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Classes | Typedefs | Functions
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< CoreDunbrackFilterCoreDunbrackFilterOP
 
typedef utility::pointer::shared_ptr< CoreDunbrackFilter const > CoreDunbrackFilterCOP
 
typedef utility::pointer::shared_ptr< FragQualFilterFragQualFilterOP
 
typedef utility::pointer::shared_ptr< FragQualFilter const > FragQualFilterCOP
 
typedef utility::pointer::shared_ptr< HelixBendFilterHelixBendFilterOP
 
typedef utility::pointer::shared_ptr< HelixBendFilter const > HelixBendFilterCOP
 
typedef utility::pointer::shared_ptr< HelixKinkFilterHelixKinkFilterOP
 
typedef utility::pointer::shared_ptr< HelixKinkFilter const > HelixKinkFilterCOP
 
typedef utility::pointer::shared_ptr< HelixPairingFilterHelixPairingFilterOP
 
typedef utility::pointer::shared_ptr< HelixPairingFilter const > HelixPairingFilterCOP
 
typedef utility::pointer::shared_ptr< HSSTripletFilterHSSTripletFilterOP
 
typedef utility::pointer::shared_ptr< HSSTripletFilter const > HSSTripletFilterCOP
 
typedef utility::pointer::shared_ptr< InterlockingAromaFilterInterlockingAromaFilterOP
 
typedef utility::pointer::shared_ptr< InterlockingAromaFilter const > InterlockingAromaFilterCOP
 
typedef utility::pointer::shared_ptr< NcontactsFilterNcontactsFilterOP
 
typedef utility::pointer::shared_ptr< NcontactsFilter const > NcontactsFilterCOP
 
typedef utility::pointer::shared_ptr< ParallelBetaPairingPreferenceFilterParallelBetaPairingPreferenceFilterOP
 
typedef utility::pointer::shared_ptr< ParallelBetaPairingPreferenceFilter const > ParallelBetaPairingPreferenceFilterCOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureCountFilterSecondaryStructureCountFilterOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureCountFilter const > SecondaryStructureCountFilterCOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureFilterSecondaryStructureFilterOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureFilter const > SecondaryStructureFilterCOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureHasResidueFilterSecondaryStructureHasResidueFilterOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureHasResidueFilter const > SecondaryStructureHasResidueFilterCOP
 
typedef utility::pointer::shared_ptr< SheetTopologyFilterSheetTopologyFilterOP
 
typedef utility::pointer::shared_ptr< SheetTopologyFilter const > SheetTopologyFilterCOP
 
typedef utility::pointer::shared_ptr< StrandCurvatureByLevelsStrandCurvatureByLevelsOP
 
typedef utility::pointer::shared_ptr< StrandCurvatureByLevels const > StrandCurvatureByLevelsCOP
 
typedef utility::pointer::shared_ptr< StrandHelixGeometryFilterStrandHelixGeometryFilterOP
 
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

◆ CoreDunbrackFilterCOP

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

◆ CoreDunbrackFilterOP

◆ FragQualFilterCOP

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

◆ FragQualFilterOP

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

◆ HelixBendFilterCOP

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

◆ HelixBendFilterOP

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

◆ HelixKinkFilterCOP

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

◆ HelixKinkFilterOP

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

◆ HelixPairingFilterCOP

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

◆ HelixPairingFilterOP

◆ HSSTripletFilterCOP

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

◆ HSSTripletFilterOP

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

◆ InterlockingAromaFilterCOP

◆ InterlockingAromaFilterOP

◆ NcontactsFilterCOP

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

◆ NcontactsFilterOP

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

◆ ParallelBetaPairingPreferenceFilterCOP

◆ ParallelBetaPairingPreferenceFilterOP

◆ SecondaryStructureCountFilterCOP

◆ SecondaryStructureCountFilterOP

◆ SecondaryStructureFilterCOP

◆ SecondaryStructureFilterOP

◆ SecondaryStructureHasResidueFilterCOP

◆ SecondaryStructureHasResidueFilterOP

◆ SheetTopologyFilterCOP

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

◆ SheetTopologyFilterOP

◆ StrandCurvatureByLevelsCOP

◆ StrandCurvatureByLevelsOP

◆ StrandHelixGeometryFilterCOP

◆ StrandHelixGeometryFilterOP

Function Documentation

◆ compute_max_strand()

core::Size protocols::fldsgn::filters::compute_max_strand ( std::string const &  sheet_topology)

◆ find_pairing()

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().

◆ find_pairing_idx()

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().

◆ remove_register_shift_single_pair()

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().

◆ 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().