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protocols::denovo_design::components::Segment Class Reference

manages information about segments of residues More...

#include <Segment.hh>

Inheritance diagram for protocols::denovo_design::components::Segment:
Inheritance graph
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Public Member Functions

 Segment (std::string const &id_val)
 
 Segment (std::string const &id_val, std::string const &ss_val, std::string const &abego_val, bool const start_inc, bool const stop_inc)
 
 ~Segment () override
 
virtual SegmentOP clone () const
 
void parse_tag (utility::tag::TagCOP tag)
 construct from xml tag More...
 
void parse_motif (std::string const &motif_str)
 construct from motif string (i.e. '1LX-10HA-1LA-1LB') More...
 
bool nterm_included () const
 
bool cterm_included () const
 
void set_nterm_included (bool const inc)
 Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is "padding") More...
 
void set_cterm_included (bool const inc)
 Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is "padding") More...
 
void set_pose_start (core::Size const pose_resid)
 
core::Size lower () const
 returns the n-terminal residue of this segment More...
 
core::Size upper () const
 returns the n-terminal residue of this segment More...
 
core::Size start () const
 
core::Size stop () const
 
core::Size safe () const
 
core::Size cutpoint () const
 
bool contains (core::Size const pose_resid) const
 
core::Size segment_to_pose (SegmentResid const segment_resid) const
 converts a internal segment resid to a pose resid 1 --> segment_start - 1 + 1 2 --> segment_start - 1 + 2 N --> segment_start - 1 + N More...
 
SegmentResid pose_to_segment (core::Size const pose_resid) const
 converts a internal segment resid to a pose resid segment_start - 1 + 1 --> 1 segment_start - 1 + 2 --> 2 segment_start - 1 + N --> N More...
 
std::string const & id () const
 
void set_id (std::string const &id_val)
 
std::string const & ss () const
 
void set_ss (SegmentResid const segment_resid, char ss_type)
 
void set_ss (std::string const &secstruct)
 
std::string const & abego () const
 
char abego (SegmentResid const segment_resid) const
 
void set_abego (std::string const &abego_str)
 
void set_abego (utility::vector1< std::string > const &abego)
 
core::Size length () const
 
core::Size elem_length () const
 
bool has_template_pose () const
 returns whether or not this segment contains a template pose More...
 
core::pose::PoseCOP template_pose () const
 returns template pose More...
 
void set_template_pose (core::pose::Pose const &template_pose, core::Size const start_resid, core::Size const stop_resid)
 sets template pose to be the given residues from template_pose More...
 
void extend (std::string const &secstruct, std::string const &abego)
 appends segment by the given secstruct and abego More...
 
core::Size movable_group () const
 
void set_movable_group (core::Size const mg)
 
SegmentResid safe_segment () const
 segment residue number for "safe" residue More...
 
void set_safe (SegmentResid const segment_resid)
 sets safe residue for this segment to be the ith residue in the segment safe = segment_start - 1 + cut_res More...
 
SegmentResid cutpoint_segment () const
 segment residue number for cutpoint More...
 
void set_cutpoint (SegmentResid const segment_resid)
 sets cutpoint for this segment to be the ith residue in the segment cut = segment_start - 1 + cut_res More...
 
core::Size n_residues_before_cutpoint () const
 number of residues before the cutpoint, 0 if cutpoint not set More...
 
core::Size n_residues_after_cutpoint () const
 number of residues after the cutpoint, length() if cutpoint not set More...
 
std::string const & upper_segment () const
 
std::string const & lower_segment () const
 
bool has_free_lower_terminus () const
 
bool has_free_upper_terminus () const
 
void set_upper_segment (std::string const &comp)
 
void set_lower_segment (std::string const &comp)
 
ResidueDihedrals const & lower_dihedrals () const
 
ResidueDihedrals const & upper_dihedrals () const
 
void set_lower_dihedrals (ResidueDihedrals const &dih)
 
void set_upper_dihedrals (ResidueDihedrals const &dih)
 
bool has_lower_residue () const
 
bool has_upper_residue () const
 
core::conformation::Residue const & lower_residue () const
 
core::conformation::Residue const & upper_residue () const
 
void set_lower_residue (core::conformation::ResidueCOP rsd)
 
void set_upper_residue (core::conformation::ResidueCOP rsd)
 
core::Size lower_padding () const
 
core::Size upper_padding () const
 
void add_lower_padding ()
 adds "padding" residue before the fixed portion of this segment More...
 
void add_upper_padding ()
 adds "padding" residue after the fixed portion of this segment More...
 
void delete_lower_padding ()
 deletes dummy residues before the fixed portion of this segment More...
 
void delete_upper_padding ()
 deletes dummy residues after the fixed portion of this segment More...
 
void delete_residue (SegmentResid const segment_resid)
 given a segment residue number, delete that residue. Resid for start_local() == 1 More...
 
core::Size lower_local () const
 on the chopping block More...
 
core::Size upper_local () const
 
core::Size start_local () const
 
core::Size stop_local () const
 
core::Size segment_to_local (SegmentResid const segment_resid) const
 converts a segment resid to a "local" resid More...
 

Private Member Functions

void delete_residues (core::Size const local_resnum_start, core::Size const local_resnum_stop)
 given a residue number range local to this 1=start, length=end, delete the residue More...
 
core::Size pose_to_local (core::Size const pose_resid) const
 converts a pose resid to a "local" resid More...
 
SegmentResid local_to_segment (core::Size const local_resid) const
 converts a local resid to a segment resid More...
 
core::Size local_to_pose (core::Size const local_resid) const
 converts a internal segment "local" resid to a pose resid 1 --> posestart - 1 + 1 2 --> posestart - 1 + 2 N --> posestart - 1 + N More...
 
void clear ()
 
core::Size template_resid (SegmentResid const segment_resid) const
 expands this residue set to include the dummy trailing residues More...
 

Private Attributes

std::string id_
 
core::Size posestart_
 
core::Size movable_group_
 
core::Size saferes_
 
core::Size cutpoint_
 
std::string ss_
 
std::string abego_
 
bool nterm_included_
 
bool cterm_included_
 
std::string lower_segment_
 
std::string upper_segment_
 
core::pose::PoseOP template_pose_
 
ResidueDihedrals lower_dihedrals_
 
ResidueDihedrals upper_dihedrals_
 
core::conformation::ResidueCOP lower_residue_
 
core::conformation::ResidueCOP upper_residue_
 

Friends

std::ostream & operator<< (std::ostream &os, Segment const &res)
 output residueinfo More...
 

Detailed Description

manages information about segments of residues

Constructor & Destructor Documentation

◆ Segment() [1/2]

protocols::denovo_design::components::Segment::Segment ( std::string const &  id_val)

◆ Segment() [2/2]

protocols::denovo_design::components::Segment::Segment ( std::string const &  id_val,
std::string const &  ss_val,
std::string const &  abego_val,
bool const  start_inc,
bool const  stop_inc 
)

References abego_, and ss_.

◆ ~Segment()

protocols::denovo_design::components::Segment::~Segment ( )
inlineoverride

Member Function Documentation

◆ abego() [1/2]

std::string const & protocols::denovo_design::components::Segment::abego ( ) const

References abego_.

Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::count_bulges(), extend(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::IdealAbegoGenerator::note_fwd_element_extensions(), protocols::denovo_design::components::IdealAbegoGenerator::note_rev_element_extensions(), parse_motif(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ abego() [2/2]

char protocols::denovo_design::components::Segment::abego ( SegmentResid const  segment_resid) const

References abego_, and segment_to_local().

◆ add_lower_padding()

void protocols::denovo_design::components::Segment::add_lower_padding ( )

adds "padding" residue before the fixed portion of this segment

References abego_, cutpoint_, nterm_included_, saferes_, set_abego(), and ss_.

Referenced by protocols::denovo_design::components::StructureData::slice().

◆ add_upper_padding()

void protocols::denovo_design::components::Segment::add_upper_padding ( )

adds "padding" residue after the fixed portion of this segment

References abego_, cterm_included_, set_abego(), and ss_.

Referenced by protocols::denovo_design::components::StructureData::slice().

◆ clear()

void protocols::denovo_design::components::Segment::clear ( )
private

References set_abego(), ss_, and template_pose_.

Referenced by parse_motif().

◆ clone()

SegmentOP protocols::denovo_design::components::Segment::clone ( ) const
virtual

◆ contains()

bool protocols::denovo_design::components::Segment::contains ( core::Size const  pose_resid) const

References lower(), and upper().

◆ cterm_included()

bool protocols::denovo_design::components::Segment::cterm_included ( ) const
inline

References cterm_included_.

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings(), and protocols::denovo_design::components::StructureData::merge_segments().

◆ cutpoint()

core::Size protocols::denovo_design::components::Segment::cutpoint ( ) const

References cutpoint_, and local_to_pose().

Referenced by protocols::denovo_design::add_cutpoints(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::connection::AreConnectablePredicate::check_movable_groups(), protocols::denovo_design::components::StructureData::connected_segments(), protocols::denovo_design::components::StructureData::cutpoints(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::components::FoldGraph::find_cutpoint_in_range(), protocols::denovo_design::components::FoldGraph::find_cutpoints(), and protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints().

◆ cutpoint_segment()

SegmentResid protocols::denovo_design::components::Segment::cutpoint_segment ( ) const

segment residue number for cutpoint

References cutpoint_, and local_to_segment().

◆ delete_lower_padding()

void protocols::denovo_design::components::Segment::delete_lower_padding ( )

deletes dummy residues before the fixed portion of this segment

References abego_, cutpoint_, lower_padding(), nterm_included_, saferes_, set_abego(), and ss_.

Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::components::StructureData::delete_leading_residues(), protocols::denovo_design::components::StructureData::delete_residue(), protocols::denovo_design::architects::PoseArchitect::design(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ delete_residue()

void protocols::denovo_design::components::Segment::delete_residue ( SegmentResid const  segment_resid)

given a segment residue number, delete that residue. Resid for start_local() == 1

References abego_, protocols::grafting::simple_movers::DeleteRegionMover::apply(), cutpoint_, saferes_, segment_to_local(), set_abego(), set_ss(), ss_, template_pose_, and template_resid().

Referenced by protocols::denovo_design::components::StructureData::delete_residue().

◆ delete_residues()

void protocols::denovo_design::components::Segment::delete_residues ( core::Size const  local_resnum_start,
core::Size const  local_resnum_stop 
)
private

given a residue number range local to this 1=start, length=end, delete the residue

References abego_, cutpoint_, saferes_, set_abego(), set_ss(), ss_, start_local(), and stop_local().

◆ delete_upper_padding()

void protocols::denovo_design::components::Segment::delete_upper_padding ( )

deletes dummy residues after the fixed portion of this segment

References abego_, cterm_included_, set_abego(), ss_, and stop_local().

Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::components::StructureData::delete_residue(), protocols::denovo_design::components::StructureData::delete_trailing_residues(), protocols::denovo_design::architects::PoseArchitect::design(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ elem_length()

core::Size protocols::denovo_design::components::Segment::elem_length ( ) const

References start_local(), and stop_local().

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::components::IdealAbegoGenerator::note_fwd_element_extensions(), protocols::denovo_design::components::IdealAbegoGenerator::note_rev_element_extensions(), parse_tag(), protocols::denovo_design::architects::BetaSheetArchitect::retrieve_lengths(), safe(), segment_to_local(), set_cutpoint(), set_safe(), set_template_pose(), and template_resid().

◆ extend()

void protocols::denovo_design::components::Segment::extend ( std::string const &  secstruct,
std::string const &  abego 
)

appends segment by the given secstruct and abego

References abego(), abego_, and ss_.

Referenced by parse_motif().

◆ has_free_lower_terminus()

bool protocols::denovo_design::components::Segment::has_free_lower_terminus ( ) const
inline

References lower_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::components::StructureData::available_lower_termini(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::StructureData::connected_segments(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::StructureData::has_free_lower_terminus(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::components::StructureData::num_chains(), and protocols::denovo_design::connection::AreConnectablePredicate::operator()().

◆ has_free_upper_terminus()

bool protocols::denovo_design::components::Segment::has_free_upper_terminus ( ) const
inline

References upper_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::components::StructureData::available_upper_termini(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::StructureData::connected_segments(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::components::StructureData::has_free_upper_terminus(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::components::StructureData::num_chains(), and protocols::denovo_design::connection::AreConnectablePredicate::operator()().

◆ has_lower_residue()

bool protocols::denovo_design::components::Segment::has_lower_residue ( ) const

References lower_residue_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment().

◆ has_template_pose()

bool protocols::denovo_design::components::Segment::has_template_pose ( ) const

returns whether or not this segment contains a template pose

Returns whether or not this segment has a template pose.

References template_pose_.

Referenced by protocols::denovo_design::components::StructureSlicePredicate::operator()().

◆ has_upper_residue()

bool protocols::denovo_design::components::Segment::has_upper_residue ( ) const

References upper_residue_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), and protocols::denovo_design::components::append_residues_from_template_segment().

◆ id()

std::string const & protocols::denovo_design::components::Segment::id ( ) const

References id_.

Referenced by protocols::denovo_design::components::StructureData::add_segment(), protocols::denovo_design::components::add_segment(), and set_template_pose().

◆ length()

core::Size protocols::denovo_design::components::Segment::length ( ) const

References ss_.

Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::architects::BlueprintArchitect::get_template_segments(), local_to_pose(), lower_local(), protocols::denovo_design::components::StructureData::merge_segments(), n_residues_after_cutpoint(), parse_tag(), segment_to_local(), set_abego(), start_local(), stop_local(), upper_local(), and upper_padding().

◆ local_to_pose()

core::Size protocols::denovo_design::components::Segment::local_to_pose ( core::Size const  local_resid) const
private

converts a internal segment "local" resid to a pose resid 1 --> posestart - 1 + 1 2 --> posestart - 1 + 2 N --> posestart - 1 + N

converts an internal local resid to a pose resid 1 --> posestart - 1 + 1 2 --> posestart - 1 + 2 N --> posestart - 1 + N

References length(), and posestart_.

Referenced by cutpoint(), lower(), safe(), segment_to_pose(), start(), stop(), and upper().

◆ local_to_segment()

SegmentResid protocols::denovo_design::components::Segment::local_to_segment ( core::Size const  local_resid) const
private

converts a local resid to a segment resid

converts an internal local resid to a segment resid

References start_local().

Referenced by cutpoint_segment(), pose_to_segment(), and safe_segment().

◆ lower()

core::Size protocols::denovo_design::components::Segment::lower ( ) const

returns the n-terminal residue of this segment

References local_to_pose(), and lower_local().

Referenced by protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::StructureData::check_improper_termini(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment(), contains(), protocols::denovo_design::components::FoldGraph::create_loops(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::denovo_design::architects::BlueprintArchitect::get_template_segments(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::components::StructureData::segment_name(), protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues(), protocols::denovo_design::components::StructureData::set_abego(), and protocols::denovo_design::architects::BlueprintArchitect::set_template_segments().

◆ lower_dihedrals()

ResidueDihedrals const & protocols::denovo_design::components::Segment::lower_dihedrals ( ) const

References lower_dihedrals_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), and protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ lower_local()

core::Size protocols::denovo_design::components::Segment::lower_local ( ) const

on the chopping block

References length().

Referenced by lower(), and lower_padding().

◆ lower_padding()

core::Size protocols::denovo_design::components::Segment::lower_padding ( ) const

References lower_local(), and start_local().

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), delete_lower_padding(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ lower_residue()

core::conformation::Residue const & protocols::denovo_design::components::Segment::lower_residue ( ) const

References lower_residue_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment().

◆ lower_segment()

std::string const& protocols::denovo_design::components::Segment::lower_segment ( ) const
inline

References lower_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::components::StructureData::available_lower_termini(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::connection::AreConnectablePredicate::check_movable_groups(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::StructureData::connected_segments(), protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose(), protocols::denovo_design::components::ConnectionPerturber::enumerate(), protocols::denovo_design::movers::FoldArchitectMover::find_roots(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::connection::AreConnectablePredicate::operator()(), protocols::denovo_design::components::StructureData::rename_segment(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), and protocols::denovo_design::components::StructureData::slice().

◆ movable_group()

core::Size protocols::denovo_design::components::Segment::movable_group ( ) const

References movable_group_.

Referenced by protocols::denovo_design::movers::AlignResiduesMover::add_metadata(), protocols::denovo_design::components::FoldGraph::check_solution(), protocols::denovo_design::connection::AreConnectablePredicate::connected_movable_groups(), protocols::denovo_design::components::map_mgs(), protocols::denovo_design::components::map_nodes(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::StructureData::movable_group(), protocols::denovo_design::components::StructureData::renumber_movable_group(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), and protocols::denovo_design::components::StructureData::segments_in_movable_group().

◆ n_residues_after_cutpoint()

core::Size protocols::denovo_design::components::Segment::n_residues_after_cutpoint ( ) const

number of residues after the cutpoint, length() if cutpoint not set

References cutpoint_, and length().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ n_residues_before_cutpoint()

core::Size protocols::denovo_design::components::Segment::n_residues_before_cutpoint ( ) const

number of residues before the cutpoint, 0 if cutpoint not set

References cutpoint_.

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ nterm_included()

bool protocols::denovo_design::components::Segment::nterm_included ( ) const
inline

References nterm_included_.

Referenced by protocols::denovo_design::components::StructureData::merge_segments().

◆ parse_motif()

void protocols::denovo_design::components::Segment::parse_motif ( std::string const &  motif_str)

construct from motif string (i.e. '1LX-10HA-1LA-1LB')

References abego(), clear(), extend(), and protocols::denovo_design::parse_motif_string().

◆ parse_tag()

void protocols::denovo_design::components::Segment::parse_tag ( utility::tag::TagCOP  tag)

construct from xml tag

References abego_, cterm_included_, cutpoint_, elem_length(), length(), movable_group_, nterm_included_, posestart_, saferes_, set_abego(), set_cterm_included(), set_cutpoint(), set_lower_segment(), set_movable_group(), set_nterm_included(), set_pose_start(), set_safe(), set_ss(), set_upper_segment(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureData::parse_subtag().

◆ pose_to_local()

core::Size protocols::denovo_design::components::Segment::pose_to_local ( core::Size const  pose_resid) const
private

converts a pose resid to a "local" resid

converts a pose resid to an internal local resid

References posestart_.

Referenced by pose_to_segment().

◆ pose_to_segment()

SegmentResid protocols::denovo_design::components::Segment::pose_to_segment ( core::Size const  pose_resid) const

converts a internal segment resid to a pose resid segment_start - 1 + 1 --> 1 segment_start - 1 + 2 --> 2 segment_start - 1 + N --> N

converts a pose resid to a segment resid Numbering starts at start_res start() --> N - posestart - start_local() + 1 start() + 1 --> N - posestart - start_local() + 2

References local_to_segment(), and pose_to_local().

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::components::StructureData::delete_residue(), protocols::denovo_design::components::StructureData::generic_enzdes_header(), protocols::denovo_design::components::StructureData::set_alias(), protocols::denovo_design::components::StructureData::set_cutpoint(), and protocols::denovo_design::components::StructureData::set_ss().

◆ safe()

core::Size protocols::denovo_design::components::Segment::safe ( ) const

References elem_length(), local_to_pose(), saferes_, and segment_to_pose().

Referenced by protocols::denovo_design::components::add_paired_residues(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::HelixPairing::pairing_string(), protocols::denovo_design::components::StrandPairing::pairing_string(), protocols::denovo_design::components::HelixSheetPairing::pairing_string(), and protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel().

◆ safe_segment()

SegmentResid protocols::denovo_design::components::Segment::safe_segment ( ) const

segment residue number for "safe" residue

References local_to_segment(), and saferes_.

◆ segment_to_local()

core::Size protocols::denovo_design::components::Segment::segment_to_local ( SegmentResid const  segment_resid) const

converts a segment resid to a "local" resid

converts a segment resid into a local resid

References elem_length(), length(), start_local(), and stop_local().

Referenced by abego(), delete_residue(), segment_to_pose(), set_cutpoint(), set_safe(), and set_ss().

◆ segment_to_pose()

core::Size protocols::denovo_design::components::Segment::segment_to_pose ( SegmentResid const  segment_resid) const

converts a internal segment resid to a pose resid 1 --> segment_start - 1 + 1 2 --> segment_start - 1 + 2 N --> segment_start - 1 + N

converts a local resid to a pose resid 1 --> start_res - 1 + 1 2 --> start_res - 1 + 1 N --> start_res - 1 + N

References local_to_pose(), and segment_to_local().

Referenced by protocols::denovo_design::components::StructureData::alias(), protocols::denovo_design::architects::bulge_residues(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment(), and safe().

◆ set_abego() [1/2]

void protocols::denovo_design::components::Segment::set_abego ( std::string const &  abego_str)

References abego_, protocols::denovo_design::abego_str(), and length().

Referenced by add_lower_padding(), add_upper_padding(), clear(), delete_lower_padding(), delete_residue(), delete_residues(), delete_upper_padding(), parse_tag(), protocols::denovo_design::components::StructureData::set_abego(), and set_abego().

◆ set_abego() [2/2]

void protocols::denovo_design::components::Segment::set_abego ( utility::vector1< std::string > const &  abego)

References protocols::denovo_design::abego_str(), and set_abego().

◆ set_cterm_included()

void protocols::denovo_design::components::Segment::set_cterm_included ( bool const  inc)
inline

Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is "padding")

References cterm_included_.

Referenced by parse_tag().

◆ set_cutpoint()

void protocols::denovo_design::components::Segment::set_cutpoint ( SegmentResid const  segment_resid)

sets cutpoint for this segment to be the ith residue in the segment cut = segment_start - 1 + cut_res

References cutpoint_, elem_length(), and segment_to_local().

Referenced by protocols::denovo_design::components::StructureData::delete_jump_and_intervening_cutpoint(), parse_tag(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), and protocols::denovo_design::components::StructureData::set_cutpoint().

◆ set_id()

void protocols::denovo_design::components::Segment::set_id ( std::string const &  id_val)

References id_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::components::add_segment(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), and protocols::denovo_design::components::StructureData::rename_segment().

◆ set_lower_dihedrals()

void protocols::denovo_design::components::Segment::set_lower_dihedrals ( ResidueDihedrals const &  dih)
inline

References lower_dihedrals_.

Referenced by set_template_pose().

◆ set_lower_residue()

void protocols::denovo_design::components::Segment::set_lower_residue ( core::conformation::ResidueCOP  rsd)
inline

References lower_residue_.

Referenced by set_template_pose().

◆ set_lower_segment()

void protocols::denovo_design::components::Segment::set_lower_segment ( std::string const &  comp)

References lower_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::StructureData::mark_disconnected(), parse_tag(), protocols::denovo_design::components::StructureData::rename_segment(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), and protocols::denovo_design::components::StructureData::slice().

◆ set_movable_group()

void protocols::denovo_design::components::Segment::set_movable_group ( core::Size const  mg)

References core::scoring::mg, and movable_group_.

Referenced by protocols::denovo_design::components::StructureData::merge(), protocols::denovo_design::components::StructureData::merge_before(), protocols::denovo_design::components::StructureData::merge_segments(), parse_tag(), protocols::denovo_design::components::StructureData::renumber_movable_group(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ set_nterm_included()

void protocols::denovo_design::components::Segment::set_nterm_included ( bool const  inc)
inline

Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is "padding")

References nterm_included_.

Referenced by parse_tag().

◆ set_pose_start()

void protocols::denovo_design::components::Segment::set_pose_start ( core::Size const  pose_resid)

References posestart_.

Referenced by parse_tag().

◆ set_safe()

void protocols::denovo_design::components::Segment::set_safe ( SegmentResid const  segment_resid)

sets safe residue for this segment to be the ith residue in the segment safe = segment_start - 1 + cut_res

References elem_length(), saferes_, and segment_to_local().

Referenced by parse_tag().

◆ set_ss() [1/2]

void protocols::denovo_design::components::Segment::set_ss ( SegmentResid const  segment_resid,
char  ss_type 
)

References segment_to_local(), and ss_.

Referenced by delete_residue(), delete_residues(), protocols::denovo_design::components::IdealAbegoGenerator::note_fwd_element_extensions(), protocols::denovo_design::components::IdealAbegoGenerator::note_rev_element_extensions(), parse_tag(), and protocols::denovo_design::components::StructureData::set_ss().

◆ set_ss() [2/2]

void protocols::denovo_design::components::Segment::set_ss ( std::string const &  secstruct)
inline

References ss_.

◆ set_template_pose()

void protocols::denovo_design::components::Segment::set_template_pose ( core::pose::Pose const &  template_pose,
core::Size const  start_resid,
core::Size const  stop_resid 
)

sets template pose to be the given residues from template_pose

sets template pose

References core::conformation::Residue::clone(), core::pose::Pose::dump_pdb(), elem_length(), id(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), set_lower_dihedrals(), set_lower_residue(), set_upper_dihedrals(), set_upper_residue(), core::pose::Pose::size(), template_pose_, protocols::TR(), and core::conformation::Residue::xyz().

◆ set_upper_dihedrals()

void protocols::denovo_design::components::Segment::set_upper_dihedrals ( ResidueDihedrals const &  dih)
inline

References upper_dihedrals_.

Referenced by set_template_pose().

◆ set_upper_residue()

void protocols::denovo_design::components::Segment::set_upper_residue ( core::conformation::ResidueCOP  rsd)
inline

References upper_residue_.

Referenced by set_template_pose().

◆ set_upper_segment()

void protocols::denovo_design::components::Segment::set_upper_segment ( std::string const &  comp)

References upper_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::StructureData::mark_disconnected(), parse_tag(), protocols::denovo_design::components::StructureData::rename_segment(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), and protocols::denovo_design::components::StructureData::slice().

◆ ss()

std::string const & protocols::denovo_design::components::Segment::ss ( ) const

References ss_.

Referenced by protocols::denovo_design::count_bulges(), protocols::denovo_design::components::StructureData::merge_segments(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ start()

core::Size protocols::denovo_design::components::Segment::start ( ) const

References local_to_pose(), and start_local().

Referenced by protocols::denovo_design::components::StructureData::add_covalent_bond(), protocols::denovo_design::movers::FoldArchitectMover::build_in_phases(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::denovo_design::components::StructureData::lower_anchor(), and protocols::denovo_design::connection::ConnectionArchitect::motifs_for_pair().

◆ start_local()

core::Size protocols::denovo_design::components::Segment::start_local ( ) const

References length(), and nterm_included_.

Referenced by delete_residues(), elem_length(), local_to_segment(), lower_padding(), segment_to_local(), and start().

◆ stop()

core::Size protocols::denovo_design::components::Segment::stop ( ) const

References local_to_pose(), and stop_local().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::build_in_phases(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::denovo_design::connection::ConnectionArchitect::motifs_for_pair(), protocols::denovo_design::components::StructureData::substitute_variables(), and protocols::denovo_design::components::StructureData::upper_anchor().

◆ stop_local()

core::Size protocols::denovo_design::components::Segment::stop_local ( ) const

References cterm_included_, and length().

Referenced by delete_residues(), delete_upper_padding(), elem_length(), segment_to_local(), stop(), and upper_padding().

◆ template_pose()

core::pose::PoseCOP protocols::denovo_design::components::Segment::template_pose ( ) const

returns template pose

References template_pose_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::components::ExtendedPoseBuilder::find_template_segments(), protocols::denovo_design::components::StructureData::merge(), protocols::denovo_design::components::StructureData::merge_before(), protocols::denovo_design::movers::FoldArchitectMover::segments_to_fold(), and protocols::denovo_design::components::StructureData::slice().

◆ template_resid()

core::Size protocols::denovo_design::components::Segment::template_resid ( SegmentResid const  segment_resid) const
private

expands this residue set to include the dummy trailing residues

References elem_length().

Referenced by delete_residue().

◆ upper()

core::Size protocols::denovo_design::components::Segment::upper ( ) const

returns the n-terminal residue of this segment

References local_to_pose(), and upper_local().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::StructureData::check_improper_termini(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment(), contains(), protocols::denovo_design::components::FoldGraph::create_loops(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::denovo_design::architects::BlueprintArchitect::get_template_segments(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::components::StructureData::segment_name(), protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues(), protocols::denovo_design::components::StructureData::set_abego(), and protocols::denovo_design::architects::BlueprintArchitect::set_template_segments().

◆ upper_dihedrals()

ResidueDihedrals const & protocols::denovo_design::components::Segment::upper_dihedrals ( ) const

References upper_dihedrals_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), and protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ upper_local()

core::Size protocols::denovo_design::components::Segment::upper_local ( ) const

References length().

Referenced by upper().

◆ upper_padding()

core::Size protocols::denovo_design::components::Segment::upper_padding ( ) const

References length(), and stop_local().

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

◆ upper_residue()

core::conformation::Residue const & protocols::denovo_design::components::Segment::upper_residue ( ) const

References upper_residue_.

Referenced by protocols::denovo_design::components::append_new_chain_from_template_segment(), and protocols::denovo_design::components::append_residues_from_template_segment().

◆ upper_segment()

std::string const& protocols::denovo_design::components::Segment::upper_segment ( ) const
inline

References upper_segment_.

Referenced by protocols::denovo_design::components::StructureData::add_prefix_to_segments(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::components::StructureData::available_upper_termini(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::connection::AreConnectablePredicate::check_movable_groups(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::StructureData::connected_segments(), protocols::denovo_design::components::ConnectionPerturber::enumerate(), protocols::denovo_design::movers::FoldArchitectMover::find_roots(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::connection::AreConnectablePredicate::operator()(), protocols::denovo_design::components::StructureData::rename_segment(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), and protocols::denovo_design::components::StructureData::slice().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<< ( std::ostream &  os,
Segment const &  res 
)
friend

output residueinfo

Member Data Documentation

◆ abego_

std::string protocols::denovo_design::components::Segment::abego_
private

Referenced by abego(), add_lower_padding(), add_upper_padding(), delete_lower_padding(), delete_residue(), delete_residues(), delete_upper_padding(), extend(), parse_tag(), Segment(), and set_abego().

◆ cterm_included_

bool protocols::denovo_design::components::Segment::cterm_included_
private

Referenced by add_upper_padding(), cterm_included(), delete_upper_padding(), parse_tag(), set_cterm_included(), and stop_local().

◆ cutpoint_

core::Size protocols::denovo_design::components::Segment::cutpoint_
private

Referenced by add_lower_padding(), cutpoint(), cutpoint_segment(), delete_lower_padding(), delete_residue(), delete_residues(), n_residues_after_cutpoint(), n_residues_before_cutpoint(), parse_tag(), and set_cutpoint().

◆ id_

std::string protocols::denovo_design::components::Segment::id_
private

Referenced by id(), and set_id().

◆ lower_dihedrals_

ResidueDihedrals protocols::denovo_design::components::Segment::lower_dihedrals_
private

Referenced by lower_dihedrals(), and set_lower_dihedrals().

◆ lower_residue_

core::conformation::ResidueCOP protocols::denovo_design::components::Segment::lower_residue_
private

Referenced by has_lower_residue(), lower_residue(), and set_lower_residue().

◆ lower_segment_

std::string protocols::denovo_design::components::Segment::lower_segment_
private

Referenced by has_free_lower_terminus(), lower_segment(), and set_lower_segment().

◆ movable_group_

core::Size protocols::denovo_design::components::Segment::movable_group_
private

Referenced by movable_group(), parse_tag(), and set_movable_group().

◆ nterm_included_

bool protocols::denovo_design::components::Segment::nterm_included_
private

Referenced by add_lower_padding(), delete_lower_padding(), nterm_included(), parse_tag(), set_nterm_included(), and start_local().

◆ posestart_

core::Size protocols::denovo_design::components::Segment::posestart_
private

Referenced by local_to_pose(), parse_tag(), pose_to_local(), and set_pose_start().

◆ saferes_

core::Size protocols::denovo_design::components::Segment::saferes_
private

Referenced by add_lower_padding(), delete_lower_padding(), delete_residue(), delete_residues(), parse_tag(), safe(), safe_segment(), and set_safe().

◆ ss_

std::string protocols::denovo_design::components::Segment::ss_
private

Referenced by add_lower_padding(), add_upper_padding(), clear(), delete_lower_padding(), delete_residue(), delete_residues(), delete_upper_padding(), extend(), length(), Segment(), set_ss(), and ss().

◆ template_pose_

core::pose::PoseOP protocols::denovo_design::components::Segment::template_pose_
private

Referenced by clear(), delete_residue(), has_template_pose(), set_template_pose(), and template_pose().

◆ upper_dihedrals_

ResidueDihedrals protocols::denovo_design::components::Segment::upper_dihedrals_
private

Referenced by set_upper_dihedrals(), and upper_dihedrals().

◆ upper_residue_

core::conformation::ResidueCOP protocols::denovo_design::components::Segment::upper_residue_
private

Referenced by has_upper_residue(), set_upper_residue(), and upper_residue().

◆ upper_segment_

std::string protocols::denovo_design::components::Segment::upper_segment_
private

Referenced by has_free_upper_terminus(), set_upper_segment(), and upper_segment().

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