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

AverageDegreeCountFilterCOP

typedef utility::pointer::shared_ptr< AtomicContactCountFilter const > protocols::protein_interface_design::filters::AverageDegreeCountFilterCOP

AverageDegreeCountFilterOP

typedef utility::pointer::shared_ptr< AtomicContactCountFilter > protocols::protein_interface_design::filters::AverageDegreeCountFilterOP

AverageDegreeFilterCOP

typedef utility::pointer::shared_ptr< AverageDegreeFilter const > protocols::protein_interface_design::filters::AverageDegreeFilterCOP

AverageDegreeFilterOP

typedef utility::pointer::shared_ptr< AverageDegreeFilter > protocols::protein_interface_design::filters::AverageDegreeFilterOP

BindingStrainFilterCOP

typedef utility::pointer::shared_ptr< BindingStrainFilter const > protocols::protein_interface_design::filters::BindingStrainFilterCOP

BindingStrainFilterOP

typedef utility::pointer::shared_ptr< BindingStrainFilter > protocols::protein_interface_design::filters::BindingStrainFilterOP

BoltzmannFilterCOP

typedef utility::pointer::shared_ptr< BoltzmannFilter const > protocols::protein_interface_design::filters::BoltzmannFilterCOP

BoltzmannFilterOP

typedef utility::pointer::shared_ptr< BoltzmannFilter > protocols::protein_interface_design::filters::BoltzmannFilterOP

DesignableResiduesFilterCOP

typedef utility::pointer::shared_ptr< DesignableResiduesFilter const > protocols::protein_interface_design::filters::DesignableResiduesFilterCOP

DesignableResiduesFilterOP

typedef utility::pointer::shared_ptr< DesignableResiduesFilter > protocols::protein_interface_design::filters::DesignableResiduesFilterOP

FilterScanFilterCOP

typedef utility::pointer::shared_ptr< FilterScanFilter const > protocols::protein_interface_design::filters::FilterScanFilterCOP

FilterScanFilterOP

typedef utility::pointer::shared_ptr< FilterScanFilter > protocols::protein_interface_design::filters::FilterScanFilterOP

HbondsToResidueFilterCOP

typedef utility::pointer::shared_ptr< HbondsToResidueFilter const > protocols::protein_interface_design::filters::HbondsToResidueFilterCOP

HbondsToResidueFilterCOPs

typedef utility::vector1<HbondsToResidueFilterCOP> protocols::protein_interface_design::filters::HbondsToResidueFilterCOPs

HbondsToResidueFilterOP

typedef utility::pointer::shared_ptr< HbondsToResidueFilter > protocols::protein_interface_design::filters::HbondsToResidueFilterOP

HbondsToResidueFilterOPs

typedef utility::vector1<HbondsToResidueFilterOP> protocols::protein_interface_design::filters::HbondsToResidueFilterOPs

RelativeSegmentCOP

typedef utility::pointer::shared_ptr< RelativeSegment const > protocols::protein_interface_design::filters::RelativeSegmentCOP

RelativeSegmentOP

typedef utility::pointer::shared_ptr< RelativeSegment > protocols::protein_interface_design::filters::RelativeSegmentOP

SequenceRecoveryFilterCOP

typedef utility::pointer::shared_ptr< SequenceRecoveryFilter const > protocols::protein_interface_design::filters::SequenceRecoveryFilterCOP

SequenceRecoveryFilterOP

typedef utility::pointer::shared_ptr< SequenceRecoveryFilter > protocols::protein_interface_design::filters::SequenceRecoveryFilterOP

SpecificResiduesNearInterfaceFilterCOP

typedef utility::pointer::shared_ptr< SpecificResiduesNearInterfaceFilter const > protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCOP

SpecificResiduesNearInterfaceFilterOP

typedef utility::pointer::shared_ptr< SpecificResiduesNearInterfaceFilter > protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterOP

StubScoreFilterCOP

typedef utility::pointer::shared_ptr< StubScoreFilter const > protocols::protein_interface_design::filters::StubScoreFilterCOP

StubScoreFilterOP

typedef utility::pointer::shared_ptr< StubScoreFilter > protocols::protein_interface_design::filters::StubScoreFilterOP

StubScoreLoopsFilterCOP

typedef utility::pointer::shared_ptr< StubScoreLoopsFilter const > protocols::protein_interface_design::filters::StubScoreLoopsFilterCOP

StubScoreLoopsFilterOP

typedef utility::pointer::shared_ptr< StubScoreLoopsFilter > protocols::protein_interface_design::filters::StubScoreLoopsFilterOP

TorsionCOP

typedef utility::pointer::shared_ptr< Torsion const > protocols::protein_interface_design::filters::TorsionCOP

TorsionOP

typedef utility::pointer::shared_ptr< Torsion > protocols::protein_interface_design::filters::TorsionOP

Function Documentation

atom_distance()

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 protocols::hybridization::r1, and protocols::hybridization::r2.

Referenced by res_rmsd().

Ca_coords()

utility::vector1< numeric::xyzVector< core::Real > > protocols::protein_interface_design::filters::Ca_coords	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	positions
	)

References protocols::simple_filters::coords(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().

res_rmsd()

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
	)

References atom_distance(), core::pose::Pose::conformation(), protocols::hybridization::r1, protocols::hybridization::r2, and core::conformation::Conformation::residue().

Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().

TR() [1/22]

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

TR() [2/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.AverageDegreeFilter"  )

static

TR() [3/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.BindingStrainFilter"  )

static

TR() [4/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.BoltzmannFilter"  )

static

TR() [5/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.ClashWithTargetFilter"  )

static

TR() [6/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.DesignableResiduesFilter"  )

static

TR() [7/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.DisulfideFilter"  )

static

TR() [8/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.FilterScanFilter"  )

static

TR() [9/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.FNatFilter"  )

static

TR() [10/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.HbondsToAtomFilter"  )

static

TR() [11/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.HbondsToResidueFilter"  )

static

TR() [12/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.InterfaceHolesFilter"  )

static

TR() [13/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.IRmsdFilter"  )

static

TR() [14/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.LRmsdFilter"  )

static

TR() [15/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RelativeSegmentFilter"  )

static

TR() [16/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RmsdFilter"  )

static

TR() [17/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.RmsdSimpleFilter"  )

static

TR() [18/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SequenceRecoveryFilter"  )

static

TR() [19/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter"  )

static

TR() [20/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.SSamountFilter"  )

static

TR() [21/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.StubScoreFilter"  )

static

tr()

static basic::Tracer protocols::protein_interface_design::filters::tr ( "protocols.protein_interface_design.filters.StubScoreLoopsFilter"  )

static

Referenced by protocols::protein_interface_design::filters::StubScoreLoopsFilter::get_score(), and protocols::protein_interface_design::filters::StubScoreLoopsFilter::parse_my_tag().

TR() [22/22]

static basic::Tracer protocols::protein_interface_design::filters::TR ( "protocols.protein_interface_design.filters.Torsion"  )

static

TR_database()

static basic::Tracer protocols::protein_interface_design::filters::TR_database ( "protocols.protein_interface_design.filters.Torsion_database"  )

static

Referenced by protocols::protein_interface_design::filters::Torsion::apply().

TR_pymol()

static basic::Tracer protocols::protein_interface_design::filters::TR_pymol ( "protocols.protein_interface_design.filters.DesignableResiduesFilter_pymol"  )

static

Referenced by protocols::protein_interface_design::filters::DesignableResiduesFilter::compute().

TR_residue_scan()

static basic::Tracer protocols::protein_interface_design::filters::TR_residue_scan ( "ResidueScan"  )

static

Referenced by protocols::protein_interface_design::filters::FilterScanFilter::apply().