protocols::denovo_design::architects Namespace Reference

Classes
class	BetaSheetArchitect
	Architect that creates a beta sheet. More...
class	BetaSheetArchitectCreator
class	BlueprintArchitect
	Designs a structure using a Blueprint file. More...
class	BlueprintArchitectCreator
class	CompoundArchitect
	Architect that creates a StructureData using multiple architects. More...
class	CompoundArchitectCreator
class	DeNovoArchitect
	for planning ideal pieces of structures More...
class	DeNovoArchitectCreator
class	DeNovoArchitectFactory
	Creates DeNovo architects. More...
class	EXCN_PreFilterFailed
class	HelixArchitect
	Architect for helices. More...
class	HelixArchitectCreator
class	MotifArchitect
	for planning arbitrary motifs More...
class	MotifArchitectCreator
class	PoseArchitect
	Design segments based on a pose. More...
class	PoseArchitectCreator
struct	SecStructInfo
class	StrandArchitect
	Architect that creates a beta strand. More...
class	StrandArchitectCreator
class	StructureArchitect
	Designs topologies. More...

Typedefs
typedef utility::pointer::shared_ptr < BetaSheetArchitect >	BetaSheetArchitectOP
typedef utility::pointer::shared_ptr < BetaSheetArchitect const >	BetaSheetArchitectCOP
typedef utility::pointer::shared_ptr < BlueprintArchitect >	BlueprintArchitectOP
typedef utility::pointer::shared_ptr < BlueprintArchitect const >	BlueprintArchitectCOP
typedef utility::pointer::shared_ptr < CompoundArchitect >	CompoundArchitectOP
typedef utility::pointer::shared_ptr < CompoundArchitect const >	CompoundArchitectCOP
typedef utility::pointer::shared_ptr < DeNovoArchitect >	DeNovoArchitectOP
typedef utility::pointer::shared_ptr < DeNovoArchitect const >	DeNovoArchitectCOP
typedef utility::vector1 < DeNovoArchitectOP >	DeNovoArchitectOPs
typedef utility::vector1 < DeNovoArchitectCOP >	DeNovoArchitectCOPs
typedef utility::pointer::shared_ptr < DeNovoArchitectCreator >	DeNovoArchitectCreatorOP
typedef utility::pointer::shared_ptr < DeNovoArchitectCreator const >	DeNovoArchitectCreatorCOP
typedef utility::pointer::shared_ptr < DeNovoArchitectFactory >	DeNovoArchitectFactoryOP
typedef utility::pointer::shared_ptr < DeNovoArchitectFactory const >	DeNovoArchitectFactoryCOP
typedef utility::pointer::shared_ptr < HelixArchitect >	HelixArchitectOP
typedef utility::pointer::shared_ptr < HelixArchitect const >	HelixArchitectCOP
typedef utility::pointer::shared_ptr < MotifArchitect >	MotifArchitectOP
typedef utility::pointer::shared_ptr < MotifArchitect const >	MotifArchitectCOP
typedef utility::vector1 < MotifArchitectOP >	MotifArchitectOPs
typedef utility::vector1 < MotifArchitectCOP >	MotifArchitectCOPs
typedef utility::pointer::shared_ptr < PoseArchitect >	PoseArchitectOP
typedef utility::pointer::shared_ptr < PoseArchitect const >	PoseArchitectCOP
typedef utility::pointer::shared_ptr < StrandArchitect >	StrandArchitectOP
typedef utility::pointer::shared_ptr < StrandArchitect const >	StrandArchitectCOP
typedef utility::vector1 < core::Size >	StrandExtensions
typedef components::SegmentResid	SegmentResid
typedef utility::vector1 < SegmentResid >	StrandBulges
typedef utility::vector1 < StrandBulges >	AllowedStrandBulges
typedef utility::vector1 < SegmentResid >	StrandExtended
typedef utility::vector1 < StrandExtended >	AllowedStrandExtended
typedef utility::pointer::shared_ptr < StructureArchitect >	StructureArchitectOP
typedef utility::pointer::shared_ptr < StructureArchitect const >	StructureArchitectCOP
typedef utility::vector1 < core::Size >	Lengths
typedef utility::vector1 < std::string >	Abego

Functions
BetaSheetArchitect::PairingsInfoVector	fill_orientation_info (BetaSheetArchitect::PairingsInfoVector const &by_strand)
BetaSheetArchitect::ResidueVector	bulge_residues (components::StructureData const &sd, StrandArchitect const &strand)
void	invalid_hhpair (std::string const &hhpair_str)
SecStructInfo	generate_secstruct_for_length (char const ss_char, std::string const &abego, core::Size const len)
	Creates a "len"-residue long SecStructInfo object with SS and ABEGO as specified here. More...
DeNovoArchitectCOP	retrieve_denovo_architect (std::string const &architect_name, basic::datacache::DataMap &data)
void	store_denovo_architect (DeNovoArchitectOP architect, basic::datacache::DataMap &data)

Typedef Documentation

typedef utility::vector1< std::string > protocols::denovo_design::architects::Abego

typedef utility::vector1< StrandBulges > protocols::denovo_design::architects::AllowedStrandBulges

typedef utility::vector1< StrandExtended > protocols::denovo_design::architects::AllowedStrandExtended

typedef utility::pointer::shared_ptr< BetaSheetArchitect const > protocols::denovo_design::architects::BetaSheetArchitectCOP

typedef utility::pointer::shared_ptr< BetaSheetArchitect > protocols::denovo_design::architects::BetaSheetArchitectOP

typedef utility::pointer::shared_ptr< BlueprintArchitect const > protocols::denovo_design::architects::BlueprintArchitectCOP

typedef utility::pointer::shared_ptr< BlueprintArchitect > protocols::denovo_design::architects::BlueprintArchitectOP

typedef utility::pointer::shared_ptr< CompoundArchitect const > protocols::denovo_design::architects::CompoundArchitectCOP

typedef utility::pointer::shared_ptr< CompoundArchitect > protocols::denovo_design::architects::CompoundArchitectOP

typedef utility::pointer::shared_ptr< DeNovoArchitect const > protocols::denovo_design::architects::DeNovoArchitectCOP

typedef utility::vector1< DeNovoArchitectCOP > protocols::denovo_design::architects::DeNovoArchitectCOPs

typedef utility::pointer::shared_ptr< DeNovoArchitectCreator const > protocols::denovo_design::architects::DeNovoArchitectCreatorCOP

typedef utility::pointer::shared_ptr< DeNovoArchitectCreator > protocols::denovo_design::architects::DeNovoArchitectCreatorOP

typedef utility::pointer::shared_ptr< DeNovoArchitectFactory const > protocols::denovo_design::architects::DeNovoArchitectFactoryCOP

typedef utility::pointer::shared_ptr< DeNovoArchitectFactory > protocols::denovo_design::architects::DeNovoArchitectFactoryOP

typedef utility::pointer::shared_ptr< DeNovoArchitect > protocols::denovo_design::architects::DeNovoArchitectOP

typedef utility::vector1< DeNovoArchitectOP > protocols::denovo_design::architects::DeNovoArchitectOPs

typedef utility::pointer::shared_ptr< HelixArchitect const > protocols::denovo_design::architects::HelixArchitectCOP

typedef utility::pointer::shared_ptr< HelixArchitect > protocols::denovo_design::architects::HelixArchitectOP

typedef utility::vector1< core::Size > protocols::denovo_design::architects::Lengths

typedef utility::pointer::shared_ptr< MotifArchitect const > protocols::denovo_design::architects::MotifArchitectCOP

typedef utility::vector1< MotifArchitectCOP > protocols::denovo_design::architects::MotifArchitectCOPs

typedef utility::pointer::shared_ptr< MotifArchitect > protocols::denovo_design::architects::MotifArchitectOP

typedef utility::vector1< MotifArchitectOP > protocols::denovo_design::architects::MotifArchitectOPs

typedef utility::pointer::shared_ptr< PoseArchitect const > protocols::denovo_design::architects::PoseArchitectCOP

typedef utility::pointer::shared_ptr< PoseArchitect > protocols::denovo_design::architects::PoseArchitectOP

typedef components::SegmentResid protocols::denovo_design::architects::SegmentResid

typedef utility::pointer::shared_ptr< StrandArchitect const > protocols::denovo_design::architects::StrandArchitectCOP

typedef utility::pointer::shared_ptr< StrandArchitect > protocols::denovo_design::architects::StrandArchitectOP

typedef utility::vector1< SegmentResid > protocols::denovo_design::architects::StrandBulges

typedef utility::vector1< SegmentResid > protocols::denovo_design::architects::StrandExtended

typedef utility::vector1< core::Size > protocols::denovo_design::architects::StrandExtensions

typedef utility::pointer::shared_ptr< StructureArchitect const > protocols::denovo_design::architects::StructureArchitectCOP

typedef utility::pointer::shared_ptr< StructureArchitect > protocols::denovo_design::architects::StructureArchitectOP

Function Documentation

BetaSheetArchitect::ResidueVector protocols::denovo_design::architects::bulge_residues	(	components::StructureData const &	sd,
		StrandArchitect const &	strand
	)

References protocols::match::upstream::b, protocols::denovo_design::architects::StructureArchitect::id(), core::select::resids(), protocols::denovo_design::architects::StrandArchitect::retrieve_bulges(), and protocols::denovo_design::components::StructureData::segment().

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::check_permutation().

BetaSheetArchitect::PairingsInfoVector protocols::denovo_design::architects::fill_orientation_info

(

BetaSheetArchitect::PairingsInfoVector const &

by_strand

)

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::add_pairings().

SecStructInfo protocols::denovo_design::architects::generate_secstruct_for_length	(	char const	ss_char,
		std::string const &	abego,
		core::Size const	len
	)

Creates a "len"-residue long SecStructInfo object with SS and ABEGO as specified here.

References protocols::denovo_design::architects::SecStructInfo::abego, and protocols::denovo_design::architects::SecStructInfo::ss.

void protocols::denovo_design::architects::invalid_hhpair

(

std::string const &

hhpair_str

)

Referenced by protocols::denovo_design::architects::BlueprintArchitect::get_helix_pairings().

DeNovoArchitectCOP protocols::denovo_design::architects::retrieve_denovo_architect	(	std::string const &	architect_name,
		basic::datacache::DataMap &	data
	)

References protocols::denovo_design::architects::DeNovoArchitect::DATA_MAP_NAME.

void protocols::denovo_design::architects::store_denovo_architect	(	DeNovoArchitectOP	architect,
		basic::datacache::DataMap &	data
	)

References protocols::denovo_design::architects::DeNovoArchitect::DATA_MAP_NAME.

Referenced by protocols::denovo_design::architects::DeNovoArchitectFactory::create_from_tag().