protocols::fldsgn::filters Namespace Reference

Classes
class	CoreDunbrackFilter
class	CoreDunbrackFilterCreator
class	FragQualFilter
class	FragQualFilterCreator
class	HelixBendFilter
	Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry. More...
class	HelixBendFilterCreator
class	HelixKinkFilter
class	HelixKinkFilterCreator
class	HelixPairingFilter
class	HelixPairingFilterCreator
class	HSSTripletFilter
class	HSSTripletFilterCreator
class	InterlockingAromaFilter
class	InterlockingAromaFilterCreator
class	NcontactsFilter
class	NcontactsFilterCreator
class	ParallelBetaPairingPreferenceFilter
class	ParallelBetaPairingPreferenceFilterCreator
class	SecondaryStructureCountFilter
class	SecondaryStructureCountFilterCreator
class	SecondaryStructureFilter
class	SecondaryStructureFilterCreator
class	SecondaryStructureHasResidueFilter
class	SecondaryStructureHasResidueFilterCreator
class	SheetTopologyFilter
class	SheetTopologyFilterCreator
class	StrandCurvatureByLevels
	Newer version of filter used in Marcos & Basanta et al. 2017. More...
class	StrandCurvatureByLevelsCreator
class	StrandHelixGeometryFilter
	Another filter used in Marcos & Basanta et al. 2017 that needs to be updated. More...
class	StrandHelixGeometryFilterCreator

Typedefs
typedef utility::pointer::shared_ptr < CoreDunbrackFilter >	CoreDunbrackFilterOP
typedef utility::pointer::shared_ptr < CoreDunbrackFilter const >	CoreDunbrackFilterCOP
typedef utility::pointer::shared_ptr < FragQualFilter >	FragQualFilterOP
typedef utility::pointer::shared_ptr < FragQualFilter const >	FragQualFilterCOP
typedef utility::pointer::shared_ptr < HelixBendFilter >	HelixBendFilterOP
typedef utility::pointer::shared_ptr < HelixBendFilter const >	HelixBendFilterCOP
typedef utility::pointer::shared_ptr < HelixKinkFilter >	HelixKinkFilterOP
typedef utility::pointer::shared_ptr < HelixKinkFilter const >	HelixKinkFilterCOP
typedef utility::pointer::shared_ptr < HelixPairingFilter >	HelixPairingFilterOP
typedef utility::pointer::shared_ptr < HelixPairingFilter const >	HelixPairingFilterCOP
typedef utility::pointer::shared_ptr < HSSTripletFilter >	HSSTripletFilterOP
typedef utility::pointer::shared_ptr < HSSTripletFilter const >	HSSTripletFilterCOP
typedef utility::pointer::shared_ptr < InterlockingAromaFilter >	InterlockingAromaFilterOP
typedef utility::pointer::shared_ptr < InterlockingAromaFilter const >	InterlockingAromaFilterCOP
typedef utility::pointer::shared_ptr < NcontactsFilter >	NcontactsFilterOP
typedef utility::pointer::shared_ptr < NcontactsFilter const >	NcontactsFilterCOP
typedef utility::pointer::shared_ptr < ParallelBetaPairingPreferenceFilter >	ParallelBetaPairingPreferenceFilterOP
typedef utility::pointer::shared_ptr < ParallelBetaPairingPreferenceFilter const >	ParallelBetaPairingPreferenceFilterCOP
typedef utility::pointer::shared_ptr < SecondaryStructureCountFilter >	SecondaryStructureCountFilterOP
typedef utility::pointer::shared_ptr < SecondaryStructureCountFilter const >	SecondaryStructureCountFilterCOP
typedef utility::pointer::shared_ptr < SecondaryStructureFilter >	SecondaryStructureFilterOP
typedef utility::pointer::shared_ptr < SecondaryStructureFilter const >	SecondaryStructureFilterCOP
typedef utility::pointer::shared_ptr < SecondaryStructureHasResidueFilter >	SecondaryStructureHasResidueFilterOP
typedef utility::pointer::shared_ptr < SecondaryStructureHasResidueFilter const >	SecondaryStructureHasResidueFilterCOP
typedef utility::pointer::shared_ptr < SheetTopologyFilter >	SheetTopologyFilterOP
typedef utility::pointer::shared_ptr < SheetTopologyFilter const >	SheetTopologyFilterCOP
typedef utility::pointer::shared_ptr < StrandCurvatureByLevels >	StrandCurvatureByLevelsOP
typedef utility::pointer::shared_ptr < StrandCurvatureByLevels const >	StrandCurvatureByLevelsCOP
typedef utility::pointer::shared_ptr < StrandHelixGeometryFilter >	StrandHelixGeometryFilterOP
typedef utility::pointer::shared_ptr < StrandHelixGeometryFilter const >	StrandHelixGeometryFilterCOP

Functions
core::Size	compute_max_strand (std::string const &sheet_topology)
std::string	remove_register_shift_single_pair (std::string const &pair_str)
	helper function for replacing register shift of a pair with 99 More...
std::string	remove_register_shifts (std::string const &pair_str)
	helper function for replacing register shift of all pairs with 99 More...
topology::StrandPairingOP	find_pairing (topology::StrandPairingSet &spairset, core::Size const s1, core::Size const s2)
	Searches the StrandPairingSet for a pairing containing s1 and s2. Returns OP to it. More...
core::Size	find_pairing_idx (topology::StrandPairingSet &spairset, core::Size const s1, core::Size const s2)
	Searches the StrandPairingSet for a pairing containing s1 and s2. Returns its 1-based index. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< CoreDunbrackFilter const > protocols::fldsgn::filters::CoreDunbrackFilterCOP

typedef utility::pointer::shared_ptr< CoreDunbrackFilter > protocols::fldsgn::filters::CoreDunbrackFilterOP

typedef utility::pointer::shared_ptr< FragQualFilter const > protocols::fldsgn::filters::FragQualFilterCOP

typedef utility::pointer::shared_ptr< FragQualFilter > protocols::fldsgn::filters::FragQualFilterOP

typedef utility::pointer::shared_ptr< HelixBendFilter const > protocols::fldsgn::filters::HelixBendFilterCOP

typedef utility::pointer::shared_ptr< HelixBendFilter > protocols::fldsgn::filters::HelixBendFilterOP

typedef utility::pointer::shared_ptr< HelixKinkFilter const > protocols::fldsgn::filters::HelixKinkFilterCOP

typedef utility::pointer::shared_ptr< HelixKinkFilter > protocols::fldsgn::filters::HelixKinkFilterOP

typedef utility::pointer::shared_ptr< HelixPairingFilter const > protocols::fldsgn::filters::HelixPairingFilterCOP

typedef utility::pointer::shared_ptr< HelixPairingFilter > protocols::fldsgn::filters::HelixPairingFilterOP

typedef utility::pointer::shared_ptr< HSSTripletFilter const > protocols::fldsgn::filters::HSSTripletFilterCOP

typedef utility::pointer::shared_ptr< HSSTripletFilter > protocols::fldsgn::filters::HSSTripletFilterOP

typedef utility::pointer::shared_ptr< InterlockingAromaFilter const > protocols::fldsgn::filters::InterlockingAromaFilterCOP

typedef utility::pointer::shared_ptr< InterlockingAromaFilter > protocols::fldsgn::filters::InterlockingAromaFilterOP

typedef utility::pointer::shared_ptr< NcontactsFilter const > protocols::fldsgn::filters::NcontactsFilterCOP

typedef utility::pointer::shared_ptr< NcontactsFilter > protocols::fldsgn::filters::NcontactsFilterOP

typedef utility::pointer::shared_ptr< ParallelBetaPairingPreferenceFilter const > protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCOP

typedef utility::pointer::shared_ptr< ParallelBetaPairingPreferenceFilter > protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterOP

typedef utility::pointer::shared_ptr< SecondaryStructureCountFilter const > protocols::fldsgn::filters::SecondaryStructureCountFilterCOP

typedef utility::pointer::shared_ptr< SecondaryStructureCountFilter > protocols::fldsgn::filters::SecondaryStructureCountFilterOP

typedef utility::pointer::shared_ptr< SecondaryStructureFilter const > protocols::fldsgn::filters::SecondaryStructureFilterCOP

typedef utility::pointer::shared_ptr< SecondaryStructureFilter > protocols::fldsgn::filters::SecondaryStructureFilterOP

typedef utility::pointer::shared_ptr< SecondaryStructureHasResidueFilter const > protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCOP

typedef utility::pointer::shared_ptr< SecondaryStructureHasResidueFilter > protocols::fldsgn::filters::SecondaryStructureHasResidueFilterOP

typedef utility::pointer::shared_ptr< SheetTopologyFilter const > protocols::fldsgn::filters::SheetTopologyFilterCOP

typedef utility::pointer::shared_ptr< SheetTopologyFilter > protocols::fldsgn::filters::SheetTopologyFilterOP

typedef utility::pointer::shared_ptr< StrandCurvatureByLevels const > protocols::fldsgn::filters::StrandCurvatureByLevelsCOP

typedef utility::pointer::shared_ptr< StrandCurvatureByLevels > protocols::fldsgn::filters::StrandCurvatureByLevelsOP

typedef utility::pointer::shared_ptr< StrandHelixGeometryFilter const > protocols::fldsgn::filters::StrandHelixGeometryFilterCOP

typedef utility::pointer::shared_ptr< StrandHelixGeometryFilter > protocols::fldsgn::filters::StrandHelixGeometryFilterOP

Function Documentation

core::Size protocols::fldsgn::filters::compute_max_strand

(

std::string const &

sheet_topology

)

References core::scoring::pair, protocols::loops::loop_closure::ccd::strand, and tr().

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute().

topology::StrandPairingOP protocols::fldsgn::filters::find_pairing	(	topology::StrandPairingSet &	spairset,
		core::Size const	s1,
		core::Size const	s2
	)

Searches the StrandPairingSet for a pairing containing s1 and s2. Returns OP to it.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::replace_register_shifts().

core::Size protocols::fldsgn::filters::find_pairing_idx	(	topology::StrandPairingSet &	spairset,
		core::Size const	s1,
		core::Size const	s2
	)

Searches the StrandPairingSet for a pairing containing s1 and s2. Returns its 1-based index.

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

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute().

std::string protocols::fldsgn::filters::remove_register_shift_single_pair

(

std::string const &

pair_str

)

helper function for replacing register shift of a pair with 99

Referenced by remove_register_shifts().

std::string protocols::fldsgn::filters::remove_register_shifts

(

std::string const &

pair_str

)

helper function for replacing register shift of all pairs with 99

References core::scoring::pair, and remove_register_shift_single_pair().

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute().