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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_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)
 
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
 
bool has_lower_residue () const
 
bool has_upper_residue () const
 
core::conformation::Residue const & lower_residue () const
 
core::conformation::Residue const & upper_residue () const
 
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

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

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

Member Function Documentation

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

References abego_, and segment_to_local().

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().

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().

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

References set_abego(), ss_, and template_pose_.

Referenced by parse_motif().

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

References lower(), and upper().

bool protocols::denovo_design::components::Segment::cterm_included ( ) const
inline
core::Size protocols::denovo_design::components::Segment::cutpoint ( ) const
SegmentResid protocols::denovo_design::components::Segment::cutpoint_segment ( ) const

segment residue number for cutpoint

References cutpoint_, and local_to_segment().

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

void protocols::denovo_design::components::Segment::delete_lower_padding ( )
void protocols::denovo_design::components::Segment::delete_residue ( SegmentResid const  segment_resid)
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(), ss_, start_local(), and stop_local().

void protocols::denovo_design::components::Segment::delete_upper_padding ( )
core::Size protocols::denovo_design::components::Segment::elem_length ( ) const
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().

bool protocols::denovo_design::components::Segment::has_free_lower_terminus ( ) const
inline
bool protocols::denovo_design::components::Segment::has_free_upper_terminus ( ) const
inline
bool protocols::denovo_design::components::Segment::has_lower_residue ( ) const
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()().

bool protocols::denovo_design::components::Segment::has_upper_residue ( ) const
std::string const & protocols::denovo_design::components::Segment::id ( ) const
core::Size protocols::denovo_design::components::Segment::length ( ) const
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().

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().

core::Size protocols::denovo_design::components::Segment::lower ( ) const
ResidueDihedrals const & protocols::denovo_design::components::Segment::lower_dihedrals ( ) const
core::Size protocols::denovo_design::components::Segment::lower_local ( ) const

on the chopping block

References length().

Referenced by lower(), and lower_padding().

core::Size protocols::denovo_design::components::Segment::lower_padding ( ) const
core::conformation::Residue const & protocols::denovo_design::components::Segment::lower_residue ( ) const
std::string const& protocols::denovo_design::components::Segment::lower_segment ( ) const
inline
core::Size protocols::denovo_design::components::Segment::movable_group ( ) const
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().

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().

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

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

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

segment residue number for "safe" residue

References local_to_segment(), and saferes_.

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

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().

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::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment(), and safe().

void protocols::denovo_design::components::Segment::set_abego ( std::string const &  abego_str)
void protocols::denovo_design::components::Segment::set_abego ( utility::vector1< std::string > const &  abego)
void protocols::denovo_design::components::Segment::set_cutpoint ( SegmentResid const  segment_resid)
void protocols::denovo_design::components::Segment::set_id ( std::string const &  id_val)
void protocols::denovo_design::components::Segment::set_lower_segment ( std::string const &  comp)
void protocols::denovo_design::components::Segment::set_movable_group ( core::Size const  mg)
void protocols::denovo_design::components::Segment::set_pose_start ( core::Size const  pose_resid)

References posestart_.

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().

void protocols::denovo_design::components::Segment::set_ss ( SegmentResid const  segment_resid,
char  ss_type 
)
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 
)
void protocols::denovo_design::components::Segment::set_upper_segment ( std::string const &  comp)
std::string const & protocols::denovo_design::components::Segment::ss ( ) const
core::Size protocols::denovo_design::components::Segment::start ( ) const
core::Size protocols::denovo_design::components::Segment::start_local ( ) const
core::Size protocols::denovo_design::components::Segment::stop ( ) const
core::Size protocols::denovo_design::components::Segment::stop_local ( ) const
core::pose::PoseCOP protocols::denovo_design::components::Segment::template_pose ( ) const
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().

core::Size protocols::denovo_design::components::Segment::upper ( ) const
ResidueDihedrals const & protocols::denovo_design::components::Segment::upper_dihedrals ( ) const
core::Size protocols::denovo_design::components::Segment::upper_local ( ) const

References length().

Referenced by upper().

core::Size protocols::denovo_design::components::Segment::upper_padding ( ) const
core::conformation::Residue const & protocols::denovo_design::components::Segment::upper_residue ( ) const
std::string const& protocols::denovo_design::components::Segment::upper_segment ( ) const
inline

Friends And Related Function Documentation

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

output residueinfo

Member Data Documentation

std::string protocols::denovo_design::components::Segment::abego_
private
bool protocols::denovo_design::components::Segment::cterm_included_
private
core::Size protocols::denovo_design::components::Segment::cutpoint_
private
std::string protocols::denovo_design::components::Segment::id_
private

Referenced by id(), and set_id().

ResidueDihedrals protocols::denovo_design::components::Segment::lower_dihedrals_
private
core::conformation::ResidueCOP protocols::denovo_design::components::Segment::lower_residue_
private
std::string protocols::denovo_design::components::Segment::lower_segment_
private
core::Size protocols::denovo_design::components::Segment::movable_group_
private
bool protocols::denovo_design::components::Segment::nterm_included_
private
core::Size protocols::denovo_design::components::Segment::posestart_
private
core::Size protocols::denovo_design::components::Segment::saferes_
private
std::string protocols::denovo_design::components::Segment::ss_
private
core::pose::PoseOP protocols::denovo_design::components::Segment::template_pose_
private
ResidueDihedrals protocols::denovo_design::components::Segment::upper_dihedrals_
private
core::conformation::ResidueCOP protocols::denovo_design::components::Segment::upper_residue_
private
std::string protocols::denovo_design::components::Segment::upper_segment_
private

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