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protocols::denovo_design::components::StructureData Class Reference

#include <StructureData.hh>

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

 StructureData ()
 
 StructureData (std::string const &id_val)
 
 ~StructureData () override
 destructors More...
 
CacheableDataOP clone () const override
 
void write (std::ostream &os) const override
 
std::string datatype () const override
 
void parse_tag (utility::tag::TagCOP tag)
 Retrieves data from an XML tag. More...
 
void parse_subtag (utility::tag::TagCOP tag)
 Retrieves data from an XML subtag. More...
 
void set_id (std::string const &id_str)
 sets id name More...
 
void set_template_pose (std::string const &segment, core::pose::Pose const &template_pose, core::Size const start_resid, core::Size const stop_resid)
 attaches a template pose to the given segment More...
 
void add_prefix_to_segments (std::string const &prefix)
 renames a residue segment and updates all connections More...
 
void rename_segment (std::string const &old_name, std::string const &new_name)
 renames a residue segment and updates all connections More...
 
void move_segment (std::string const &segment1, std::string const &segment2)
 re-arranges segments suchs that segment2 follows segment1 in sequence More...
 
void connect_segments (std::string const &segment1, std::string const &segment2)
 connects the given chains together, doesn't update anything – don't call this on its own unless you know what you're doing More...
 
void disconnect_segments (std::string const &segment1, std::string const &segment2)
 connects the given chains together, doesn't update anything – don't call this on its own unless you know what you're doing More...
 
void merge_segments (std::string const &segment1, std::string const &segment2, std::string const &new_name)
 merges two segments into one that has the name new_name. They must be next to each other in sequence. More...
 
void delete_segment (std::string const &segment)
 removes all traces of the given segment from the object More...
 
void delete_residue (core::Size const pose_resid)
 delete residue at resid More...
 
void declare_covalent_bond (std::string const &seg1, core::Size const res1, std::string const &atom1, std::string const &seg2, core::Size const res2, std::string const &atom2)
 declares a covalent bond between the specified atoms More...
 
void declare_covalent_bond (core::Size const res1, std::string const &atom1, core::Size const res2, std::string const &atom2)
 declares a covalent bond using pose residues More...
 
Cutpoints cutpoints () const
 returns list of all cutpoints, in N–>C order More...
 
void set_cutpoint (core::Size const resid)
 marks the ith residue as a cutpoint More...
 
void set_cutpoint (std::string const &seg, SegmentResid const resi)
 marks the resi-th residue of segment as a cutpoint More...
 
void replace_segment (SegmentName const &seg_name, Segment const &segment)
 replace segment named seg_name with the given new segment More...
 
void add_segment (Segment const &resis)
 adds a residues segment to the end of the list More...
 
void add_segment (Segment const &resis, std::string const &insert_before_segment)
 adds a residues segment – will be ordered before the given segment More...
 
void add_segment (Segment const &resis, SegmentNameList::iterator insert_pos)
 adds a residues segment – will be inserted just before at given iterator More...
 
StructureData slice (SegmentNameSet const &segments, bool const force_padding) const
 Returns a StructureData containing only the given segments The resulting StructureData will contain all data from the current. More...
 
void merge (StructureData const &other)
 merge all data and segments from "other" into this StructureData More...
 
void merge (StructureData const &other, SegmentNames const &segments)
 merge given data and segments from "other" into this StructureData More...
 
void merge_before (StructureData const &other, std::string const &position)
 merge all data and segments from "other" into this StructureData before the given position More...
 
void merge_before (StructureData const &other, std::string const &position, SegmentNames const &segments)
 merge all data and given segments from "other" into this StructureData before the given position More...
 
bool has_alias (std::string const &alias) const
 Aliases. More...
 
core::Size alias (std::string const &alias) const
 given a residue alias, returns a pose residue number More...
 
void set_alias (std::string const &alias_name, std::string const &segment_name, core::Size const resi)
 sets an "alias" for a particular residue inside a segment which allows for it to be easily accessed More...
 
void set_alias (std::string const &alias_name, core::Size const resi)
 sets an "alias" for a particular residue which allows for it to be easily accessed More...
 
bool has_data_int (std::string const &segment_id, std::string const &data_name) const
 User-specified Data. More...
 
bool has_data_real (std::string const &segment_id, std::string const &data_name) const
 check for real number data More...
 
bool has_data_str (std::string const &segment_id, std::string const &data_name) const
 gets real number data More...
 
int get_data_int (std::string const &segment_id, std::string const &data_name) const
 gets integer data More...
 
core::Real get_data_real (std::string const &segment_id, std::string const &data_name) const
 gets real number data More...
 
std::string const & get_data_str (std::string const &segment_id, std::string const &data_name) const
 gets real number data More...
 
void set_data_int (std::string const &segment_id, std::string const &data_name, int const val)
 sets real number data More...
 
void set_data_real (std::string const &segment_id, std::string const &data_name, core::Real const val)
 sets real number data More...
 
void set_data_str (std::string const &segment_id, std::string const &data_name, std::string const &val)
 sets real number data More...
 
void copy_data (StructureData const &perm)
 copies user data fields from one permutation to this one – overwrites existing data More...
 
core::Size num_chains () const
 Total number of chains WARNING: This is an O(n) operation, where n is number of residue segments. More...
 
core::Size pose_residue (std::string const &segment_name, core::Size const local_res) const
 returns the actual residue number of the given name and res # More...
 
bool has_segment (std::string const &seg) const
 true if this permutation contains a residue segment named seg More...
 
SegmentNameList connected_segments (std::string const &seg, bool const stop_at_cutpoint) const
 returns an ordered list of segments which are all connected containing seg More...
 
SegmentNames segments_in_movable_group (core::Size const group) const
 computes and returns a set of segments which are in the given movable group More...
 
MovableGroups const & movable_groups () const
 computes and returns a set of movable groups More...
 
core::Size movable_group (core::Size const resid) const
 movable group of segment which contains residue resid More...
 
SegmentNames available_lower_termini () const
 returns segments which have free lower termini More...
 
SegmentNames available_upper_termini () const
 returns segments which have free upper termini More...
 
SegmentNameList::const_iterator segments_begin () const
 start of segments list More...
 
SegmentNameList::const_iterator segments_end () const
 end of segment list More...
 
BondInfos::const_iterator covalent_bonds_begin () const
 start/end of covalent bonds list More...
 
BondInfos::const_iterator covalent_bonds_end () const
 end of covalent bonds list More...
 
bool non_polymer_bond_exists (std::string const &seg1, std::string const &seg2) const
 tells whether a non-polymer bond exists between the given segments More...
 
BondInfo const & non_polymer_bond (std::string const &seg1, std::string const &seg2) const
 finds a non-peptide bond between two segments, returns end() if there isn't one More...
 
BondInfos::const_iterator find_non_polymer_bond (std::string const &seg1, std::string const &seg2) const
 finds a non-peptide bond between two segments, returns end() if there isn't one More...
 
Segment const & segment (std::string const &id_val) const
 Segment retrieval. More...
 
SegmentNameList::const_iterator find_segment_name (std::string const &segname) const
 finds a segment in the segment_order list and returns an iterator to it More...
 
SegmentMap::const_iterator find_segment (std::string const &segname) const
 finds a segment in the segment map and returns an iterator to it More...
 
core::Size lower_anchor (std::string const &id_val) const
 returns n-terminal residue of the chain represented by given string More...
 
core::Size upper_anchor (std::string const &id_val) const
 returns c-terminal residue of the chain represented by given string More...
 
std::string const & segment_name (core::Size const res) const
 returns segment which includes residue number res More...
 
std::pair< std::string,
std::string > 
termini (std::string const &seg) const
 returns n and c terminal segments of the chain which includes seg More...
 
bool has_free_lower_terminus (std::string const &id_val) const
 tells if the segment given has an available lower terminus More...
 
bool has_free_upper_terminus (std::string const &id_val) const
 tells if the segment given has an available lower terminus More...
 
std::string const & id () const
 returns the id of this permutation More...
 
core::Size length () const
 returns the length of this permutation More...
 
core::Size pose_length () const
 returns the total length of this permutation, including n-, c-terminal loop residues which are basically for show More...
 
bool has_segment_group (std::string const &sname) const
 Data storage/access. More...
 
SegmentNames segment_group (std::string const &sname) const
 returns true if this object has a group of segments with the given name More...
 
std::map< std::string, int >
const & 
data_int () const
 gets all real number data More...
 
std::map< std::string,
core::Real > const & 
data_real () const
 gets all real number data More...
 
std::map< std::string,
std::string > const & 
data_str () const
 gets all string data More...
 
AliasMap const & aliases () const
 gets all alias data More...
 
std::string const & ss () const
 return secondary structure string More...
 
char ss (core::Size const resid) const
 abego of residue resid More...
 
void set_ss (core::Size const resid, char const ss_type)
 sets secondary structure for residue resid More...
 
std::string const & abego () const
 return abego string More...
 
char abego (core::Size const resid) const
 abego of residue resid More...
 
void set_abego (std::string const &segment, std::string const &abego)
 
void set_abego (std::string const &segment, utility::vector1< std::string > const &abego)
 
std::string substitute_variables (std::istream &input) const
 given an input stream, substitute all variables More...
 
void check_consistency () const
 checks consistency of the data More...
 
void check_pose_consistency (core::pose::Pose const &pose) const
 checks the permutation for internal consistency vs a pose More...
 
void mark_connected (std::string const &lower_seg, std::string const &upper_seg)
 marks the given segments as covanlently connected More...
 
void mark_disconnected (std::string const &seg1, std::string const &seg2)
 unmarks the given segments as covalently connected More...
 
void delete_jump_and_intervening_cutpoint (std::string const &segment1, std::string const &segment2)
 removes jump and cutpoint between the two segments to create a single polymer chain More...
 
void delete_leading_residues (std::string const &seg)
 deletes the residues between the segment N terminus and the N anchor point More...
 
void delete_trailing_residues (std::string const &seg)
 deletes the residues between the segment C terminus and the C anchor point More...
 
core::Size choose_new_movable_group () const
 chooses a new movable group which doesn't conflict with existing ones More...
 
void set_movable_group (std::string const &id, core::Size const mg)
 sets movable group of a segment More...
 
void renumber_movable_group (core::Size const oldg, core::Size const newg)
 renumbers movable group "oldg" to have new number "newg" More...
 
void update_numbering ()
 updates numbering based on the saved order of Segment objects More...
 
void save_remarks (core::io::Remarks const &remarks)
 Saves given remarks changes enzdes residues to generic segment name/number. More...
 
core::io::Remarks retrieve_remarks (core::pose::Pose const &pose) const
 retrieves saved remarks, makes any enzdes residues specific to the given pose More...
 
void add_covalent_bond (core::Size const res1, std::string const &atom1, core::Size const res2, std::string const &atom2)
 
void clear_pairings ()
 
void add_pairing (SegmentPairing const &pairing)
 
SegmentPairingCOP pairing (SegmentNames const &segments) const
 
SegmentPairingCOPs::const_iterator pairings_begin () const
 
SegmentPairingCOPs::const_iterator pairings_end () const
 

Static Public Member Functions

static std::string class_name ()
 

Static Public Attributes

static char const DATA_DELIMETER = '#'
 

Protected Member Functions

void on_change ()
 overridden by derived classes if they need to do anything when the SD changes More...
 
int get_data_int (std::string const &data_name) const
 helper functions for data access More...
 
core::Real get_data_real (std::string const &data_name) const
 gets real number data More...
 
std::string const & get_data_str (std::string const &data_name) const
 gets string data More...
 
bool has_data_int (std::string const &data_name) const
 
bool has_data_real (std::string const &data_name) const
 
bool has_data_str (std::string const &data_name) const
 
void set_data_int (std::string const &data_name, int const val)
 sets integer number data More...
 
void set_data_real (std::string const &data_name, core::Real const val)
 sets real number data More...
 
void set_data_str (std::string const &data_name, std::string const &val)
 sets string data More...
 
SegmentMap const & segments () const
 returns constant list of residue ranges More...
 
Segmentsegment_nonconst (std::string const &id_val)
 returns non-const access to residue range of the segment represented by given string More...
 
SegmentNameList::iterator find_segment_name (std::string const &segname)
 finds a segment in the segment_order list and returns an iterator to it More...
 
SegmentNameList::iterator segments_end_nonconst ()
 non-const iterator to end of segment names list More...
 
SegmentMap::iterator find_segment (std::string const &segname)
 finds a segment in the segments map and returns a non-const iterator More...
 
std::string find_lower_terminus (std::set< std::string > &visited, std::string const &seg) const
 performs dfs in lower direction looking for termini More...
 
std::string find_upper_terminus (std::set< std::string > &visited, std::string const &seg) const
 performs dfs in upper direction looking for termini More...
 
core::kinematics::FoldTree slide_jump (core::kinematics::FoldTree const &ft_orig, core::Size const jump_idx, core::Size const new_start, core::Size const new_stop) const
 safely slide a jump, avoiding foldtree segmentation faults More...
 
void add_covalent_bond (std::string const &seg1, core::Size const res1, std::string const &atom1, std::string const &seg2, core::Size const res2, std::string const &atom2)
 
void add_covalent_bond (BondInfo const &bi)
 
void add_prefix_to_segments (std::string const &prefix, char const delimeter)
 renames a residue segment and updates all connections More...
 
void move_segments (std::string const &segment1, std::string const &segment2_lower, std::string const &segment2_upper)
 

Private Types

typedef
basic::datacache::CacheableDataOP 
CacheableDataOP
 
typedef std::string SegmentName
 
typedef std::set< SegmentNameSegmentNameSet
 

Private Member Functions

void copy_data (StructureData const &perm, bool const overwrite)
 copies user data fields from one permutation to this one – optionally overwrites More...
 
void block_signals ()
 blocks on_change() signals More...
 
void unblock_signals ()
 unblocks on_change() signals and calls on_change() More...
 
void changed ()
 should be called when something changes More...
 
void check_pose (core::pose::Pose const &pose) const
 checks pose vs. StructureData info More...
 
void check_residues () const
 checks residues in SD – makes sure everything is sequential and accounted for More...
 
void check_improper_termini (core::pose::Pose const &pose) const
 checks chain termini in pose vs SD More...
 
void check_chains (core::pose::Pose const &pose) const
 
void check_movable_groups () const
 check pose movable groups vs SD More...
 
std::string generic_enzdes_header (std::string const &remark_str) const
 called to generalize an enzdes header to track it as pose changes More...
 
std::string specific_enzdes_header (core::pose::Pose const &pose, std::string const &generic_remark_str) const
 called to make an enzdes header specific to a pose More...
 

Private Attributes

std::string id_
 
std::string ss_
 
std::string abego_
 
core::Size pose_length_
 
core::Size length_
 
std::map< std::string, int > data_int_
 
std::map< std::string, core::Realdata_real_
 
StringMap data_str_
 
SegmentMap segments_
 
AliasMap aliases_
 
utility::vector1< BondInfocovalent_bonds_
 
SegmentNameList segment_order_
 
MovableGroups movable_groups_
 
SegmentPairingCOPs pairings_
 
bool block_signals_
 

Friends

std::ostream & operator<< (std::ostream &os, StructureData const &perm)
 for output More...
 

Member Typedef Documentation

typedef basic::datacache::CacheableDataOP protocols::denovo_design::components::StructureData::CacheableDataOP
private

Constructor & Destructor Documentation

protocols::denovo_design::components::StructureData::StructureData ( )
protocols::denovo_design::components::StructureData::StructureData ( std::string const &  id_val)
protocols::denovo_design::components::StructureData::~StructureData ( )
overridedefault

destructors

Member Function Documentation

std::string const & protocols::denovo_design::components::StructureData::abego ( ) const
char protocols::denovo_design::components::StructureData::abego ( core::Size const  resid) const

abego of residue resid

return secondary structure at residue resid

References abego_.

void protocols::denovo_design::components::StructureData::add_covalent_bond ( core::Size const  res1,
std::string const &  atom1,
core::Size const  res2,
std::string const &  atom2 
)
void protocols::denovo_design::components::StructureData::add_covalent_bond ( std::string const &  seg1,
core::Size const  res1,
std::string const &  atom1,
std::string const &  seg2,
core::Size const  res2,
std::string const &  atom2 
)
protected

References add_covalent_bond().

void protocols::denovo_design::components::StructureData::add_covalent_bond ( BondInfo const &  bi)
protected
void protocols::denovo_design::components::StructureData::add_pairing ( SegmentPairing const &  pairing)
void protocols::denovo_design::components::StructureData::add_prefix_to_segments ( std::string const &  prefix)

renames a residue segment and updates all connections

renames a residue segment and updates all connections. If the prefix is already there for a given segment name, it does nothing

References protocols::denovo_design::PARENT_DELIMETER.

void protocols::denovo_design::components::StructureData::add_prefix_to_segments ( std::string const &  prefix,
char const  delimeter 
)
protected
void protocols::denovo_design::components::StructureData::add_segment ( Segment const &  resis)
void protocols::denovo_design::components::StructureData::add_segment ( Segment const &  resis,
std::string const &  insert_before_segment 
)

adds a residues segment – will be ordered before the given segment

adds a residues segment – final will be inserted before segment named "insert_segment" if "after_seg" is empty, or not found in the list of segments, the new segment will be inserted at the end

References add_segment(), and find_segment_name().

void protocols::denovo_design::components::StructureData::add_segment ( Segment const &  resis,
SegmentNameList::iterator  insert_pos 
)

adds a residues segment – will be inserted just before at given iterator

adds a residues segment – final will be inserted before the iterator given as insert_pose

References protocols::denovo_design::components::Segment::id(), segment_order_, segments_, protocols::TR(), and update_numbering().

core::Size protocols::denovo_design::components::StructureData::alias ( std::string const &  alias) const
AliasMap const& protocols::denovo_design::components::StructureData::aliases ( ) const
inline

gets all alias data

References aliases_.

Referenced by copy_data().

SegmentNames protocols::denovo_design::components::StructureData::available_lower_termini ( ) const
SegmentNames protocols::denovo_design::components::StructureData::available_upper_termini ( ) const
void protocols::denovo_design::components::StructureData::block_signals ( )
private

blocks on_change() signals

References block_signals_.

Referenced by save_remarks().

void protocols::denovo_design::components::StructureData::changed ( )
private
void protocols::denovo_design::components::StructureData::check_chains ( core::pose::Pose const &  pose) const
private
void protocols::denovo_design::components::StructureData::check_consistency ( ) const

checks consistency of the data

Exceptions
EXCN_PoseInconsistentif there is a problem

References check_movable_groups(), and check_residues().

void protocols::denovo_design::components::StructureData::check_improper_termini ( core::pose::Pose const &  pose) const
private
void protocols::denovo_design::components::StructureData::check_movable_groups ( ) const
private

check pose movable groups vs SD

References movable_group(), movable_groups_, and protocols::TR().

Referenced by check_consistency(), and check_pose_consistency().

void protocols::denovo_design::components::StructureData::check_pose ( core::pose::Pose const &  pose) const
private

checks pose vs. StructureData info

Exceptions
EXCN_PoseInconsistentif things don't match
EXCN_BadInputif things don't match

References core::conformation::Residue::aa(), core::chemical::aa_vrt, id(), pose_length(), core::pose::Pose::residue(), core::pose::Pose::size(), ss(), and protocols::TR().

Referenced by check_pose_consistency().

void protocols::denovo_design::components::StructureData::check_pose_consistency ( core::pose::Pose const &  pose) const
void protocols::denovo_design::components::StructureData::check_residues ( ) const
private

checks residues in SD – makes sure everything is sequential and accounted for

References pose_length(), protocols::hybridization::r2, segments_, and protocols::TR().

Referenced by check_consistency(), and check_pose_consistency().

core::Size protocols::denovo_design::components::StructureData::choose_new_movable_group ( ) const

chooses a new movable group which doesn't conflict with existing ones

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

Referenced by protocols::denovo_design::connection::ConnectionArchitect::connect(), merge(), and merge_before().

std::string protocols::denovo_design::components::StructureData::class_name ( )
static
void protocols::denovo_design::components::StructureData::clear_pairings ( )

References pairings_.

StructureData::CacheableDataOP protocols::denovo_design::components::StructureData::clone ( ) const
override
void protocols::denovo_design::components::StructureData::connect_segments ( std::string const &  segment1,
std::string const &  segment2 
)

connects the given chains together, doesn't update anything – don't call this on its own unless you know what you're doing

connects the given chains together, doesn't update anything – don't call this on its own unless you know what you're doing.

References changed(), has_free_lower_terminus(), has_free_upper_terminus(), mark_connected(), segment(), and protocols::TR().

Referenced by protocols::denovo_design::connection::ConnectionArchitect::connect(), and merge_segments().

SegmentNameList protocols::denovo_design::components::StructureData::connected_segments ( std::string const &  seg,
bool const  stop_at_cutpoint 
) const
void protocols::denovo_design::components::StructureData::copy_data ( StructureData const &  perm)

copies user data fields from one permutation to this one – overwrites existing data

copies user data fields from one permutation to this one – existing data is overridden

Referenced by merge(), merge_before(), and slice().

void protocols::denovo_design::components::StructureData::copy_data ( StructureData const &  perm,
bool const  overwrite 
)
private

copies user data fields from one permutation to this one – optionally overwrites

copies user data fields from one permutation to this one – gives the option to not overwrite data

References core::pose::motif::a(), add_covalent_bond(), add_pairing(), aliases(), aliases_, changed(), covalent_bonds_begin(), covalent_bonds_end(), data_int(), data_int_, data_real(), data_real_, data_str(), data_str_, has_segment(), pairings_begin(), pairings_end(), segment_order_, protocols::denovo_design::components::set_map_data(), and protocols::TR().

BondInfos::const_iterator protocols::denovo_design::components::StructureData::covalent_bonds_begin ( ) const

start/end of covalent bonds list

References covalent_bonds_.

Referenced by copy_data(), find_non_polymer_bond(), and protocols::denovo_design::components::operator<<().

BondInfos::const_iterator protocols::denovo_design::components::StructureData::covalent_bonds_end ( ) const
Cutpoints protocols::denovo_design::components::StructureData::cutpoints ( ) const

returns list of all cutpoints, in N–>C order

returns a list of valid cutpoints, in N–>C order

References protocols::denovo_design::components::Segment::cutpoint(), segment(), segments_begin(), and segments_end().

Referenced by check_chains().

std::map< std::string, int > const& protocols::denovo_design::components::StructureData::data_int ( ) const
inline

gets all real number data

References data_int_.

Referenced by copy_data().

std::map< std::string, core::Real > const& protocols::denovo_design::components::StructureData::data_real ( ) const
inline

gets all real number data

References data_real_.

Referenced by copy_data().

std::map< std::string, std::string > const& protocols::denovo_design::components::StructureData::data_str ( ) const
inline

gets all string data

References data_str_.

Referenced by copy_data().

std::string protocols::denovo_design::components::StructureData::datatype ( ) const
override

References class_name().

void protocols::denovo_design::components::StructureData::declare_covalent_bond ( std::string const &  seg1,
core::Size const  res1,
std::string const &  atom1,
std::string const &  seg2,
core::Size const  res2,
std::string const &  atom2 
)

declares a covalent bond between the specified atoms

References pose_residue().

Referenced by protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply().

void protocols::denovo_design::components::StructureData::declare_covalent_bond ( core::Size const  res1,
std::string const &  atom1,
core::Size const  res2,
std::string const &  atom2 
)

declares a covalent bond using pose residues

References add_covalent_bond(), and protocols::TR().

void protocols::denovo_design::components::StructureData::delete_jump_and_intervening_cutpoint ( std::string const &  segment1,
std::string const &  segment2 
)

removes jump and cutpoint between the two segments to create a single polymer chain

References changed(), segment(), segment_nonconst(), and protocols::denovo_design::components::Segment::set_cutpoint().

void protocols::denovo_design::components::StructureData::delete_leading_residues ( std::string const &  seg)
void protocols::denovo_design::components::StructureData::delete_residue ( core::Size const  pose_resid)
void protocols::denovo_design::components::StructureData::delete_segment ( std::string const &  segment)
void protocols::denovo_design::components::StructureData::delete_trailing_residues ( std::string const &  seg)
void protocols::denovo_design::components::StructureData::disconnect_segments ( std::string const &  segment1,
std::string const &  segment2 
)

connects the given chains together, doesn't update anything – don't call this on its own unless you know what you're doing

disconnects the given chains doesn't update anything – don't call this on its own unless you know what you're doing.

References mark_disconnected().

std::string protocols::denovo_design::components::StructureData::find_lower_terminus ( std::set< std::string > &  visited,
std::string const &  seg 
) const
protected

performs dfs in lower direction looking for termini

References has_free_lower_terminus(), and segment().

Referenced by termini().

BondInfos::const_iterator protocols::denovo_design::components::StructureData::find_non_polymer_bond ( std::string const &  seg1,
std::string const &  seg2 
) const

finds a non-peptide bond between two segments, returns end() if there isn't one

References covalent_bonds_begin(), and covalent_bonds_end().

Referenced by protocols::denovo_design::components::FoldGraph::fold_tree(), non_polymer_bond(), and non_polymer_bond_exists().

SegmentMap::const_iterator protocols::denovo_design::components::StructureData::find_segment ( std::string const &  segname) const

finds a segment in the segment map and returns an iterator to it

finds a segment in the segments map and returns an iterator to it

Exceptions
utility_exitif not found

References core::pack::dunbrack::c, segment_order_, and segments_.

Referenced by delete_segment(), rename_segment(), and replace_segment().

SegmentMap::iterator protocols::denovo_design::components::StructureData::find_segment ( std::string const &  segname)
protected

finds a segment in the segments map and returns a non-const iterator

finds a segment in the segments map and returns an iterator to it

Exceptions
utility_exitif not found

References segment_order_, and segments_.

SegmentNameList::const_iterator protocols::denovo_design::components::StructureData::find_segment_name ( std::string const &  segname) const

finds a segment in the segment_order list and returns an iterator to it

finds a segment in the segment_order list and returns a const iterator to it

Exceptions
utility_exitif not found

References core::pack::dunbrack::c, and segment_order_.

Referenced by add_prefix_to_segments(), add_segment(), delete_segment(), merge_before(), merge_segments(), move_segments(), and rename_segment().

SegmentNameList::iterator protocols::denovo_design::components::StructureData::find_segment_name ( std::string const &  segname)
protected

finds a segment in the segment_order list and returns an iterator to it

Exceptions
utility_exitif not found

References core::pack::dunbrack::c, and segment_order_.

std::string protocols::denovo_design::components::StructureData::find_upper_terminus ( std::set< std::string > &  visited,
std::string const &  seg 
) const
protected

performs dfs in upper direction looking for termini

References has_free_upper_terminus(), and segment().

Referenced by termini().

std::string protocols::denovo_design::components::StructureData::generic_enzdes_header ( std::string const &  remark_str) const
private

called to generalize an enzdes header to track it as pose changes

References DATA_DELIMETER, protocols::denovo_design::components::Segment::pose_to_segment(), segment(), segment_name(), ss(), protocols::loops::start, and protocols::loops::stop.

Referenced by save_remarks().

int protocols::denovo_design::components::StructureData::get_data_int ( std::string const &  segment_id,
std::string const &  data_name 
) const

gets integer data

gets int number data

References DATA_DELIMETER.

int protocols::denovo_design::components::StructureData::get_data_int ( std::string const &  data_name) const
protected

helper functions for data access

gets real number data

References data_int_, and id().

core::Real protocols::denovo_design::components::StructureData::get_data_real ( std::string const &  segment_id,
std::string const &  data_name 
) const

gets real number data

References DATA_DELIMETER.

core::Real protocols::denovo_design::components::StructureData::get_data_real ( std::string const &  data_name) const
protected

gets real number data

References data_real_, and id().

std::string const & protocols::denovo_design::components::StructureData::get_data_str ( std::string const &  segment_id,
std::string const &  data_name 
) const

gets real number data

gets string data

References DATA_DELIMETER.

Referenced by protocols::denovo_design::architects::StrandArchitect::retrieve_bulges_s().

std::string const & protocols::denovo_design::components::StructureData::get_data_str ( std::string const &  data_name) const
protected

gets string data

References data_str_, and id().

bool protocols::denovo_design::components::StructureData::has_alias ( std::string const &  alias) const
inline

Aliases.

given a residue alias, returns a pose residue number

References aliases_.

Referenced by protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), pose_residue(), and set_alias().

bool protocols::denovo_design::components::StructureData::has_data_int ( std::string const &  segment_id,
std::string const &  data_name 
) const

User-specified Data.

check for integer data

References DATA_DELIMETER.

bool protocols::denovo_design::components::StructureData::has_data_int ( std::string const &  data_name) const
inlineprotected

References data_int_.

bool protocols::denovo_design::components::StructureData::has_data_real ( std::string const &  segment_id,
std::string const &  data_name 
) const

check for real number data

References DATA_DELIMETER.

bool protocols::denovo_design::components::StructureData::has_data_real ( std::string const &  data_name) const
inlineprotected

References data_real_.

bool protocols::denovo_design::components::StructureData::has_data_str ( std::string const &  segment_id,
std::string const &  data_name 
) const

gets real number data

References DATA_DELIMETER.

bool protocols::denovo_design::components::StructureData::has_data_str ( std::string const &  data_name) const
inlineprotected

References data_str_.

bool protocols::denovo_design::components::StructureData::has_free_lower_terminus ( std::string const &  id_val) const
bool protocols::denovo_design::components::StructureData::has_free_upper_terminus ( std::string const &  id_val) const
bool protocols::denovo_design::components::StructureData::has_segment ( std::string const &  seg) const
bool protocols::denovo_design::components::StructureData::has_segment_group ( std::string const &  sname) const

Data storage/access.

returns true if this object has a group of segments with the given name

References core::pack::dunbrack::c, has_segment(), protocols::denovo_design::PARENT_DELIMETER, segments_begin(), and segments_end().

Referenced by protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset().

std::string const & protocols::denovo_design::components::StructureData::id ( ) const
core::Size protocols::denovo_design::components::StructureData::length ( ) const

returns the length of this permutation

References length_.

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

core::Size protocols::denovo_design::components::StructureData::lower_anchor ( std::string const &  id_val) const

returns n-terminal residue of the chain represented by given string

References segment(), and protocols::denovo_design::components::Segment::start().

void protocols::denovo_design::components::StructureData::mark_connected ( std::string const &  lower_seg,
std::string const &  upper_seg 
)

marks the given segments as covanlently connected

References changed(), and segments_.

Referenced by protocols::denovo_design::components::add_segments_for_chain(), and connect_segments().

void protocols::denovo_design::components::StructureData::mark_disconnected ( std::string const &  seg1,
std::string const &  seg2 
)
void protocols::denovo_design::components::StructureData::merge ( StructureData const &  other)

merge all data and segments from "other" into this StructureData

References segments_begin(), and segments_end().

void protocols::denovo_design::components::StructureData::merge ( StructureData const &  other,
SegmentNames const &  segments 
)
void protocols::denovo_design::components::StructureData::merge_before ( StructureData const &  other,
std::string const &  position 
)

merge all data and segments from "other" into this StructureData before the given position

References segments_begin(), and segments_end().

void protocols::denovo_design::components::StructureData::merge_before ( StructureData const &  other,
std::string const &  position,
SegmentNames const &  segments 
)
void protocols::denovo_design::components::StructureData::merge_segments ( std::string const &  segment1,
std::string const &  segment2,
std::string const &  new_name 
)
core::Size protocols::denovo_design::components::StructureData::movable_group ( core::Size const  resid) const

movable group of segment which contains residue resid

References protocols::denovo_design::components::Segment::movable_group(), segment(), and segment_name().

Referenced by check_movable_groups().

MovableGroups const & protocols::denovo_design::components::StructureData::movable_groups ( ) const

computes and returns a set of movable groups

References movable_groups_.

Referenced by protocols::denovo_design::components::FoldGraph::FoldGraph(), and merge_segments().

void protocols::denovo_design::components::StructureData::move_segment ( std::string const &  segment1,
std::string const &  segment2 
)
void protocols::denovo_design::components::StructureData::move_segments ( std::string const &  segment1,
std::string const &  segment2_lower,
std::string const &  segment2_upper 
)
protected
BondInfo const & protocols::denovo_design::components::StructureData::non_polymer_bond ( std::string const &  seg1,
std::string const &  seg2 
) const

finds a non-peptide bond between two segments, returns end() if there isn't one

References covalent_bonds_end(), and find_non_polymer_bond().

bool protocols::denovo_design::components::StructureData::non_polymer_bond_exists ( std::string const &  seg1,
std::string const &  seg2 
) const

tells whether a non-polymer bond exists between the given segments

References covalent_bonds_, and find_non_polymer_bond().

Referenced by protocols::denovo_design::components::FoldGraph::check_solution().

core::Size protocols::denovo_design::components::StructureData::num_chains ( ) const

Total number of chains WARNING: This is an O(n) operation, where n is number of residue segments.

the total number of free termini in the permutation

References protocols::denovo_design::components::Segment::has_free_lower_terminus(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), segment(), segments_, and protocols::TR().

void protocols::denovo_design::components::StructureData::on_change ( )
protected

overridden by derived classes if they need to do anything when the SD changes

References protocols::TR().

Referenced by changed().

SegmentPairingCOP protocols::denovo_design::components::StructureData::pairing ( SegmentNames const &  segments) const
SegmentPairingCOPs::const_iterator protocols::denovo_design::components::StructureData::pairings_begin ( ) const
SegmentPairingCOPs::const_iterator protocols::denovo_design::components::StructureData::pairings_end ( ) const
void protocols::denovo_design::components::StructureData::parse_subtag ( utility::tag::TagCOP  tag)
void protocols::denovo_design::components::StructureData::parse_tag ( utility::tag::TagCOP  tag)
core::Size protocols::denovo_design::components::StructureData::pose_length ( ) const
core::Size protocols::denovo_design::components::StructureData::pose_residue ( std::string const &  segment_name,
core::Size const  local_res 
) const
void protocols::denovo_design::components::StructureData::rename_segment ( std::string const &  old_name,
std::string const &  new_name 
)
void protocols::denovo_design::components::StructureData::renumber_movable_group ( core::Size const  oldg,
core::Size const  newg 
)
void protocols::denovo_design::components::StructureData::replace_segment ( SegmentName const &  seg_name,
Segment const &  segment 
)
core::io::Remarks protocols::denovo_design::components::StructureData::retrieve_remarks ( core::pose::Pose const &  pose) const

retrieves saved remarks, makes any enzdes residues specific to the given pose

retrieves cached remarks specific to the given pose

References DATA_DELIMETER, data_str_, core::io::rna::numbers, specific_enzdes_header(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::save_into_pose().

void protocols::denovo_design::components::StructureData::save_remarks ( core::io::Remarks const &  remarks)

Saves given remarks changes enzdes residues to generic segment name/number.

Saves remarks of the given pose into the pose's datacache – changes enzdes residues to segment name/number.

References block_signals(), changed(), generic_enzdes_header(), protocols::denovo_design::components::StructureDataFactory::REMARK_NUM, set_data_str(), protocols::TR(), and unblock_signals().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_pose().

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

Segment retrieval.

returns residue range of the segment represented by given string

returns segment represented by given string

References id(), protocols::denovo_design::PARENT_DELIMETER, and segments_.

Referenced by add_covalent_bond(), protocols::denovo_design::add_cutpoints(), protocols::denovo_design::movers::AlignResiduesMover::add_metadata(), protocols::denovo_design::components::add_paired_residues(), add_prefix_to_segments(), alias(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), available_lower_termini(), available_upper_termini(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::build_in_phases(), protocols::denovo_design::architects::bulge_residues(), protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings(), check_chains(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), check_improper_termini(), protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::components::FoldGraph::check_solution(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), connect_segments(), protocols::denovo_design::connection::AreConnectablePredicate::connected_movable_groups(), connected_segments(), protocols::denovo_design::count_bulges(), protocols::denovo_design::components::FoldGraph::create_loops(), protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose(), cutpoints(), delete_jump_and_intervening_cutpoint(), delete_residue(), protocols::denovo_design::components::ConnectionPerturber::enumerate(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::components::FoldGraph::find_cutpoint_in_range(), protocols::denovo_design::components::FoldGraph::find_cutpoints(), find_lower_terminus(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::find_roots(), protocols::denovo_design::components::ExtendedPoseBuilder::find_template_segments(), find_upper_terminus(), 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::Picker::fragments_for_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), generic_enzdes_header(), protocols::denovo_design::architects::BlueprintArchitect::get_template_segments(), has_free_lower_terminus(), has_free_upper_terminus(), lower_anchor(), protocols::denovo_design::components::map_mgs(), protocols::denovo_design::components::map_nodes(), merge(), merge_before(), merge_segments(), protocols::denovo_design::connection::ConnectionArchitect::motifs_for_pair(), movable_group(), move_segment(), move_segments(), num_chains(), protocols::denovo_design::components::StructureSlicePredicate::operator()(), protocols::denovo_design::connection::AreConnectablePredicate::operator()(), protocols::denovo_design::components::operator<<(), protocols::denovo_design::components::HelixPairing::pairing_string(), protocols::denovo_design::components::StrandPairing::pairing_string(), protocols::denovo_design::components::HelixSheetPairing::pairing_string(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), rename_segment(), renumber_movable_group(), replace_segment(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), protocols::denovo_design::architects::BetaSheetArchitect::retrieve_lengths(), segment_name(), segments_in_movable_group(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::segments_to_fold(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::select_movable_residues(), set_alias(), set_cutpoint(), set_ss(), protocols::denovo_design::architects::BlueprintArchitect::set_template_segments(), slice(), substitute_variables(), and upper_anchor().

SegmentNames protocols::denovo_design::components::StructureData::segment_group ( std::string const &  sname) const
std::string const & protocols::denovo_design::components::StructureData::segment_name ( core::Size const  res) const
Segment & protocols::denovo_design::components::StructureData::segment_nonconst ( std::string const &  id_val)
protected

returns non-const access to residue range of the segment represented by given string

returns non-const residue range of the segment represented by given string

References id(), protocols::denovo_design::PARENT_DELIMETER, and segments_.

Referenced by delete_jump_and_intervening_cutpoint(), delete_leading_residues(), delete_residue(), delete_trailing_residues(), mark_disconnected(), set_abego(), set_cutpoint(), and set_ss().

SegmentMap const& protocols::denovo_design::components::StructureData::segments ( ) const
inlineprotected

returns constant list of residue ranges

References segments_.

Referenced by pairing(), and segments_in_movable_group().

SegmentNameList::const_iterator protocols::denovo_design::components::StructureData::segments_begin ( ) const
SegmentNameList::const_iterator protocols::denovo_design::components::StructureData::segments_end ( ) const

end of segment list

References segment_order_.

Referenced by protocols::denovo_design::add_cutpoints(), available_lower_termini(), available_upper_termini(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::build_in_phases(), protocols::denovo_design::components::FoldGraph::build_seg2node(), protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings(), check_chains(), protocols::denovo_design::components::FoldGraph::check_solution(), protocols::denovo_design::components::DivideAndConqueror::compute_all_units(), cutpoints(), protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::components::FoldGraph::find_cutpoints(), protocols::denovo_design::components::ExtendedPoseBuilder::find_template_segments(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::architects::BlueprintArchitect::get_template_segments(), has_segment_group(), protocols::denovo_design::components::map_mgs(), protocols::denovo_design::components::map_nodes(), merge(), merge_before(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel(), protocols::denovo_design::movers::SealFoldTreeMover::SealFoldTreeMover(), segment_group(), protocols::denovo_design::connection::ConnectionArchitect::segment_pairs(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::segments_to_fold(), slice(), and update_numbering().

SegmentNameList::iterator protocols::denovo_design::components::StructureData::segments_end_nonconst ( )
protected

non-const iterator to end of segment names list

References segment_order_.

SegmentNames protocols::denovo_design::components::StructureData::segments_in_movable_group ( core::Size const  group) const

computes and returns a set of segments which are in the given movable group

References protocols::denovo_design::components::Segment::movable_group(), segment(), segments(), and segments_.

Referenced by protocols::denovo_design::components::FoldGraph::FoldGraph(), and merge_segments().

void protocols::denovo_design::components::StructureData::set_abego ( std::string const &  segment,
std::string const &  abego 
)
void protocols::denovo_design::components::StructureData::set_abego ( std::string const &  segment,
utility::vector1< std::string > const &  abego 
)
void protocols::denovo_design::components::StructureData::set_alias ( std::string const &  alias_name,
std::string const &  segment_name,
core::Size const  resi 
)

sets an "alias" for a particular residue inside a segment which allows for it to be easily accessed

References aliases_, changed(), has_alias(), has_segment(), segment(), segment_name(), and ss().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::add_metadata(), protocols::denovo_design::movers::SetResidueAliasMover::apply(), parse_subtag(), and set_alias().

void protocols::denovo_design::components::StructureData::set_alias ( std::string const &  alias_name,
core::Size const  resi 
)

sets an "alias" for a particular residue which allows for it to be easily accessed

References pose_length(), protocols::denovo_design::components::Segment::pose_to_segment(), segment(), segment_name(), set_alias(), and protocols::TR().

void protocols::denovo_design::components::StructureData::set_cutpoint ( core::Size const  resid)
void protocols::denovo_design::components::StructureData::set_cutpoint ( std::string const &  seg,
SegmentResid const  resi 
)

marks the resi-th residue of segment as a cutpoint

marks the resi-th residue of seg as a cutpoint

References changed(), segment_nonconst(), and protocols::denovo_design::components::Segment::set_cutpoint().

void protocols::denovo_design::components::StructureData::set_data_int ( std::string const &  segment_id,
std::string const &  data_name,
int const  val 
)

sets real number data

sets integer number data

References DATA_DELIMETER.

Referenced by parse_subtag(), and protocols::denovo_design::architects::BetaSheetArchitect::store_sheet_idx().

void protocols::denovo_design::components::StructureData::set_data_int ( std::string const &  data_name,
int const  val 
)
protected

sets integer number data

References changed(), data_int_, and protocols::hybridization::val.

void protocols::denovo_design::components::StructureData::set_data_real ( std::string const &  segment_id,
std::string const &  data_name,
core::Real const  val 
)

sets real number data

References DATA_DELIMETER.

Referenced by parse_subtag().

void protocols::denovo_design::components::StructureData::set_data_real ( std::string const &  data_name,
core::Real const  val 
)
protected

sets real number data

References changed(), data_real_, and protocols::hybridization::val.

void protocols::denovo_design::components::StructureData::set_data_str ( std::string const &  segment_id,
std::string const &  data_name,
std::string const &  val 
)
void protocols::denovo_design::components::StructureData::set_data_str ( std::string const &  data_name,
std::string const &  val 
)
protected

sets string data

References changed(), data_str_, and protocols::hybridization::val.

void protocols::denovo_design::components::StructureData::set_id ( std::string const &  id_str)

sets id name

References id_.

Referenced by parse_tag().

void protocols::denovo_design::components::StructureData::set_movable_group ( std::string const &  id,
core::Size const  mg 
)

sets movable group of a segment

References changed(), and segments_.

Referenced by protocols::denovo_design::connection::ConnectionArchitect::connect().

void protocols::denovo_design::components::StructureData::set_ss ( core::Size const  resid,
char const  ss_type 
)
void protocols::denovo_design::components::StructureData::set_template_pose ( std::string const &  segment,
core::pose::Pose const &  template_pose,
core::Size const  start_resid,
core::Size const  stop_resid 
)
StructureData protocols::denovo_design::components::StructureData::slice ( SegmentNameSet const &  segments,
bool const  force_padding 
) const
core::kinematics::FoldTree protocols::denovo_design::components::StructureData::slide_jump ( core::kinematics::FoldTree const &  ft_orig,
core::Size const  jump_idx,
core::Size const  new_start,
core::Size const  new_stop 
) const
protected

safely slide a jump, avoiding foldtree segmentation faults

std::string protocols::denovo_design::components::StructureData::specific_enzdes_header ( core::pose::Pose const &  pose,
std::string const &  generic_remark_str 
) const
private

called to make an enzdes header specific to a pose

References core::pose::Pose::chain(), core::pose::Pose::pdb_info(), ss(), and substitute_variables().

Referenced by retrieve_remarks().

std::string const & protocols::denovo_design::components::StructureData::ss ( ) const
char protocols::denovo_design::components::StructureData::ss ( core::Size const  resid) const

abego of residue resid

return secondary structure at residue resid

References ss_.

std::string protocols::denovo_design::components::StructureData::substitute_variables ( std::istream &  input) const

given an input stream, substitute all variables

variables are of the form: %SEGMENTNAME#residue%% SEGMENTNAME = name of the segment residue = local residue number within the segment The substituted value will be an core::Size corresponding to the pose residue

References DATA_DELIMETER, pose_residue(), segment(), protocols::loops::start, protocols::denovo_design::components::Segment::stop(), and protocols::TR().

Referenced by protocols::denovo_design::constraints::FileConstraintGenerator::apply(), protocols::denovo_design::get_resid(), and specific_enzdes_header().

std::pair< std::string, std::string > protocols::denovo_design::components::StructureData::termini ( std::string const &  seg) const

returns n and c terminal segments of the chain which includes seg

returns n and c terminal segments of the chain which includes res

References find_lower_terminus(), find_upper_terminus(), and protocols::TR().

Referenced by protocols::denovo_design::connection::AreConnectablePredicate::operator()().

void protocols::denovo_design::components::StructureData::unblock_signals ( )
private

unblocks on_change() signals and calls on_change()

References block_signals_.

Referenced by save_remarks().

void protocols::denovo_design::components::StructureData::update_numbering ( )
core::Size protocols::denovo_design::components::StructureData::upper_anchor ( std::string const &  id_val) const

returns c-terminal residue of the chain represented by given string

References segment(), and protocols::denovo_design::components::Segment::stop().

void protocols::denovo_design::components::StructureData::write ( std::ostream &  os) const
override

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
StructureData const &  perm 
)
friend

for output

Member Data Documentation

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

Referenced by abego(), and update_numbering().

AliasMap protocols::denovo_design::components::StructureData::aliases_
private
bool protocols::denovo_design::components::StructureData::block_signals_
private
utility::vector1< BondInfo > protocols::denovo_design::components::StructureData::covalent_bonds_
private
char const protocols::denovo_design::components::StructureData::DATA_DELIMETER = '#'
static
std::map< std::string, int > protocols::denovo_design::components::StructureData::data_int_
private
std::map< std::string, core::Real > protocols::denovo_design::components::StructureData::data_real_
private
StringMap protocols::denovo_design::components::StructureData::data_str_
private
std::string protocols::denovo_design::components::StructureData::id_
private

Referenced by id(), and set_id().

core::Size protocols::denovo_design::components::StructureData::length_
private

Referenced by length(), parse_tag(), and update_numbering().

MovableGroups protocols::denovo_design::components::StructureData::movable_groups_
private
SegmentPairingCOPs protocols::denovo_design::components::StructureData::pairings_
private
core::Size protocols::denovo_design::components::StructureData::pose_length_
private
SegmentNameList protocols::denovo_design::components::StructureData::segment_order_
private
SegmentMap protocols::denovo_design::components::StructureData::segments_
private
std::string protocols::denovo_design::components::StructureData::ss_
private

Referenced by ss(), and update_numbering().


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