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Classes | Typedefs | Functions
protocols::protein_interface_design::filters Namespace Reference

Classes

class  AtomicContactCountFilter
 
class  AtomicContactCountFilterCreator
 
class  AverageDegreeFilter
 
class  AverageDegreeFilterCreator
 
class  BindingStrainFilter
 
class  BindingStrainFilterCreator
 
class  BoltzmannFilter
 
class  BoltzmannFilterCreator
 
class  ClashWithTargetFilter
 
class  ClashWithTargetFilterCreator
 
class  DesignableResiduesFilter
 
class  DesignableResiduesFilterCreator
 
class  DisulfideFilter
 Filters for structures which could form a disulfide bond across the docking interface. More...
 
class  DisulfideFilterCreator
 
class  FilterScanFilter
 
class  FilterScanFilterCreator
 
class  FNatFilter
 
class  FNatFilterCreator
 
class  HbondsToAtomFilter
 returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class More...
 
class  HbondsToAtomFilterCreator
 
class  HbondsToResidueFilter
 returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class More...
 
class  HbondsToResidueFilterCreator
 
class  InterfaceHolesFilter
 
class  InterfaceHolesFilterCreator
 
class  IRmsdFilter
 
class  IRmsdFilterCreator
 
class  LRmsdFilter
 
class  LRmsdFilterCreator
 
class  RelativeSegmentFilter
 returns the residues aligned to a segment on the input pdb to the source pdb More...
 
class  RelativeSegmentFilterCreator
 
class  RmsdFilter
 
class  RmsdFilterCreator
 
class  RmsdSimpleFilter
 
class  RmsdSimpleFilterCreator
 
class  SequenceRecoveryFilter
 
class  SequenceRecoveryFilterCreator
 
class  SpecificResiduesNearInterfaceFilter
 
class  SpecificResiduesNearInterfaceFilterCreator
 
class  SSamountFilter
 
class  SSamountFilterCreator
 
class  StubScoreFilter
 
class  StubScoreFilterCreator
 
class  StubScoreLoopsFilter
 
class  StubScoreLoopsFilterCreator
 
class  Torsion
 
class  TorsionCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AtomicContactCountFilter
AverageDegreeCountFilterOP
 
typedef
utility::pointer::shared_ptr
< AtomicContactCountFilter
const > 
AverageDegreeCountFilterCOP
 
typedef
utility::pointer::shared_ptr
< AverageDegreeFilter
AverageDegreeFilterOP
 
typedef
utility::pointer::shared_ptr
< AverageDegreeFilter const > 
AverageDegreeFilterCOP
 
typedef
utility::pointer::shared_ptr
< BindingStrainFilter
BindingStrainFilterOP
 
typedef
utility::pointer::shared_ptr
< BindingStrainFilter const > 
BindingStrainFilterCOP
 
typedef
utility::pointer::shared_ptr
< BoltzmannFilter
BoltzmannFilterOP
 
typedef
utility::pointer::shared_ptr
< BoltzmannFilter const > 
BoltzmannFilterCOP
 
typedef
utility::pointer::shared_ptr
< DesignableResiduesFilter
DesignableResiduesFilterOP
 
typedef
utility::pointer::shared_ptr
< DesignableResiduesFilter
const > 
DesignableResiduesFilterCOP
 
typedef
utility::pointer::shared_ptr
< FilterScanFilter
FilterScanFilterOP
 
typedef
utility::pointer::shared_ptr
< FilterScanFilter const > 
FilterScanFilterCOP
 
typedef
utility::pointer::shared_ptr
< HbondsToResidueFilter
HbondsToResidueFilterOP
 
typedef
utility::pointer::shared_ptr
< HbondsToResidueFilter const > 
HbondsToResidueFilterCOP
 
typedef utility::vector1
< HbondsToResidueFilterOP
HbondsToResidueFilterOPs
 
typedef utility::vector1
< HbondsToResidueFilterCOP
HbondsToResidueFilterCOPs
 
typedef
utility::pointer::shared_ptr
< RelativeSegment > 
RelativeSegmentOP
 
typedef
utility::pointer::shared_ptr
< RelativeSegment const > 
RelativeSegmentCOP
 
typedef
utility::pointer::shared_ptr
< SequenceRecoveryFilter
SequenceRecoveryFilterOP
 
typedef
utility::pointer::shared_ptr
< SequenceRecoveryFilter const > 
SequenceRecoveryFilterCOP
 
typedef
utility::pointer::shared_ptr
< SpecificResiduesNearInterfaceFilter
SpecificResiduesNearInterfaceFilterOP
 
typedef
utility::pointer::shared_ptr
< SpecificResiduesNearInterfaceFilter
const > 
SpecificResiduesNearInterfaceFilterCOP
 
typedef
utility::pointer::shared_ptr
< StubScoreFilter
StubScoreFilterOP
 
typedef
utility::pointer::shared_ptr
< StubScoreFilter const > 
StubScoreFilterCOP
 
typedef
utility::pointer::shared_ptr
< StubScoreLoopsFilter
StubScoreLoopsFilterOP
 
typedef
utility::pointer::shared_ptr
< StubScoreLoopsFilter const > 
StubScoreLoopsFilterCOP
 
typedef
utility::pointer::shared_ptr
< Torsion
TorsionOP
 
typedef
utility::pointer::shared_ptr
< Torsion const > 
TorsionCOP
 

Functions

static basic::Tracer TR ("protocols.protein_interface_design.filters.AtomicContactCountFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.AverageDegreeFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.BindingStrainFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.BoltzmannFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.ClashWithTargetFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.DesignableResiduesFilter")
 
static basic::Tracer TR_pymol ("protocols.protein_interface_design.filters.DesignableResiduesFilter_pymol")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.DisulfideFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.FilterScanFilter")
 
static basic::Tracer TR_residue_scan ("ResidueScan")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.FNatFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.HbondsToAtomFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.HbondsToResidueFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.InterfaceHolesFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.IRmsdFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.LRmsdFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.RelativeSegmentFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.RmsdFilter")
 
core::Real atom_distance (core::conformation::Residue const &r1, std::string const &a1, core::conformation::Residue const &r2, std::string const &a2)
 
core::Real res_rmsd (utility::vector1< core::Size > const pose_res_for_rmsd, utility::vector1< core::Size > const template_res_for_rmsd, core::pose::Pose const &copy_pose, core::pose::Pose const &template_pose)
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
Ca_coords (core::pose::Pose const &pose, utility::vector1< core::Size > const &positions)
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.RmsdSimpleFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.SequenceRecoveryFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.SSamountFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.StubScoreFilter")
 
static basic::Tracer tr ("protocols.protein_interface_design.filters.StubScoreLoopsFilter")
 
static basic::Tracer TR ("protocols.protein_interface_design.filters.Torsion")
 
static basic::Tracer TR_database ("protocols.protein_interface_design.filters.Torsion_database")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< RelativeSegment const > protocols::protein_interface_design::filters::RelativeSegmentCOP
typedef utility::pointer::shared_ptr< RelativeSegment > protocols::protein_interface_design::filters::RelativeSegmentOP
typedef utility::pointer::shared_ptr< Torsion const > protocols::protein_interface_design::filters::TorsionCOP
typedef utility::pointer::shared_ptr< Torsion > protocols::protein_interface_design::filters::TorsionOP

Function Documentation

core::Real protocols::protein_interface_design::filters::atom_distance ( core::conformation::Residue const &  r1,
std::string const &  a1,
core::conformation::Residue const &  r2,
std::string const &  a2 
)

References core::conformation::Residue::xyz().

Referenced by res_rmsd().

utility::vector1< numeric::xyzVector< core::Real > > protocols::protein_interface_design::filters::Ca_coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  positions 
)
core::Real protocols::protein_interface_design::filters::res_rmsd ( utility::vector1< core::Size > const  pose_res_for_rmsd,
utility::vector1< core::Size > const  template_res_for_rmsd,
core::pose::Pose const &  copy_pose,
core::pose::Pose const &  template_pose 
)
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RelativeSegmentFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.BoltzmannFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.AverageDegreeFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.Torsion"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.InterfaceHolesFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.DesignableResiduesFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SequenceRecoveryFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::tr ( "protocols.protein_interface_design.filters.StubScoreLoopsFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.BindingStrainFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.StubScoreFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.AtomicContactCountFilter"  )
static

Referenced by protocols::protein_interface_design::filters::ClashWithTargetFilter::apply(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::protein_interface_design::filters::InterfaceHolesFilter::apply(), protocols::protein_interface_design::filters::RmsdFilter::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply(), protocols::protein_interface_design::filters::LRmsdFilter::apply(), protocols::protein_interface_design::filters::IRmsdFilter::apply(), protocols::protein_interface_design::filters::FNatFilter::apply(), protocols::protein_interface_design::filters::StubScoreFilter::apply(), protocols::protein_interface_design::filters::RmsdSimpleFilter::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::filters::SSamountFilter::apply(), protocols::protein_interface_design::filters::DisulfideFilter::apply(), protocols::protein_interface_design::filters::HbondsToResidueFilter::apply(), protocols::protein_interface_design::filters::BoltzmannFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::protein_interface_design::filters::StubScoreFilter::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::protein_interface_design::filters::RmsdSimpleFilter::compute(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::protein_interface_design::filters::ClashWithTargetFilter::parse_my_tag(), protocols::protein_interface_design::filters::RelativeSegmentFilter::parse_my_tag(), protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::StubScoreFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::InterfaceHolesFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::SSamountFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdSimpleFilter::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::single_substitution(), and protocols::protein_interface_design::filters::BindingStrainFilter::unbind().

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.FilterScanFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.DisulfideFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.LRmsdFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.FNatFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.IRmsdFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.ClashWithTargetFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.HbondsToAtomFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.HbondsToResidueFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RmsdSimpleFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SSamountFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RmsdFilter"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR_database ( "protocols.protein_interface_design.filters.Torsion_database"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR_pymol ( "protocols.protein_interface_design.filters.DesignableResiduesFilter_pymol"  )
static
static basic::Tracer protocols::protein_interface_design::filters::TR_residue_scan ( "ResidueScan"  )
static