protocols::fldsgn::topology Namespace Reference

Classes
class	BB_Pos
class	BetaAlphaBetaMotif
class	BetaAlphaBetaMotifSet
class	DimerPairing
class	DimerPairings
class	HelixPairing
class	HelixPairingSet
struct	TripletID
class	HSSTriplet
class	HSSTripletSet
class	Sheet
class	SheetSet
class	SheetFoldTypeManager
class	SS_Base
class	Strand
class	Helix
class	Loop
class	SS_Info2
class	StrandPairing
class	StrandPairingSet

Typedefs
typedef utility::pointer::shared_ptr< BetaAlphaBetaMotif >	BetaAlphaBetaMotifOP
typedef utility::pointer::shared_ptr< BetaAlphaBetaMotif const >	BetaAlphaBetaMotifCOP
typedef utility::vector1< BetaAlphaBetaMotifOP >	BetaAlphaBetaMotifs
typedef utility::pointer::shared_ptr< BetaAlphaBetaMotifSet >	BetaAlphaBetaMotifSetOP
typedef utility::pointer::shared_ptr< BetaAlphaBetaMotifSet const >	BetaAlphaBetaMotifSetCOP
typedef utility::pointer::shared_ptr< DimerPairing >	DimerPairingOP
typedef utility::pointer::shared_ptr< DimerPairing const >	DimerPairingCOP
typedef utility::pointer::shared_ptr< HelixPairing >	HelixPairingOP
typedef utility::pointer::shared_ptr< HelixPairingSet >	HelixPairingSetOP
typedef utility::pointer::shared_ptr< HelixPairing const >	HelixPairingCOP
typedef utility::pointer::shared_ptr< HelixPairingSet const >	HelixPairingSetCOP
typedef utility::vector1< HelixPairingOP >	HelixPairings
typedef utility::pointer::shared_ptr< HSSTriplet >	HSSTripletOP
typedef utility::pointer::shared_ptr< HSSTripletSet >	HSSTripletSetOP
typedef utility::pointer::shared_ptr< HSSTriplet const >	HSSTripletCOP
typedef utility::pointer::shared_ptr< HSSTripletSet const >	HSSTripletSetCOP
typedef utility::vector1< HSSTripletOP >	HSSTriplets
typedef HSSTriplets::const_iterator	HSSConstIterator
typedef HSSTriplets::iterator	HSSIterator
typedef utility::pointer::shared_ptr< Sheet >	SheetOP
typedef utility::pointer::shared_ptr< Sheet const >	SheetCOP
typedef utility::vector1< SheetOP >	Sheets
typedef utility::pointer::shared_ptr< SheetSet >	SheetSetOP
typedef utility::pointer::shared_ptr< SheetSet const >	SheetSetCOP
typedef utility::pointer::shared_ptr< SS_Base >	SS_BaseOP
typedef utility::pointer::shared_ptr< Helix >	HelixOP
typedef utility::pointer::shared_ptr< Strand >	StrandOP
typedef utility::pointer::shared_ptr< Loop >	LoopOP
typedef utility::pointer::shared_ptr< SS_Base const >	SS_BaseCOP
typedef utility::pointer::shared_ptr< Helix const >	HelixCOP
typedef utility::pointer::shared_ptr< Strand const >	StrandCOP
typedef utility::pointer::shared_ptr< Loop const >	LoopCOP
typedef utility::vector1< HelixOP >	Helices
typedef utility::vector1< StrandOP >	Strands
typedef utility::vector1< LoopOP >	Loops
typedef utility::pointer::shared_ptr< SS_Info2 >	SS_Info2_OP
typedef utility::pointer::shared_ptr< SS_Info2 const >	SS_Info2_COP
typedef utility::pointer::shared_ptr< StrandPairing >	StrandPairingOP
typedef utility::pointer::shared_ptr< StrandPairingSet >	StrandPairingSetOP
typedef utility::pointer::shared_ptr< StrandPairing const >	StrandPairingCOP
typedef utility::pointer::shared_ptr< StrandPairingSet const >	StrandPairingSetCOP
typedef utility::vector1< StrandPairingOP >	StrandPairings
typedef utility::vector1< StrandPairingCOP >	StrandPairingCOPs

Enumerations
enum	SheetFoldType : char {   BABx1 = 1 , RosI , RosO , BABx2 ,   Thio , BFr , EFr , CFr ,   DFr , Rsmn2x2 , Rsmn3x3_Half , BABx3 ,   PG_like , Thioredoxin , BAB_CFr , DFr_BAB ,   BEFr , Fd_like , RFd_like , CDFr ,   HPN_CFr , DFr_HPN , Flavodoxin , Ploop2x3 ,   RNAseH , Top7 , Rsmn3x3 , Ploop3x3 ,   UNFOLD , NO_STRANDS , UNKNOWN , n_fold_types = UNKNOWN }
	List of topologies determined by strand pairings. More...

Functions
std::ostream &	operator<< (std::ostream &out, const BetaAlphaBetaMotif &s)
	IO operator. More...
bool	compare (std::map< core::Size, Real >::const_iterator a, std::map< core::Size, Real >::const_iterator b)
std::ostream &	operator<< (std::ostream &out, const BetaAlphaBetaMotifSet &s)
std::ostream &	operator<< (std::ostream &out, const DimerPairing &dp)
bool	pointer_sorter (DimerPairingCOP const a, DimerPairingCOP const b)
std::ostream &	operator<< (std::ostream &out, const DimerPairings &dps)
std::ostream &	operator<< (std::ostream &out, const HelixPairing &hp)
	return name More...
std::ostream &	operator<< (std::ostream &out, const HelixPairingSet &s)
	return helix pairing More...
std::ostream &	operator<< (std::ostream &os, TripletID const &id)
std::ostream &	operator<< (std::ostream &out, const HSSTriplet &s)
	IO Operator. More...
std::ostream &	operator<< (std::ostream &out, const HSSTripletSet &s)
	IO Operator. More...
std::ostream &	operator<< (std::ostream &out, const Sheet &s)
	return strand pairing More...
std::ostream &	operator<< (std::ostream &out, const SheetSet &s)
	return strand pairing More...
std::ostream &	operator<< (std::ostream &out, const Strand &st)
std::ostream &	operator<< (std::ostream &out, const Helix &hx)
std::ostream &	operator<< (std::ostream &out, const Loop &lp)
std::ostream &	operator<< (std::ostream &out, const SS_Info2 &ssinfo)
std::ostream &	operator<< (std::ostream &out, const StrandPairing &sp)
	return name More...
std::set< core::Size >	compute_bulges (core::Size const strand_begin, core::Size const strand_end, utility::vector1< String > const &abego)
std::ostream &	operator<< (std::ostream &out, const StrandPairingSet &s)
	output detail of strand pairing set More...
bool	pointer_sorter (StrandPairingCOP const a, StrandPairingCOP const b)
bool	sort_by_length (protocols::fldsgn::topology::StrandPairingCOP const a, protocols::fldsgn::topology::StrandPairingCOP const b)
protocols::fldsgn::topology::StrandPairingSet	calc_strand_pairing_set (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2_COP const ssinfo, core::Size minimum_pair_length)
	convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet More...
core::Real	calc_delta_sasa (core::pose::Pose const &pose, utility::vector1< protocols::forge::build::Interval > intervals, Real const pore_radius)
	calc delta sasa, when a molecule is splited to 2parts. More...
core::Size	check_kink_helix (core::pose::Pose const &pose, core::Size const begin, core::Size const end)
	check kink of helix, return number of loosen hydrogen More...
utility::vector1< core::scoring::hbonds::HBond >	check_internal_hbonds (core::pose::Pose const &pose, core::Size const begin, core::Size const end)
	check kink of helix, return number of loosen hydrogen More...
core::Real	calc_strand_helix_angle (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2_COP const ssinfo, core::Size const strand_id1, core::Size const strand_id2, core::Size const helix_id, std::string const &geom_type)

Typedef Documentation

BetaAlphaBetaMotifCOP

typedef utility::pointer::shared_ptr< BetaAlphaBetaMotif const > protocols::fldsgn::topology::BetaAlphaBetaMotifCOP

BetaAlphaBetaMotifOP

typedef utility::pointer::shared_ptr< BetaAlphaBetaMotif > protocols::fldsgn::topology::BetaAlphaBetaMotifOP

BetaAlphaBetaMotifs

typedef utility::vector1< BetaAlphaBetaMotifOP > protocols::fldsgn::topology::BetaAlphaBetaMotifs

BetaAlphaBetaMotifSetCOP

typedef utility::pointer::shared_ptr< BetaAlphaBetaMotifSet const > protocols::fldsgn::topology::BetaAlphaBetaMotifSetCOP

BetaAlphaBetaMotifSetOP

typedef utility::pointer::shared_ptr< BetaAlphaBetaMotifSet > protocols::fldsgn::topology::BetaAlphaBetaMotifSetOP

DimerPairingCOP

typedef utility::pointer::shared_ptr< DimerPairing const > protocols::fldsgn::topology::DimerPairingCOP

DimerPairingOP

typedef utility::pointer::shared_ptr< DimerPairing > protocols::fldsgn::topology::DimerPairingOP

Helices

typedef utility::vector1< HelixOP > protocols::fldsgn::topology::Helices

HelixCOP

typedef utility::pointer::shared_ptr< Helix const > protocols::fldsgn::topology::HelixCOP

HelixOP

typedef utility::pointer::shared_ptr< Helix > protocols::fldsgn::topology::HelixOP

HelixPairingCOP

typedef utility::pointer::shared_ptr< HelixPairing const > protocols::fldsgn::topology::HelixPairingCOP

HelixPairingOP

typedef utility::pointer::shared_ptr< HelixPairing > protocols::fldsgn::topology::HelixPairingOP

HelixPairings

typedef utility::vector1< HelixPairingOP > protocols::fldsgn::topology::HelixPairings

HelixPairingSetCOP

typedef utility::pointer::shared_ptr< HelixPairingSet const > protocols::fldsgn::topology::HelixPairingSetCOP

HelixPairingSetOP

typedef utility::pointer::shared_ptr< HelixPairingSet > protocols::fldsgn::topology::HelixPairingSetOP

HSSConstIterator

typedef HSSTriplets::const_iterator protocols::fldsgn::topology::HSSConstIterator

HSSIterator

typedef HSSTriplets::iterator protocols::fldsgn::topology::HSSIterator

HSSTripletCOP

typedef utility::pointer::shared_ptr< HSSTriplet const > protocols::fldsgn::topology::HSSTripletCOP

HSSTripletOP

typedef utility::pointer::shared_ptr< HSSTriplet > protocols::fldsgn::topology::HSSTripletOP

HSSTriplets

typedef utility::vector1< HSSTripletOP > protocols::fldsgn::topology::HSSTriplets

HSSTripletSetCOP

typedef utility::pointer::shared_ptr< HSSTripletSet const > protocols::fldsgn::topology::HSSTripletSetCOP

HSSTripletSetOP

typedef utility::pointer::shared_ptr< HSSTripletSet > protocols::fldsgn::topology::HSSTripletSetOP

LoopCOP

typedef utility::pointer::shared_ptr< Loop const > protocols::fldsgn::topology::LoopCOP

LoopOP

typedef utility::pointer::shared_ptr< Loop > protocols::fldsgn::topology::LoopOP

Loops

typedef utility::vector1< LoopOP > protocols::fldsgn::topology::Loops

SheetCOP

typedef utility::pointer::shared_ptr< Sheet const > protocols::fldsgn::topology::SheetCOP

SheetOP

typedef utility::pointer::shared_ptr< Sheet > protocols::fldsgn::topology::SheetOP

Sheets

typedef utility::vector1< SheetOP > protocols::fldsgn::topology::Sheets

SheetSetCOP

typedef utility::pointer::shared_ptr< SheetSet const > protocols::fldsgn::topology::SheetSetCOP

SheetSetOP

typedef utility::pointer::shared_ptr< SheetSet > protocols::fldsgn::topology::SheetSetOP

SS_BaseCOP

typedef utility::pointer::shared_ptr< SS_Base const > protocols::fldsgn::topology::SS_BaseCOP

SS_BaseOP

typedef utility::pointer::shared_ptr< SS_Base > protocols::fldsgn::topology::SS_BaseOP

SS_Info2_COP

typedef utility::pointer::shared_ptr< SS_Info2 const > protocols::fldsgn::topology::SS_Info2_COP

SS_Info2_OP

typedef utility::pointer::shared_ptr< SS_Info2 > protocols::fldsgn::topology::SS_Info2_OP

StrandCOP

typedef utility::pointer::shared_ptr< Strand const > protocols::fldsgn::topology::StrandCOP

StrandOP

typedef utility::pointer::shared_ptr< Strand > protocols::fldsgn::topology::StrandOP

StrandPairingCOP

typedef utility::pointer::shared_ptr< StrandPairing const > protocols::fldsgn::topology::StrandPairingCOP

StrandPairingCOPs

typedef utility::vector1< StrandPairingCOP > protocols::fldsgn::topology::StrandPairingCOPs

StrandPairingOP

typedef utility::pointer::shared_ptr< StrandPairing > protocols::fldsgn::topology::StrandPairingOP

StrandPairings

typedef utility::vector1< StrandPairingOP > protocols::fldsgn::topology::StrandPairings

StrandPairingSetCOP

typedef utility::pointer::shared_ptr< StrandPairingSet const > protocols::fldsgn::topology::StrandPairingSetCOP

StrandPairingSetOP

typedef utility::pointer::shared_ptr< StrandPairingSet > protocols::fldsgn::topology::StrandPairingSetOP

Strands

typedef utility::vector1< StrandOP > protocols::fldsgn::topology::Strands

Enumeration Type Documentation

SheetFoldType

enum protocols::fldsgn::topology::SheetFoldType : char

List of topologies determined by strand pairings.

Enumerator
BABx1
RosI	3strands
RosO
BABx2
Thio
BFr
EFr
CFr
DFr
Rsmn2x2	4strands
Rsmn3x3_Half	rossmann2x2
BABx3	Half structure of Rossmann3x3.
PG_like
Thioredoxin
BAB_CFr
DFr_BAB
BEFr
Fd_like
RFd_like	ferredoxin-like
CDFr	reverse ferredoxin-like
HPN_CFr
DFr_HPN
Flavodoxin	5strands
Ploop2x3
RNAseH	mixture
Top7
Rsmn3x3	6 strands
Ploop3x3
UNFOLD
NO_STRANDS
UNKNOWN
n_fold_types

Function Documentation

calc_delta_sasa()

core::Real protocols::fldsgn::topology::calc_delta_sasa	(	core::pose::Pose const &	pose,
		utility::vector1< protocols::forge::build::Interval >	intervals,
		Real const	pore_radius
	)

calc delta sasa, when a molecule is splited to 2parts.

References core::scoring::calc_per_atom_sasa(), core::pose::initialize_atomid_map(), core::sequence::left, core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().

calc_strand_helix_angle()

core::Real protocols::fldsgn::topology::calc_strand_helix_angle	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::SS_Info2_COP const	ssinfo,
		core::Size const	strand_id1,
		core::Size const	strand_id2,
		core::Size const	helix_id,
		std::string const &	geom_type
	)

References core::sequence::end, core::pose::Pose::residue(), core::io::pose_from_sfr::sgn(), and core::conformation::Residue::xyz().

Referenced by protocols::fldsgn::filters::StrandHelixGeometryFilter::apply().

calc_strand_pairing_set()

protocols::fldsgn::topology::StrandPairingSet protocols::fldsgn::topology::calc_strand_pairing_set	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::SS_Info2_COP const	ssinfo,
		core::Size	minimum_pair_length
	)

convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet

References core::scoring::dssp::StrandPairing::antiparallel(), core::scoring::dssp::StrandPairing::begin1(), protocols::simple_filters::dssp(), core::scoring::dssp::StrandPairing::end1(), protocols::fldsgn::topology::StrandPairingSet::finalize(), core::scoring::dssp::StrandPairing::get_pair(), core::scoring::dssp::StrandPairing::get_pleating(), protocols::fldsgn::topology::StrandPairingSet::push_back(), core::scoring::dssp::StrandPairingSet::size(), core::scoring::dssp::StrandPairingSet::strand_pairing(), and TR().

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_pose(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::SheetTopologyFilter::compute(), protocols::denovo_design::components::find_orientations_and_lengths(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::fldsgn::NcontactsCalculator::recompute(), and protocols::denovo_design::components::reorder_chains().

check_internal_hbonds()

utility::vector1< core::scoring::hbonds::HBond > protocols::fldsgn::topology::check_internal_hbonds	(	core::pose::Pose const &	pose,
		core::Size const	begin,
		core::Size const	end
	)

check kink of helix, return number of loosen hydrogen

References core::scoring::Energies::data(), core::sequence::end, core::pose::Pose::energies(), and core::scoring::EnergiesCacheableDataType::HBOND_SET.

check_kink_helix()

core::Size protocols::fldsgn::topology::check_kink_helix	(	core::pose::Pose const &	pose,
		core::Size const	begin,
		core::Size const	end
	)

check kink of helix, return number of loosen hydrogen

References core::scoring::Energies::data(), core::sequence::end, core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::HBOND_SET, and TR().

Referenced by protocols::fldsgn::filters::HelixKinkFilter::apply().

compare()

bool protocols::fldsgn::topology::compare	(	std::map< core::Size, Real >::const_iterator	a,
		std::map< core::Size, Real >::const_iterator	b
	)

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build_hits_at_all_positions(), protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_helix_cycle(), protocols::motifs::Motif::motif_atom_match_lax(), protocols::motifs::Motif::motif_atom_match_strict(), protocols::antibody::PDBLandmark::operator!=(), protocols::antibody::PDBLandmark::operator==(), protocols::mpi_refinement::Scheduler::read_cmd(), and core::scoring::rna::RNA_TorsionPotential::RNA_TorsionPotential().

compute_bulges()

std::set< core::Size > protocols::fldsgn::topology::compute_bulges	(	core::Size const	strand_begin,
		core::Size const	strand_end,
		utility::vector1< String > const &	abego
	)

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

Referenced by protocols::fldsgn::topology::StrandPairing::redefine_begin_end().

operator<<() [1/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	os,
		TripletID const &	id
	)

operator<<() [2/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const BetaAlphaBetaMotif &	s
	)

IO operator.

IO Operator.

operator<<() [3/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const BetaAlphaBetaMotifSet &	s
	)

operator<<() [4/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const DimerPairing &	dp
	)

operator<<() [5/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const DimerPairings &	dps
	)

operator<<() [6/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const Helix &	hx
	)

operator<<() [7/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const HelixPairing &	hp
	)

return name

return strand pairing

operator<<() [8/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const HelixPairingSet &	s
	)

return helix pairing

return strand pairing

operator<<() [9/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const HSSTriplet &	s
	)

IO Operator.

operator<<() [10/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const HSSTripletSet &	s
	)

IO Operator.

operator<<() [11/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const Loop &	lp
	)

operator<<() [12/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const Sheet &	s
	)

return strand pairing

operator<<() [13/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const SheetSet &	s
	)

return strand pairing

operator<<() [14/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const SS_Info2 &	ssinfo
	)

operator<<() [15/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const Strand &	st
	)

operator<<() [16/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const StrandPairing &	sp
	)

return name

return strand pairing

operator<<() [17/17]

std::ostream& protocols::fldsgn::topology::operator<<	(	std::ostream &	out,
		const StrandPairingSet &	s
	)

output detail of strand pairing set

return strand pairing

pointer_sorter() [1/2]

bool protocols::fldsgn::topology::pointer_sorter	(	DimerPairingCOP const	a,
		DimerPairingCOP const	b
	)

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::fldsgn::topology::StrandPairingSet::finalize(), and protocols::fldsgn::topology::DimerPairings::finalize().

pointer_sorter() [2/2]

bool protocols::fldsgn::topology::pointer_sorter	(	StrandPairingCOP const	a,
		StrandPairingCOP const	b
	)

References core::pose::motif::a(), and protocols::match::upstream::b.

sort_by_length()

bool protocols::fldsgn::topology::sort_by_length	(	protocols::fldsgn::topology::StrandPairingCOP const	a,
		protocols::fldsgn::topology::StrandPairingCOP const	b
	)

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::fldsgn::topology::StrandPairingSet::make_strand_neighbor_two().