Namespaces
	architects

	calculators

	components

	connection

	constraints

	filters

	movers

	residue_selectors

	task_operations

Classes
class	DisulfidizeMover

class	DisulfidizeMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< DisulfidizerMover >	DisulfidizerMoverOP

typedef utility::pointer::shared_ptr< DisulfidizerMover const >	DisulfidizerMoverCOP

typedef utility::pointer::weak_ptr< DisulfidizerMover >	DisulfidizerMoverAP

typedef utility::pointer::weak_ptr< DisulfidizerMover const >	DisulfidizerMoverCAP

typedef std::string	SegmentName

typedef std::vector< SegmentName >	SegmentNames

typedef std::list< SegmentName >	SegmentNameList

typedef std::set< SegmentName >	SegmentNameSet

typedef std::pair< core::Size, core::Size >	SizePair

typedef std::map< std::string, core::Size >	StrandNameToNumberMap

Functions
void	add_to_list (DisulfidizeMover::DisulfideList &disulf_partners, core::Size const r1, core::Size const r2)

bool	same_pose (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Tells whether the two given poses are identical based on # resides and dihedrals. More...

core::kinematics::FoldTree	remove_all_jump_atoms (core::kinematics::FoldTree const &orig)

core::kinematics::FoldTree	remove_missing_jump_atoms (core::pose::Pose const &pose, core::kinematics::FoldTree const &orig)
	removes atoms missing from the current pose More...

void	construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, core::select::residue_selector::ResidueSubset const &set1, core::select::residue_selector::ResidueSubset const &set2, bool const keep_chirality)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...

void	construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, std::set< core::Size > const &res_set, bool const keep_chirality)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...

core::pose::PoseOP	construct_dummy_pose (std::string const &restype_name)
	builds an extended-conformation poly-XXX pose More...

core::pose::PoseOP	construct_dummy_pose (std::string const &restype_name, core::Size const length)

core::pose::PoseOP	construct_dummy_pose (core::chemical::ResidueType const &restype)

core::pose::PoseOP	construct_dummy_pose (core::chemical::ResidueType const &restype, core::Size length)

core::select::residue_selector::ResidueSelectorCOP	get_residue_selector (basic::datacache::DataMap const &data, std::string const &name)

std::string	abego_str (utility::vector1< std::string > const &abego)

utility::vector1< std::string >	abego_vector (std::string const &ab)

std::string	get_remark_line (core::io::Remarks::const_iterator &it_rem, core::io::Remarks::const_iterator const &end)

void	add_remark (core::io::Remarks &remarks, core::Size const num, std::string const &str_val)
	adds a remark to a Remarks object, splitting it into multiple remarks if it is too long More...

core::Size	loop_stop_without_overlap (core::pose::Pose const &pose, core::Size stopres, core::Size const overlap)

core::Size	loop_start_without_overlap (core::pose::Pose const &pose, core::Size startres, core::Size const overlap)

void	rebuild_missing_atoms (core::pose::Pose &pose, core::Size const resi)
	given a residue, rebuilds all missing atoms More...

int	find_jump_rec (core::kinematics::FoldTree const &ft, core::Size const residue)
	helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs More...

void	insert_peptide_edges (core::kinematics::FoldTree &ft, core::kinematics::Edge const &jedge)
	inserts the peptide edges to accomodate the new jump edge given More...

core::Size	extract_int (core::Real &num, core::Size const m, core::Size const n)
	given a number 0 <= x < 1, calculate an integer M <= x <= N NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER More...

std::pair< std::string, std::string >	parse_strand_pair (std::string const &strand_pair_str)

core::Size	count_bulges (components::StructureData const &perm, std::string const &segment)
	counts the beta-bulges in the given segment. This simply counts all abego A's in the segment More...

void	add_chain_from_pose (core::pose::PoseCOP to_add, core::pose::PoseOP combined)
	dumps a pose into another pose as a new chain More...

void	add_residues_to_pose (core::pose::Pose &pose, core::pose::Pose const &template_pose, bool const new_chain)
	adds residues from template_pose to pose. If new_chain == true, creates covalent bond More...

core::Size	get_resid (components::StructureData const &perm, std::string const &resid_str)

core::Real	linear_chainbreak (core::pose::Pose const &pose, core::Size const pos)
	evaluate linear chainbreak at a position 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)

void	add_cutpoints (core::pose::Pose &pose, components::StructureData const &sd)

std::string	symmetric_secstruct (core::pose::Pose const &pose, std::string const &asymm_secstruct)
	Given a symmetric pose and a secstruct for the asymmetric unit, constructs and returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit. More...

core::kinematics::FoldTree	symmetric_fold_tree (core::pose::Pose const &pose, core::kinematics::FoldTree const &asymm_ft)
	Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and returns a symmetric fold tree while preserving the topology of the aysmmetric unit's fold tree. More...

core::select::residue_selector::ResidueSubset	symmetric_residue_subset (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &asymm_subset)
	Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset. More...

void	parse_motif_string (std::string const &motif_str, std::string &secstruct, std::string &abego)
	Computes secondary structure string from the given motifs. More...

template<class T >
utility::vector1< T >	parse_length_string (std::string const &len_str)

template<typename Container , typename T >
Container	set_difference (typename std::set< T >::const_iterator begin1, typename std::set< T >::const_iterator const &end1, typename std::set< T >::const_iterator begin2, typename std::set< T >::const_iterator const &end2)
	Returns vector of elements found in v1 but not in v2. More...

template<typename Container >
Container	csv_to_container (std::string const &csv, char const delim=',')
	Given a comma-seperated string, convert to container. More...

Variables
static char const	PARENT_DELIMETER = '.'

Typedef Documentation

◆ DisulfidizerMoverAP

typedef utility::pointer::weak_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverAP

◆ DisulfidizerMoverCAP

typedef utility::pointer::weak_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCAP

◆ DisulfidizerMoverCOP

typedef utility::pointer::shared_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCOP

◆ DisulfidizerMoverOP

typedef utility::pointer::shared_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverOP

◆ SegmentName

typedef std::string protocols::denovo_design::SegmentName

◆ SegmentNameList

typedef std::list< SegmentName > protocols::denovo_design::SegmentNameList

◆ SegmentNames

typedef std::vector< SegmentName > protocols::denovo_design::SegmentNames

◆ SegmentNameSet

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

◆ SizePair

typedef std::pair< core::Size, core::Size > protocols::denovo_design::SizePair

◆ StrandNameToNumberMap

typedef std::map< std::string, core::Size > protocols::denovo_design::StrandNameToNumberMap

Function Documentation

◆ abego_str()

std::string protocols::denovo_design::abego_str ( utility::vector1< std::string > const & abego )

References core::pose::motif::a(), and core::scoring::abego.

Referenced by protocols::denovo_design::filters::PreProlineFilter::compute_simple(), protocols::denovo_design::architects::StrandArchitect::create_motif(), protocols::denovo_design::architects::BlueprintArchitect::design(), protocols::denovo_design::components::IdealAbegoGenerator::extract_ideal_motifs(), protocols::fldsgn::SheetConstraintGenerator::get_abego(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::denovo_design::components::Segment::set_abego(), and protocols::denovo_design::components::StructureData::set_abego().

◆ abego_vector()

utility::vector1< std::string > protocols::denovo_design::abego_vector ( std::string const & ab )

References core::scoring::abego.

Referenced by protocols::denovo_design::components::Picker::fragments_for_permutation(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::fldsgn::SheetConstraintGenerator::get_abego(), core::scoring::dssp::Dssp::get_dssp_plus_abego_L_def(), and protocols::denovo_design::components::Picker::pick_and_cache_fragments().

◆ add_chain_from_pose()

void protocols::denovo_design::add_chain_from_pose	(	core::pose::PoseCOP	to_add,
		core::pose::PoseOP	combined
	)

dumps a pose into another pose as a new chain

References protocols::TR().

◆ add_cutpoints()

void protocols::denovo_design::add_cutpoints	(	core::pose::Pose &	pose,
		components::StructureData const &	sd
	)

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), protocols::denovo_design::components::Segment::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::conformation::Residue::lower_connect_atom(), core::pose::Pose::residue(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::antibody::design::add_loops_from_bool_vector(), and protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose().

◆ add_remark()

void protocols::denovo_design::add_remark	(	core::io::Remarks &	remarks,
		core::Size const	num,
		std::string const &	str_val
	)

adds a remark to a Remarks object, splitting it into multiple remarks if it is too long

References core::io::RemarkInfo::num, and core::io::RemarkInfo::value.

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

◆ add_residues_to_pose()

void protocols::denovo_design::add_residues_to_pose	(	core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose,
		bool const	new_chain
	)

adds residues from template_pose to pose. If new_chain == true, creates covalent bond

References core::pose::Pose::append_polymer_residue_after_seqpos(), core::conformation::Conformation::buffer_signals(), core::pose::Pose::conformation(), core::pose::Pose::empty(), core::conformation::Conformation::insert_conformation_by_jump(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Conformation::unblock_signals().

◆ add_to_list()

void protocols::denovo_design::add_to_list	(	DisulfidizeMover::DisulfideList &	disulf_partners,
		core::Size const	r1,
		core::Size const	r2
	)

References protocols::hybridization::r1, and protocols::hybridization::r2.

Referenced by protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), and core::pack::palette::PackerPalette::initialize_non_terminal_types().

◆ construct_dummy_pose() [1/4]

core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( core::chemical::ResidueType const & restype )

References construct_dummy_pose().

◆ construct_dummy_pose() [2/4]

core::pose::PoseOP protocols::denovo_design::construct_dummy_pose	(	core::chemical::ResidueType const &	restype,
		core::Size	length
	)

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), and core::conformation::ResidueFactory::create_residue().

◆ construct_dummy_pose() [3/4]

core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( std::string const & restype_name )

builds an extended-conformation poly-XXX pose

Referenced by construct_dummy_pose().

◆ construct_dummy_pose() [4/4]

core::pose::PoseOP protocols::denovo_design::construct_dummy_pose	(	std::string const &	restype_name,
		core::Size const	length
	)

References construct_dummy_pose(), and core::chemical::rsd_set_from_cmd_line().

◆ construct_poly_ala_pose() [1/2]

void protocols::denovo_design::construct_poly_ala_pose	(	core::pose::Pose &	pose,
		bool const	keep_disulf,
		core::select::residue_selector::ResidueSubset const &	set1,
		core::select::residue_selector::ResidueSubset const &	set2,
		bool const	keep_chirality
	)

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

Referenced by protocols::forge::components::BDR::centroid_build(), and protocols::denovo_design::DisulfidizeMover::find_possible_disulfides().

◆ construct_poly_ala_pose() [2/2]

void protocols::denovo_design::construct_poly_ala_pose	(	core::pose::Pose &	pose,
		bool const	keep_disulf,
		std::set< core::Size > const &	res_set,
		bool const	keep_chirality
	)

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

Note: Updated for beta-3-amino acids by VKM on 26 November 2016.

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

References protocols::simple_moves::MutateResidue::apply(), core::conformation::break_disulfide(), core::pose::Pose::conformation(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose(), core::pose::Pose::fold_tree(), core::conformation::get_disulf_partner(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_d_aa(), core::chemical::ResidueType::is_disulfide_bonded(), core::conformation::Residue::is_protein(), remove_all_jump_atoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::type().

◆ count_bulges()

core::Size protocols::denovo_design::count_bulges	(	components::StructureData const &	perm,
		std::string const &	segment
	)

counts the beta-bulges in the given segment. This simply counts all abego A's in the segment

References core::scoring::abego, protocols::denovo_design::components::Segment::abego(), protocols::denovo_design::components::StructureData::segment(), and protocols::denovo_design::components::Segment::ss().

◆ csv_to_container()

template<typename Container >

Container protocols::denovo_design::csv_to_container	(	std::string const &	csv,
		char const	delim = `','`
	)

Given a comma-seperated string, convert to container.

◆ extract_int()

core::Size protocols::denovo_design::extract_int	(	core::Real &	num,
		core::Size const	m,
		core::Size const	n
	)

given a number 0 <= x < 1, calculate an integer M <= x <= N NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER

References protocols::TR(), and protocols::hybridization::val.

Referenced by protocols::denovo_design::connection::ConnectionArchitect::choose_motif(), protocols::denovo_design::architects::BetaSheetArchitect::design(), protocols::denovo_design::architects::HelixArchitect::design(), protocols::denovo_design::architects::MotifArchitect::design(), protocols::denovo_design::architects::StrandArchitect::design(), and protocols::denovo_design::components::RandomVectorSelector< T >::select().

◆ find_jump_rec()

int protocols::denovo_design::find_jump_rec	(	core::kinematics::FoldTree const &	ft,
		core::Size const	residue
	)

helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs

References core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::root(), protocols::loops::start, and protocols::loops::stop.

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), and protocols::denovo_design::movers::RotateSegmentMover::apply().

◆ get_remark_line()

std::string protocols::denovo_design::get_remark_line	(	core::io::Remarks::const_iterator &	it_rem,
		core::io::Remarks::const_iterator const &	end
	)

References core::sequence::end.

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

◆ get_resid()

core::Size protocols::denovo_design::get_resid	(	components::StructureData const &	perm,
		std::string const &	resid_str
	)

References protocols::denovo_design::components::StructureData::pose_length(), and protocols::denovo_design::components::StructureData::substitute_variables().

Referenced by protocols::denovo_design::movers::RotateSegmentMover::target_atoms().

◆ get_residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::get_residue_selector	(	basic::datacache::DataMap const &	data,
		std::string const &	name
	)

References core::select::residue_selector::get_residue_selector().

Referenced by protocols::denovo_design::DisulfidizeMover::parse_my_tag().

◆ insert_peptide_edges()

void protocols::denovo_design::insert_peptide_edges	(	core::kinematics::FoldTree &	ft,
		core::kinematics::Edge const &	jedge
	)

inserts the peptide edges to accomodate the new jump edge given

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::delete_edge(), core::kinematics::Edge::label(), core::kinematics::Edge::PEPTIDE, core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and protocols::TR().

◆ linear_chainbreak()

core::Real protocols::denovo_design::linear_chainbreak	(	core::pose::Pose const &	pose,
		core::Size const	pos
	)

evaluate linear chainbreak at a position

Remarks: If necessary, will evaluate using a copy of the Pose with a cut fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished. Eventually this should be merged into protocols/forge/methods/linear_chainbreak.cc However, the changes I needed to make to that file break certain parts of remodel

References protocols::forge::methods::add_cutpoint_variants(), core::kinematics::FoldTree::add_edge(), protocols::buns::energy, core::pose::Pose::fold_tree(), core::scoring::linear_chainbreak, core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::Edge::PEPTIDE, and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::rna::get_modeler_scorefxn().

◆ loop_start_without_overlap()

core::Size protocols::denovo_design::loop_start_without_overlap	(	core::pose::Pose const &	pose,
		core::Size	startres,
		core::Size const	overlap
	)

References core::pose::Pose::chain(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::scoring::packstat::overlap(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::find_roots().

◆ loop_stop_without_overlap()

core::Size protocols::denovo_design::loop_stop_without_overlap	(	core::pose::Pose const &	pose,
		core::Size	stopres,
		core::Size const	overlap
	)

References core::pose::Pose::chain(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::scoring::packstat::overlap(), and core::pose::Pose::residue().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::find_roots().

◆ parse_length_string()

template<class T >

utility::vector1< T > protocols::denovo_design::parse_length_string ( std::string const & len_str )

References core::sequence::end, and protocols::loops::start.

◆ parse_motif_string()

void protocols::denovo_design::parse_motif_string	(	std::string const &	motif_str,
		std::string &	secstruct,
		std::string &	abego
	)

Computes secondary structure string from the given motifs.

Parameters

[in]	motif_str	Motif string to be parsed (e.g. "5EB-2LG-5EB")
[out]	secstruct	Secondary structure string to be cleared and filled
[out]	abego	ABEGO string to be cleared and filled

References core::scoring::abego, and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_motifs(), and protocols::denovo_design::components::Segment::parse_motif().

◆ parse_strand_pair()

std::pair< std::string, std::string > protocols::denovo_design::parse_strand_pair ( std::string const & strand_pair_str )

◆ rebuild_missing_atoms()

void protocols::denovo_design::rebuild_missing_atoms	(	core::pose::Pose &	pose,
		core::Size const	resi
	)

given a residue, rebuilds all missing atoms

References core::chemical::ResidueType::atom_name(), core::pose::Pose::conformation(), core::conformation::Residue::fill_missing_atoms(), core::conformation::Residue::has(), core::conformation::Conformation::replace_residue(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Residue::type().

Referenced by protocols::denovo_design::movers::new_jump_and_cutpoint().

◆ remove_all_jump_atoms()

core::kinematics::FoldTree protocols::denovo_design::remove_all_jump_atoms ( core::kinematics::FoldTree const & orig )

References core::kinematics::FoldTree::add_edge(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop_atom(), and protocols::TR().

Referenced by construct_poly_ala_pose(), and protocols::denovo_design::DisulfidizeMover::process_pose().

◆ remove_missing_jump_atoms()

core::kinematics::FoldTree protocols::denovo_design::remove_missing_jump_atoms	(	core::pose::Pose const &	pose,
		core::kinematics::FoldTree const &	orig
	)

removes atoms missing from the current pose

References core::kinematics::FoldTree::add_edge(), core::conformation::Residue::has(), core::pose::Pose::residue(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop_atom(), and protocols::TR().

◆ same_pose()

bool protocols::denovo_design::same_pose	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Tells whether the two given poses are identical based on # resides and dihedrals.

References core::conformation::Residue::is_protein(), core::conformation::Residue::name(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ set_difference()

template<typename Container , typename T >

Container protocols::denovo_design::set_difference	(	typename std::set< T >::const_iterator	begin1,
		typename std::set< T >::const_iterator const &	end1,
		typename std::set< T >::const_iterator	begin2,
		typename std::set< T >::const_iterator const &	end2
	)

Returns vector of elements found in v1 but not in v2.

Referenced by core::io::mmtf::add_ters_via_bonds(), and protocols::rna::movers::clean_res_list().

◆ slide_jump()

core::kinematics::FoldTree protocols::denovo_design::slide_jump	(	core::kinematics::FoldTree const &	ft_orig,
		core::Size const	jump_idx,
		core::Size const	new_start,
		core::Size const	new_stop
	)

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::end(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), core::kinematics::FoldTree::slide_jump(), core::kinematics::Edge::start(), and protocols::TR().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), and protocols::denovo_design::movers::RotateSegmentMover::apply().

◆ symmetric_fold_tree()

core::kinematics::FoldTree protocols::denovo_design::symmetric_fold_tree	(	core::pose::Pose const &	pose,
		core::kinematics::FoldTree const &	asymm_ft
	)

Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and returns a symmetric fold tree while preserving the topology of the aysmmetric unit's fold tree.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::pose::Pose::conformation(), core::kinematics::FoldTree::delete_extra_vertices(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::kinematics::Edge::start(), and protocols::TR().

Referenced by protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), and protocols::denovo_design::movers::SealFoldTreeMover::apply().

◆ symmetric_residue_subset()

core::select::residue_selector::ResidueSubset protocols::denovo_design::symmetric_residue_subset	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	asymm_subset
	)

Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset.

References core::pose::Pose::conformation(), and core::pose::Pose::size().

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

◆ symmetric_secstruct()

std::string protocols::denovo_design::symmetric_secstruct	(	core::pose::Pose const &	pose,
		std::string const &	asymm_secstruct
	)

Given a symmetric pose and a secstruct for the asymmetric unit, constructs and returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit.

References core::pose::Pose::conformation(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

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

Variable Documentation

◆ PARENT_DELIMETER

char const protocols::denovo_design::PARENT_DELIMETER = '.'

static

Namespaces

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ DisulfidizerMoverAP

◆ DisulfidizerMoverCAP

◆ DisulfidizerMoverCOP

◆ DisulfidizerMoverOP

◆ SegmentName

◆ SegmentNameList

◆ SegmentNames

◆ SegmentNameSet

◆ SizePair

◆ StrandNameToNumberMap

Function Documentation

◆ abego_str()

◆ abego_vector()

◆ add_chain_from_pose()

◆ add_cutpoints()

◆ add_remark()

◆ add_residues_to_pose()

◆ add_to_list()

◆ construct_dummy_pose() [1/4]

◆ construct_dummy_pose() [2/4]

◆ construct_dummy_pose() [3/4]

◆ construct_dummy_pose() [4/4]

◆ construct_poly_ala_pose() [1/2]

◆ construct_poly_ala_pose() [2/2]

◆ count_bulges()

◆ csv_to_container()

◆ extract_int()

◆ find_jump_rec()

◆ get_remark_line()

◆ get_resid()

◆ get_residue_selector()

◆ insert_peptide_edges()

◆ linear_chainbreak()

◆ loop_start_without_overlap()

◆ loop_stop_without_overlap()

◆ parse_length_string()

◆ parse_motif_string()

◆ parse_strand_pair()

◆ rebuild_missing_atoms()

◆ remove_all_jump_atoms()

◆ remove_missing_jump_atoms()

◆ same_pose()

◆ set_difference()

◆ slide_jump()

◆ symmetric_fold_tree()

◆ symmetric_residue_subset()

◆ symmetric_secstruct()

Variable Documentation

◆ PARENT_DELIMETER