieces(), and unfolded_jump().

core::pose::PoseOP protocols::fold_from_loops::utils::Nub::unfolded_pose_
private
core::scoring::constraints::ConstraintSetOP protocols::fold_from_loops::utils::Nub::working_cst_
private

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