protocols::fldsgn::topology Namespace Reference

Classes
class	BB_Pos
class	BetaAlphaBetaMotif
class	BetaAlphaBetaMotifSet
class	DimerPairing
class	DimerPairings
class	Helix
class	HelixPairing
class	HelixPairingSet
class	HSSTriplet
class	HSSTripletSet
class	Loop
class	Sheet
class	SheetFoldTypeManager
class	SheetSet
class	SS_Base
class	SS_Info2
class	Strand
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::vector1 < SheetFoldType >	SheetFoldTypes
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

Enumerations
enum	SheetFoldType {   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< Size, Real >::const_iterator a, std::map< 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 &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::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...

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::vector1< SheetFoldType > protocols::fldsgn::topology::SheetFoldTypes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::fldsgn::topology::SheetFoldType

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

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(), left, core::id::AtomID_Map< T >::set(), and core::pose::Pose::total_residue().

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(), core::scoring::dssp::Dssp::strand_pairing_set(), and TR().

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::apply(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), and protocols::fldsgn::NcontactsCalculator::recompute().

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::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), HBOND_SET, and core::scoring::EnergiesCacheableDataType::HBOND_SET.

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::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_SET, HBOND_SET, and TR().

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

bool protocols::fldsgn::topology::compare	(	std::map< Size, Real >::const_iterator	a,
		std::map< 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::normalmode::NormalModeMultifunc::dEddofs_to_dEdvars(), protocols::normalmode::NormalModeMultifunc::dofs_to_vars(), protocols::frag_picker::quota::QuotaConfig::get_fraction(), protocols::frag_picker::quota::QuotaConfig::is_valid_quota_pool_name(), protocols::sparta::GDB::loadGDB(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::md::MDBase::parse_schfile(), protocols::normalmode::NormalMode::prepare_coord(), protocols::mpi_refinement::Scheduler::read_cmd(), and protocols::normalmode::NormalModeMultifunc::vars_to_dofs().

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

IO Operator.

References protocols::fldsgn::topology::HSSTriplet::helix(), protocols::fldsgn::topology::HSSTriplet::strand1(), and protocols::fldsgn::topology::HSSTriplet::strand2().

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

References protocols::fldsgn::topology::DimerPairing::dist(), protocols::fldsgn::topology::DimerPairing::dp(), F, I, protocols::fldsgn::topology::DimerPairing::orient(), protocols::fldsgn::topology::DimerPairing::phi(), protocols::fldsgn::topology::DimerPairing::res1(), protocols::fldsgn::topology::DimerPairing::res2(), protocols::fldsgn::topology::DimerPairing::score(), protocols::fldsgn::topology::DimerPairing::sigma(), protocols::fldsgn::topology::DimerPairing::sign1(), protocols::fldsgn::topology::DimerPairing::sign2(), and protocols::fldsgn::topology::DimerPairing::theta().

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

return strand pairing

References protocols::forge::methods::order(), protocols::fldsgn::topology::Sheet::order_strands(), and protocols::fldsgn::topology::Sheet::orient_strands().

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

IO operator.

IO Operator.

References protocols::fldsgn::topology::BetaAlphaBetaMotif::cross_over(), protocols::fldsgn::topology::BetaAlphaBetaMotif::helix(), protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle_as_string(), protocols::fldsgn::topology::BetaAlphaBetaMotif::hs1_dist(), protocols::fldsgn::topology::BetaAlphaBetaMotif::hs2_dist(), protocols::fldsgn::topology::BetaAlphaBetaMotif::hs_angle(), protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_dist(), protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_elev_angle(), protocols::fldsgn::topology::BetaAlphaBetaMotif::is_lefthanded(), protocols::fldsgn::topology::BetaAlphaBetaMotif::strand1(), and protocols::fldsgn::topology::BetaAlphaBetaMotif::strand2().

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

References protocols::fldsgn::topology::SS_Base::begin(), and protocols::fldsgn::topology::SS_Base::end().

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

return name

return strand pairing

References protocols::fldsgn::topology::HelixPairing::align_angle(), protocols::fldsgn::topology::HelixPairing::cross_angle(), protocols::fldsgn::topology::HelixPairing::dist(), F, and protocols::fldsgn::topology::HelixPairing::name().

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

References I, and LJ.

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

References protocols::fldsgn::topology::SS_Base::begin(), and protocols::fldsgn::topology::SS_Base::end().

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

return name

return strand pairing

References protocols::fldsgn::topology::StrandPairing::begin1(), protocols::fldsgn::topology::StrandPairing::begin2(), protocols::fldsgn::topology::StrandPairing::end1(), protocols::fldsgn::topology::StrandPairing::end2(), and protocols::fldsgn::topology::StrandPairing::name().

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

References protocols::fldsgn::topology::SS_Base::begin(), protocols::fldsgn::topology::SS_Base::end(), and protocols::fldsgn::topology::Loop::type().

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

return helix pairing

return strand pairing

References protocols::fldsgn::topology::HelixPairingSet::helix_pairings(), and protocols::fldsgn::topology::HelixPairingSet::name().

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

IO Operator.

References protocols::fldsgn::topology::HSSTripletSet::hss_triplets().

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

return strand pairing

References protocols::fldsgn::topology::SheetSet::num_sheets(), and protocols::fldsgn::topology::SheetSet::sheet().

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

References protocols::fldsgn::topology::SS_Info2::helices_, and protocols::fldsgn::topology::SS_Info2::strands_.

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

output detail of strand pairing set

return strand pairing

References protocols::fldsgn::topology::StrandPairingSet::name(), and protocols::fldsgn::topology::StrandPairingSet::strand_pairings().

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

References protocols::fldsgn::topology::BetaAlphaBetaMotifSet::bab_motifs().

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

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

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

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

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