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

#include <StructureData.hh>

Inheritance diagram for protocols::denovo_design::components::StructureData:

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 &abego)
	Set abego to use for the entire pose/all segments using a string. More...
void	set_abego (utility::vector1< std::string > const &abego)
	Set abego to use for the entire pose/all segments using a vector of one-character strings. More...
void	set_abego (std::string const &segment, std::string const &abego)
	Set abego to use for a specific segment using a string. More...
void	set_abego (std::string const &segment, utility::vector1< std::string > const &abego)
	Set abego to use for a specific segment using a vector of one-character strings. More...
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...
Segment &	segment_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< SegmentName >	SegmentNameSet

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::Real >	data_real_
StringMap	data_str_
SegmentMap	segments_
AliasMap	aliases_
utility::vector1< BondInfo >	covalent_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

CacheableDataOP

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

private

SegmentName

typedef std::string protocols::denovo_design::components::StructureData::SegmentName

private

SegmentNameSet

typedef std::set< SegmentName > protocols::denovo_design::components::StructureData::SegmentNameSet

private

Constructor & Destructor Documentation

StructureData() [1/2]

protocols::denovo_design::components::StructureData::StructureData

(

)

StructureData() [2/2]

protocols::denovo_design::components::StructureData::StructureData

(

std::string const &

id_val

)

~StructureData()

protocols::denovo_design::components::StructureData::~StructureData ( )

overridedefault

destructors

Member Function Documentation

abego() [1/2]

std::string const & protocols::denovo_design::components::StructureData::abego

(

)

const

return abego string

References abego_.

Referenced by protocols::denovo_design::components::add_paired_residues(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover(), protocols::denovo_design::components::Picker::fragments_for_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::StrandPairing::nobu_register_shift(), and set_abego().

abego() [2/2]

char protocols::denovo_design::components::StructureData::abego

(

core::Size const

resid

)

const

abego of residue resid

return secondary structure at residue resid

References abego_.

add_covalent_bond() [1/3]

void protocols::denovo_design::components::StructureData::add_covalent_bond ( BondInfo const &  bi )

protected

References changed(), covalent_bonds_, and protocols::TR().

add_covalent_bond() [2/3]

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
	)

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

Referenced by add_covalent_bond(), copy_data(), declare_covalent_bond(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), and parse_subtag().

add_covalent_bond() [3/3]

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().

add_pairing()

void protocols::denovo_design::components::StructureData::add_pairing

(

SegmentPairing const &

pairing

)

References pairing(), and pairings_.

Referenced by copy_data(), and parse_subtag().

add_prefix_to_segments() [1/2]

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.

add_prefix_to_segments() [2/2]

void protocols::denovo_design::components::StructureData::add_prefix_to_segments ( std::string const &  prefix, char const  delimeter  )

protected

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 aliases_, changed(), find_segment_name(), protocols::denovo_design::components::Segment::has_free_lower_terminus(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::lower_segment(), segment(), segment_order_, segments_, protocols::denovo_design::components::Segment::set_id(), protocols::denovo_design::components::Segment::set_lower_segment(), protocols::denovo_design::components::Segment::set_upper_segment(), and protocols::denovo_design::components::Segment::upper_segment().

add_segment() [1/3]

void protocols::denovo_design::components::StructureData::add_segment

(

Segment const &

resis

)

adds a residues segment to the end of the list

References segment_order_, and protocols::TR().

Referenced by add_segment(), protocols::denovo_design::components::add_segment(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::movers::AddSegmentDataMover::create_segment(), merge(), merge_before(), merge_segments(), parse_subtag(), and slice().

add_segment() [2/3]

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().

add_segment() [3/3]

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().

alias()

core::Size protocols::denovo_design::components::StructureData::alias

(

std::string const &

alias

)

const

given a residue alias, returns a pose residue number

References aliases_, has_segment(), segment(), segment_name(), protocols::denovo_design::components::Segment::segment_to_pose(), and protocols::TR().

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

aliases()

AliasMap const& protocols::denovo_design::components::StructureData::aliases ( ) const

inline

gets all alias data

References aliases_.

Referenced by copy_data().

available_lower_termini()

SegmentNames protocols::denovo_design::components::StructureData::available_lower_termini

(

)

const

returns segments which have free lower termini

returns segments which have free lower termini in sequence order

References protocols::denovo_design::components::Segment::has_free_lower_terminus(), protocols::denovo_design::components::Segment::lower_segment(), segment(), segments_begin(), segments_end(), and protocols::TR().

Referenced by protocols::denovo_design::connection::ConnectionArchitect::available_lower_termini(), and protocols::denovo_design::connection::AreConnectablePredicate::operator()().

available_upper_termini()

SegmentNames protocols::denovo_design::components::StructureData::available_upper_termini

(

)

const

returns segments which have free upper termini

returns segments which have free upper termini in sequence order

References protocols::denovo_design::components::Segment::has_free_upper_terminus(), segment(), segments_begin(), segments_end(), protocols::TR(), and protocols::denovo_design::components::Segment::upper_segment().

Referenced by protocols::denovo_design::connection::ConnectionArchitect::available_upper_termini(), and protocols::denovo_design::connection::AreConnectablePredicate::operator()().

block_signals()

void protocols::denovo_design::components::StructureData::block_signals ( )

private

blocks on_change() signals

References block_signals_.

Referenced by save_remarks().

changed()

void protocols::denovo_design::components::StructureData::changed ( )

private

should be called when something changes

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

References block_signals_, and on_change().

Referenced by add_covalent_bond(), add_prefix_to_segments(), connect_segments(), copy_data(), delete_jump_and_intervening_cutpoint(), delete_residue(), mark_connected(), mark_disconnected(), rename_segment(), renumber_movable_group(), replace_segment(), save_remarks(), set_alias(), set_cutpoint(), set_data_int(), set_data_real(), set_data_str(), and set_movable_group().

check_chains()

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

private

References protocols::denovo_design::components::advance_past_virtual_residues(), core::conformation::Conformation::chain_endings(), protocols::denovo_design::components::compute_chain_beginnings(), protocols::denovo_design::components::compute_cutpoints(), core::pose::Pose::conformation(), protocols::denovo_design::components::Segment::cutpoint(), cutpoints(), core::pose::Pose::end(), protocols::denovo_design::components::Segment::has_free_lower_terminus(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::lower(), segment(), segments_begin(), segments_end(), core::pose::Pose::size(), protocols::TR(), and protocols::denovo_design::components::Segment::upper().

Referenced by check_pose_consistency().

check_consistency()

void protocols::denovo_design::components::StructureData::check_consistency

(

)

const

checks consistency of the data

Exceptions

EXCN_PoseInconsistent

if there is a problem

References check_movable_groups(), and check_residues().

check_improper_termini()

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

private

checks chain termini in pose vs SD

Exceptions

EXCN_PoseInconsistent

if there is a problem

References core::conformation::Residue::is_terminus(), protocols::denovo_design::components::Segment::lower(), core::pose::Pose::residue(), segment(), segments_, protocols::TR(), and protocols::denovo_design::components::Segment::upper().

Referenced by check_pose_consistency().

check_movable_groups()

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().

check_pose()

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

private

checks pose vs. StructureData info

Exceptions

EXCN_PoseInconsistent	if things don't match
EXCN_BadInput	if 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().

check_pose_consistency()

void protocols::denovo_design::components::StructureData::check_pose_consistency

(

core::pose::Pose const &

pose

)

const

checks the permutation for internal consistency vs a pose

Exceptions

EXCN_PoseInconsistent

if there is a problem

References check_chains(), check_improper_termini(), check_movable_groups(), check_pose(), check_residues(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), core::pose::Pose::remove_constraints(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_pose(), protocols::denovo_design::movers::FoldArchitectMover::fold_attempt(), and protocols::denovo_design::components::StructureDataFactory::save_into_pose().

check_residues()

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().

choose_new_movable_group()

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().

class_name()

std::string protocols::denovo_design::components::StructureData::class_name ( )

static

Referenced by protocols::denovo_design::components::StructureDataFactory::clear_cached_data(), datatype(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), protocols::denovo_design::components::StructureDataCreator::keyname(), protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data(), protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data_ptr(), protocols::denovo_design::components::StructureDataFactory::set_cached_data(), and write().

clear_pairings()

void protocols::denovo_design::components::StructureData::clear_pairings

(

)

References pairings_.

clone()

StructureData::CacheableDataOP protocols::denovo_design::components::StructureData::clone ( ) const

override

connect_segments()

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().

connected_segments()

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

returns an ordered list of segments which are all connected containing seg

Parameters

stop_at_cutpoint

- if true, segments past a cutpoint will not be counted as connected

References protocols::denovo_design::components::Segment::cutpoint(), protocols::denovo_design::components::Segment::has_free_lower_terminus(), has_free_lower_terminus(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::lower_segment(), segment(), and protocols::denovo_design::components::Segment::upper_segment().

Referenced by protocols::denovo_design::components::FoldGraph::check_solution(), protocols::denovo_design::connection::AreConnectablePredicate::connected_movable_groups(), and move_segment().

copy_data() [1/2]

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().

copy_data() [2/2]

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().

covalent_bonds_begin()

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(), and find_non_polymer_bond().

covalent_bonds_end()

BondInfos::const_iterator protocols::denovo_design::components::StructureData::covalent_bonds_end

(

)

const

end of covalent bonds list

References covalent_bonds_.

Referenced by protocols::denovo_design::components::FoldGraph::add_non_polymeric_connections(), copy_data(), find_non_polymer_bond(), protocols::denovo_design::components::FoldGraph::FoldGraph(), and non_polymer_bond().

cutpoints()

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().

data_int()

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().

data_real()

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().

data_str()

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().

datatype()

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

override

References class_name().

declare_covalent_bond() [1/2]

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().

declare_covalent_bond() [2/2]

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().

delete_jump_and_intervening_cutpoint()

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().

delete_leading_residues()

void protocols::denovo_design::components::StructureData::delete_leading_residues

(

std::string const &

seg

)

deletes the residues between the segment N terminus and the N anchor point

References protocols::denovo_design::components::Segment::delete_lower_padding(), segment_nonconst(), and update_numbering().

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

delete_residue()

void protocols::denovo_design::components::StructureData::delete_residue

(

core::Size const

pose_resid

)

delete residue at resid

References changed(), protocols::denovo_design::components::Segment::delete_lower_padding(), protocols::denovo_design::components::Segment::delete_residue(), delete_segment(), protocols::denovo_design::components::Segment::delete_upper_padding(), protocols::denovo_design::components::Segment::pose_to_segment(), segment(), segment_name(), segment_nonconst(), protocols::TR(), and update_numbering().

delete_segment()

void protocols::denovo_design::components::StructureData::delete_segment

(

std::string const &

segment

)

removes all traces of the given segment from the object

References find_segment(), find_segment_name(), protocols::hybridization::r2, segment_order_, segments_, protocols::TR(), and update_numbering().

Referenced by delete_residue(), protocols::denovo_design::components::ConnectionPerturber::enumerate(), and merge_segments().

delete_trailing_residues()

void protocols::denovo_design::components::StructureData::delete_trailing_residues

(

std::string const &

seg

)

deletes the residues between the segment C terminus and the C anchor point

References protocols::denovo_design::components::Segment::delete_upper_padding(), segment_nonconst(), and update_numbering().

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

disconnect_segments()

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().

find_lower_terminus()

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().

find_non_polymer_bond()

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().

find_segment() [1/2]

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_exit

if not found

References segment_order_, and segments_.

find_segment() [2/2]

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_exit

if not found

References segment_order_, and segments_.

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

find_segment_name() [1/2]

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_exit

if not found

References segment_order_.

find_segment_name() [2/2]

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_exit

if not found

References segment_order_.

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

find_upper_terminus()

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().

generic_enzdes_header()

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().

get_data_int() [1/2]

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().

get_data_int() [2/2]

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.

get_data_real() [1/2]

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().

get_data_real() [2/2]

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.

get_data_str() [1/2]

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().

get_data_str() [2/2]

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().

has_alias()

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 alias(), and aliases_.

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

has_data_int() [1/2]

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

inlineprotected

References data_int_.

has_data_int() [2/2]

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.

has_data_real() [1/2]

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

inlineprotected

References data_real_.

has_data_real() [2/2]

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.

has_data_str() [1/2]

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

inlineprotected

References data_str_.

has_data_str() [2/2]

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.

has_free_lower_terminus()

bool protocols::denovo_design::components::StructureData::has_free_lower_terminus

(

std::string const &

id_val

)

const

tells if the segment given has an available lower terminus

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

Referenced by protocols::denovo_design::connection::ConnectionArchitect::available_lower_termini(), connect_segments(), connected_segments(), and find_lower_terminus().

has_free_upper_terminus()

bool protocols::denovo_design::components::StructureData::has_free_upper_terminus

(

std::string const &

id_val

)

const

tells if the segment given has an available lower terminus

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

Referenced by protocols::denovo_design::connection::ConnectionArchitect::available_upper_termini(), connect_segments(), and find_upper_terminus().

has_segment()

bool protocols::denovo_design::components::StructureData::has_segment

(

std::string const &

seg

)

const

true if this permutation contains a residue segment named seg

References protocols::denovo_design::PARENT_DELIMETER, and segments_.

Referenced by alias(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), copy_data(), protocols::denovo_design::components::ConnectionPerturber::enumerate(), protocols::denovo_design::components::HelixPerturber::enumerate(), has_segment_group(), merge_before(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), segment_group(), and set_alias().

has_segment_group()

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 has_segment(), protocols::denovo_design::PARENT_DELIMETER, segments_begin(), and segments_end().

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

id()

std::string const & protocols::denovo_design::components::StructureData::id

(

)

const

returns the id of this permutation

References id_.

Referenced by check_pose(), protocols::denovo_design::components::FoldGraph::FoldGraph(), get_data_int(), get_data_real(), get_data_str(), segment(), segment_nonconst(), and update_numbering().

length()

core::Size protocols::denovo_design::components::StructureData::length

(

)

const

returns the length of this permutation

References length_.

lower_anchor()

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().

mark_connected()

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().

mark_disconnected()

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

unmarks the given segments as covalently connected

References changed(), segment_nonconst(), protocols::denovo_design::components::Segment::set_lower_segment(), protocols::denovo_design::components::Segment::set_upper_segment(), and protocols::TR().

Referenced by disconnect_segments().

merge() [1/2]

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().

merge() [2/2]

void protocols::denovo_design::components::StructureData::merge	(	StructureData const &	other,
		SegmentNames const &	segments
	)

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

References add_segment(), choose_new_movable_group(), copy_data(), segment(), segment_order_, segments(), protocols::denovo_design::components::Segment::set_movable_group(), protocols::denovo_design::components::Segment::template_pose(), and protocols::TR().

merge_before() [1/2]

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().

merge_before() [2/2]

void protocols::denovo_design::components::StructureData::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

References add_segment(), choose_new_movable_group(), copy_data(), find_segment_name(), has_segment(), segment(), segments(), protocols::denovo_design::components::Segment::set_movable_group(), protocols::denovo_design::components::Segment::template_pose(), and protocols::TR().

merge_segments()

void protocols::denovo_design::components::StructureData::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.

References protocols::denovo_design::components::Segment::abego(), add_segment(), connect_segments(), protocols::denovo_design::components::Segment::cterm_included(), delete_segment(), find_segment_name(), protocols::denovo_design::components::Segment::length(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::Segment::lower_segment(), protocols::denovo_design::components::Segment::movable_group(), movable_groups(), protocols::denovo_design::components::Segment::nterm_included(), segment(), segment_order_, segments_, segments_in_movable_group(), protocols::denovo_design::components::Segment::set_movable_group(), protocols::denovo_design::components::Segment::ss(), protocols::TR(), protocols::denovo_design::components::Segment::upper(), and protocols::denovo_design::components::Segment::upper_segment().

movable_group()

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().

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().

move_segment()

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

re-arranges segments suchs that segment2 follows segment1 in sequence

re-arranges residues such that segment 2 follows segment 1 in sequence

References connected_segments(), protocols::denovo_design::components::Segment::has_free_lower_terminus(), protocols::denovo_design::components::Segment::has_free_upper_terminus(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::Segment::lower_segment(), move_segments(), segment(), protocols::denovo_design::components::Segment::upper(), and protocols::denovo_design::components::Segment::upper_segment().

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

move_segments()

void protocols::denovo_design::components::StructureData::move_segments ( std::string const &  segment1, std::string const &  segment2_lower, std::string const &  segment2_upper  )

protected

References find_segment_name(), segment(), segment_order_, segments_, and update_numbering().

Referenced by move_segment().

non_polymer_bond()

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().

non_polymer_bond_exists()

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().

num_chains()

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().

on_change()

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().

pairing()

SegmentPairingCOP protocols::denovo_design::components::StructureData::pairing

(

SegmentNames const &

segments

)

const

References core::scoring::pair, pairings_, and segments().

Referenced by add_pairing(), and protocols::denovo_design::architects::BetaSheetArchitect::retrieve_register_shifts().

pairings_begin()

SegmentPairingCOPs::const_iterator protocols::denovo_design::components::StructureData::pairings_begin

(

)

const

References pairings_.

Referenced by copy_data(), protocols::denovo_design::components::SegmentPairing::get_pairings(), protocols::denovo_design::architects::BetaSheetArchitect::retrieve_orientations(), and protocols::denovo_design::components::SegmentPairSet::SegmentPairSet().

pairings_end()

SegmentPairingCOPs::const_iterator protocols::denovo_design::components::StructureData::pairings_end

(

)

const

References pairings_.

Referenced by copy_data(), protocols::denovo_design::components::SegmentPairing::get_pairings(), protocols::denovo_design::architects::BetaSheetArchitect::retrieve_orientations(), and protocols::denovo_design::components::SegmentPairSet::SegmentPairSet().

parse_subtag()

void protocols::denovo_design::components::StructureData::parse_subtag

(

utility::tag::TagCOP

tag

)

Retrieves data from an XML subtag.

References add_covalent_bond(), add_pairing(), add_segment(), protocols::denovo_design::components::SegmentPairing::create(), protocols::denovo_design::components::Segment::parse_tag(), set_alias(), set_data_int(), set_data_real(), set_data_str(), protocols::denovo_design::components::SegmentPairing::TAG_NAME, and protocols::TR().

Referenced by parse_tag().

parse_tag()

void protocols::denovo_design::components::StructureData::parse_tag

(

utility::tag::TagCOP

tag

)

Retrieves data from an XML tag.

References length_, parse_subtag(), pose_length_, set_id(), and protocols::hybridization::t.

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

pose_length()

core::Size protocols::denovo_design::components::StructureData::pose_length

(

)

const

returns the total length of this permutation, including n-, c-terminal loop residues which are basically for show

References pose_length_.

Referenced by protocols::denovo_design::components::add_segment(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), check_pose(), check_residues(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), protocols::denovo_design::get_resid(), protocols::denovo_design::architects::BetaSheetArchitect::modify_and_add_permutation(), protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues(), and set_alias().

pose_residue()

core::Size protocols::denovo_design::components::StructureData::pose_residue	(	std::string const &	segment_name,
		core::Size const	local_res
	)		const

returns the actual residue number of the given name and res #

References alias(), has_alias(), segment_name(), and segments_.

Referenced by protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), declare_covalent_bond(), protocols::denovo_design::components::FoldGraph::fold_tree(), and substitute_variables().

rename_segment()

void protocols::denovo_design::components::StructureData::rename_segment	(	std::string const &	old_name,
		std::string const &	new_name
	)

renames a residue segment and updates all connections

References aliases_, changed(), find_segment(), find_segment_name(), protocols::denovo_design::components::Segment::lower_segment(), segment(), segments_, protocols::denovo_design::components::Segment::set_id(), protocols::denovo_design::components::Segment::set_lower_segment(), protocols::denovo_design::components::Segment::set_upper_segment(), and protocols::denovo_design::components::Segment::upper_segment().

renumber_movable_group()

void protocols::denovo_design::components::StructureData::renumber_movable_group	(	core::Size const	oldg,
		core::Size const	newg
	)

renumbers movable group "oldg" to have new number "newg"

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

Referenced by protocols::denovo_design::movers::AlignResiduesMover::add_metadata().

replace_segment()

void protocols::denovo_design::components::StructureData::replace_segment	(	SegmentName const &	seg_name,
		Segment const &	segment
	)

replace segment named seg_name with the given new segment

References changed(), find_segment(), segment(), segments_, and update_numbering().

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), and protocols::denovo_design::components::StructureDataPerturber::replace_segments().

retrieve_remarks()

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().

save_remarks()

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()

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(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), available_lower_termini(), available_upper_termini(), protocols::denovo_design::movers::FoldArchitectMover::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::FoldArchitectMover::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::connection::AreConnectablePredicate::operator()(), protocols::denovo_design::components::StructureSlicePredicate::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::FoldArchitectMover::segments_to_fold(), protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues(), set_abego(), set_alias(), set_cutpoint(), set_ss(), protocols::denovo_design::architects::BlueprintArchitect::set_template_segments(), slice(), substitute_variables(), and upper_anchor().

segment_group()

SegmentNames protocols::denovo_design::components::StructureData::segment_group

(

std::string const &

sname

)

const

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

References has_segment(), protocols::denovo_design::PARENT_DELIMETER, segments_begin(), and segments_end().

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

segment_name()

std::string const & protocols::denovo_design::components::StructureData::segment_name

(

core::Size const

res

)

const

returns segment which includes residue number res

References protocols::denovo_design::components::Segment::lower(), segment(), segments_, and protocols::denovo_design::components::Segment::upper().

Referenced by add_covalent_bond(), alias(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), delete_residue(), protocols::denovo_design::movers::FoldArchitectMover::find_roots(), generic_enzdes_header(), movable_group(), pose_residue(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::denovo_design::movers::FoldArchitectMover::remove_cutpoints(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::remove_cutpoints(), set_alias(), set_cutpoint(), and set_ss().

segment_nonconst()

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().

segments()

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

inlineprotected

returns constant list of residue ranges

References segments_.

Referenced by merge(), merge_before(), pairing(), and segments_in_movable_group().

segments_begin()

SegmentNameList::const_iterator protocols::denovo_design::components::StructureData::segments_begin

(

)

const

start of segments list

References segment_order_.

Referenced by protocols::denovo_design::add_cutpoints(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), available_lower_termini(), available_upper_termini(), protocols::denovo_design::movers::FoldArchitectMover::build_in_phases(), protocols::denovo_design::components::ExtendedPoseBuilder::calc_chain_endings(), check_chains(), cutpoints(), protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::movers::FoldArchitectMover::find_roots(), protocols::denovo_design::components::ExtendedPoseBuilder::find_template_segments(), 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::FoldArchitectMover::segments_to_fold(), set_abego(), slice(), and update_numbering().

segments_end()

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(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), available_lower_termini(), available_upper_termini(), protocols::denovo_design::movers::FoldArchitectMover::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::FoldArchitectMover::segments_to_fold(), set_abego(), slice(), and update_numbering().

segments_end_nonconst()

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

protected

non-const iterator to end of segment names list

References segment_order_.

segments_in_movable_group()

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().

set_abego() [1/4]

void protocols::denovo_design::components::StructureData::set_abego

(

std::string const &

abego

)

Set abego to use for the entire pose/all segments using a string.

References abego(), protocols::denovo_design::components::Segment::lower(), segment_nonconst(), segments_begin(), segments_end(), protocols::denovo_design::components::Segment::set_abego(), and protocols::denovo_design::components::Segment::upper().

Referenced by set_abego().

set_abego() [2/4]

void protocols::denovo_design::components::StructureData::set_abego	(	std::string const &	segment,
		std::string const &	abego
	)

Set abego to use for a specific segment using a string.

References abego(), segment(), segment_nonconst(), protocols::denovo_design::components::Segment::set_abego(), and update_numbering().

set_abego() [3/4]

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

Set abego to use for a specific segment using a vector of one-character strings.

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

set_abego() [4/4]

void protocols::denovo_design::components::StructureData::set_abego

(

utility::vector1< std::string > const &

abego

)

Set abego to use for the entire pose/all segments using a vector of one-character strings.

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

set_alias() [1/2]

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().

set_alias() [2/2]

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().

set_cutpoint() [1/2]

void protocols::denovo_design::components::StructureData::set_cutpoint

(

core::Size const

resid

)

marks the ith residue as a cutpoint

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

Referenced by protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::denovo_design::movers::FoldArchitectMover::remove_cutpoints(), and protocols::denovo_design::components::RemodelLoopMoverPoseFolder::remove_cutpoints().

set_cutpoint() [2/2]

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().

set_data_int() [1/2]

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.

set_data_int() [2/2]

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, and protocols::hybridization::val.

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

set_data_real() [1/2]

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.

set_data_real() [2/2]

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, and protocols::hybridization::val.

Referenced by parse_subtag().

set_data_str() [1/2]

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.

set_data_str() [2/2]

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

sets real number data

sets string data

References DATA_DELIMETER, and protocols::hybridization::val.

Referenced by protocols::denovo_design::connection::ConnectionArchitect::connect(), parse_subtag(), save_remarks(), and protocols::denovo_design::architects::StrandArchitect::store_bulges().

set_id()

void protocols::denovo_design::components::StructureData::set_id

(

std::string const &

id_str

)

sets id name

References id_.

Referenced by parse_tag().

set_movable_group()

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(), core::scoring::mg, and segments_.

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

set_ss()

void protocols::denovo_design::components::StructureData::set_ss	(	core::Size const	resid,
		char const	ss_type
	)

sets secondary structure for residue resid

References protocols::denovo_design::components::Segment::pose_to_segment(), segment(), segment_name(), segment_nonconst(), protocols::denovo_design::components::Segment::set_ss(), protocols::TR(), and update_numbering().

set_template_pose()

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
	)

attaches a template pose to the given segment

References segments_.

Referenced by protocols::denovo_design::movers::FoldArchitectMover::build_in_phases(), and protocols::denovo_design::architects::BlueprintArchitect::set_template_segments().

slice()

StructureData protocols::denovo_design::components::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.

Returns a StructureData containing only the given segments The resulting StructureData will contain all relevant data from the current.

References protocols::denovo_design::components::Segment::add_lower_padding(), add_segment(), protocols::denovo_design::components::Segment::add_upper_padding(), copy_data(), protocols::denovo_design::components::Segment::lower_segment(), segment(), segments_begin(), segments_end(), protocols::denovo_design::components::Segment::set_lower_segment(), protocols::denovo_design::components::Segment::set_upper_segment(), protocols::denovo_design::components::Segment::template_pose(), and protocols::denovo_design::components::Segment::upper_segment().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::apply(), and protocols::denovo_design::movers::FoldArchitectMover::build_in_phases().

slide_jump()

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

specific_enzdes_header()

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().

ss() [1/2]

std::string const & protocols::denovo_design::components::StructureData::ss

(

)

const

return secondary structure string

References ss_.

Referenced by protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(), check_pose(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover(), protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), generic_enzdes_header(), protocols::fldsgn::filters::SecondaryStructureFilter::get_filtered_secstruct(), protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs(), protocols::denovo_design::components::HelixPairing::pairing_string(), protocols::denovo_design::components::StrandPairing::pairing_string(), protocols::denovo_design::components::HelixSheetPairing::pairing_string(), set_alias(), and specific_enzdes_header().

ss() [2/2]

char protocols::denovo_design::components::StructureData::ss

(

core::Size const

resid

)

const

abego of residue resid

return secondary structure at residue resid

References ss_.

substitute_variables()

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().

termini()

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()().

unblock_signals()

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

private

unblocks on_change() signals and calls on_change()

References block_signals_.

Referenced by save_remarks().

update_numbering()

void protocols::denovo_design::components::StructureData::update_numbering

(

)

updates numbering based on the saved order of Segment objects

References abego_, id(), length_, movable_groups_, pose_length_, segment_order_, segments_, segments_begin(), segments_end(), ss_, and protocols::TR().

Referenced by add_segment(), delete_leading_residues(), delete_residue(), delete_segment(), delete_trailing_residues(), move_segments(), replace_segment(), set_abego(), and set_ss().

upper_anchor()

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().

write()

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

override

References class_name(), and protocols::denovo_design::components::clean_for_storage().

Friends And Related Function Documentation

operator<<

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

friend

for output

Member Data Documentation

abego_

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

private

Referenced by abego(), and update_numbering().

aliases_

AliasMap protocols::denovo_design::components::StructureData::aliases_

private

Referenced by add_prefix_to_segments(), alias(), aliases(), copy_data(), has_alias(), rename_segment(), and set_alias().

block_signals_

bool protocols::denovo_design::components::StructureData::block_signals_

private

Referenced by block_signals(), changed(), and unblock_signals().

covalent_bonds_

utility::vector1< BondInfo > protocols::denovo_design::components::StructureData::covalent_bonds_

private

Referenced by add_covalent_bond(), covalent_bonds_begin(), covalent_bonds_end(), and non_polymer_bond_exists().

DATA_DELIMETER

char const protocols::denovo_design::components::StructureData::DATA_DELIMETER = '#'

static

Referenced by generic_enzdes_header(), get_data_int(), get_data_real(), get_data_str(), has_data_int(), has_data_real(), has_data_str(), retrieve_remarks(), set_data_int(), set_data_real(), set_data_str(), and substitute_variables().

data_int_

std::map< std::string, int > protocols::denovo_design::components::StructureData::data_int_

private

Referenced by copy_data(), data_int(), get_data_int(), has_data_int(), and set_data_int().

data_real_

std::map< std::string, core::Real > protocols::denovo_design::components::StructureData::data_real_

private

Referenced by copy_data(), data_real(), get_data_real(), has_data_real(), and set_data_real().

data_str_

StringMap protocols::denovo_design::components::StructureData::data_str_

private

Referenced by copy_data(), data_str(), get_data_str(), has_data_str(), retrieve_remarks(), and set_data_str().

id_

std::string protocols::denovo_design::components::StructureData::id_

private

Referenced by id(), and set_id().

length_

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

private

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

movable_groups_

MovableGroups protocols::denovo_design::components::StructureData::movable_groups_

private

Referenced by check_movable_groups(), choose_new_movable_group(), movable_groups(), and update_numbering().

pairings_

SegmentPairingCOPs protocols::denovo_design::components::StructureData::pairings_

private

Referenced by add_pairing(), clear_pairings(), pairing(), pairings_begin(), and pairings_end().

pose_length_

core::Size protocols::denovo_design::components::StructureData::pose_length_

private

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

segment_order_

SegmentNameList protocols::denovo_design::components::StructureData::segment_order_

private

Referenced by add_prefix_to_segments(), add_segment(), copy_data(), delete_segment(), find_segment(), find_segment_name(), merge(), merge_segments(), move_segments(), segments_begin(), segments_end(), segments_end_nonconst(), and update_numbering().

segments_

SegmentMap protocols::denovo_design::components::StructureData::segments_

private

Referenced by add_prefix_to_segments(), add_segment(), check_improper_termini(), check_residues(), delete_segment(), find_segment(), has_free_lower_terminus(), has_free_upper_terminus(), has_segment(), mark_connected(), merge_segments(), move_segments(), num_chains(), pose_residue(), rename_segment(), renumber_movable_group(), replace_segment(), segment(), segment_name(), segment_nonconst(), segments(), segments_in_movable_group(), set_movable_group(), set_template_pose(), and update_numbering().

ss_

std::string protocols::denovo_design::components::StructureData::ss_

private

Referenced by ss(), and update_numbering().

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

• src/protocols/denovo_design/components/StructureData.hh
• src/protocols/denovo_design/components/StructureData.cc