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

Function Documentation

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