protocols::cyclic_peptide Namespace Reference

Namespaces
	crosslinker

Classes
class	CreateAngleConstraint
class	CreateAngleConstraintCreator
class	CreateDistanceConstraint
class	CreateDistanceConstraintCreator
class	CreateTorsionConstraint
class	CreateTorsionConstraintCreator
class	CrosslinkerMover
	This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure. More...
class	CrosslinkerMoverCreator
class	CycpepSymmetryFilter
	A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry. More...
class	CycpepSymmetryFilterCreator
class	DeclareBond
class	DeclareBondCreator
class	FlipChiralityMover
class	FlipChiralityMoverCreator
class	OversaturatedHbondAcceptorFilter
	This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds. More...
class	OversaturatedHbondAcceptorFilterCreator
class	PeptideCyclizeMover
class	PeptideCyclizeMoverCreator
class	PeptideInternalHbondsFilter
	A filter that thinly wraps the PeptideInternalHbondsMetric. More...
class	PeptideInternalHbondsFilterCreator
class	PeptideInternalHbondsMetric
	A simple metric for measuring the backbone hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds. More...
class	PeptideInternalHbondsMetricCreator
class	PeptideStubMover
class	PeptideStubMoverCreator
class	RamaMutationSelector
	Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type. More...
class	RamaMutationSelectorCreator
class	SymmetricCycpepAlign
	Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover. More...
class	SymmetricCycpepAlignCreator
class	TryDisulfPermutations
class	TryDisulfPermutationsCreator

Typedefs
typedef utility::pointer::shared_ptr < CreateAngleConstraint >	CreateAngleConstraintOP
typedef utility::pointer::shared_ptr < CreateAngleConstraint const >	CreateAngleConstraintCOP
typedef utility::vector1 < CreateAngleConstraintOP >	CreateAngleConstraintOPs
typedef utility::vector1 < CreateAngleConstraintCOP >	CreateAngleConstraintCOPs
typedef utility::pointer::shared_ptr < CreateDistanceConstraint >	CreateDistanceConstraintOP
typedef utility::pointer::shared_ptr < CreateDistanceConstraint const >	CreateDistanceConstraintCOP
typedef utility::vector1 < CreateDistanceConstraintOP >	CreateDistanceConstraintOPs
typedef utility::vector1 < CreateDistanceConstraintCOP >	CreateDistanceConstraintCOPs
typedef utility::pointer::shared_ptr < CreateTorsionConstraint >	CreateTorsionConstraintOP
typedef utility::pointer::shared_ptr < CreateTorsionConstraint const >	CreateTorsionConstraintCOP
typedef utility::vector1 < CreateTorsionConstraintOP >	CreateTorsionConstraintOPs
typedef utility::vector1 < CreateTorsionConstraintCOP >	CreateTorsionConstraintCOPs
typedef utility::pointer::shared_ptr < CrosslinkerMover >	CrosslinkerMoverOP
typedef utility::pointer::shared_ptr < CrosslinkerMover const >	CrosslinkerMoverCOP
typedef utility::pointer::shared_ptr < CycpepSymmetryFilter >	CycpepSymmetryFilterOP
typedef utility::pointer::shared_ptr < CycpepSymmetryFilter const >	CycpepSymmetryFilterCOP
typedef utility::pointer::shared_ptr < DeclareBond >	DeclareBondOP
typedef utility::pointer::shared_ptr < DeclareBond const >	DeclareBondCOP
typedef utility::vector1 < DeclareBondOP >	DeclareBondOPs
typedef utility::vector1 < DeclareBondCOP >	DeclareBondCOPs
typedef utility::pointer::shared_ptr < FlipChiralityMover >	FlipChiralityMoverOP
typedef utility::pointer::shared_ptr < FlipChiralityMover const >	FlipChiralityMoverCOP
typedef utility::vector1 < FlipChiralityMoverOP >	FlipChiralityMoverOPs
typedef utility::vector1 < FlipChiralityMoverCOP >	FlipChiralityMoverCOPs
typedef utility::pointer::shared_ptr < OversaturatedHbondAcceptorFilter >	OversaturatedHbondAcceptorFilterOP
typedef utility::pointer::shared_ptr < OversaturatedHbondAcceptorFilter const >	OversaturatedHbondAcceptorFilterCOP
typedef utility::pointer::shared_ptr < PeptideCyclizeMover >	PeptideCyclizeMoverOP
typedef utility::pointer::shared_ptr < PeptideCyclizeMover const >	PeptideCyclizeMoverCOP
typedef utility::vector1 < PeptideCyclizeMoverOP >	PeptideCyclizeMoverOPs
typedef utility::vector1 < PeptideCyclizeMoverCOP >	PeptideCyclizeMoverCOPs
using	PeptideInternalHbondsFilterOP = utility::pointer::shared_ptr< PeptideInternalHbondsFilter >
using	PeptideInternalHbondsFilterCOP = utility::pointer::shared_ptr< PeptideInternalHbondsFilter const >
using	PeptideInternalHbondsMetricOP = utility::pointer::shared_ptr< PeptideInternalHbondsMetric >
using	PeptideInternalHbondsMetricCOP = utility::pointer::shared_ptr< PeptideInternalHbondsMetric const >
typedef utility::pointer::shared_ptr < PeptideStubMover >	PeptideStubMoverOP
typedef utility::pointer::shared_ptr < PeptideStubMover const >	PeptideStubMoverCOP
typedef utility::vector1 < PeptideStubMoverOP >	PeptideStubMoverOPs
typedef utility::vector1 < PeptideStubMoverCOP >	PeptideStubMoverCOPs
using	FirstResidAdded = core::Size
	This type alias is meant to clarify certain return types. More...
typedef utility::pointer::shared_ptr < RamaMutationSelector >	RamaMutationSelectorOP
typedef utility::pointer::shared_ptr < RamaMutationSelector const >	RamaMutationSelectorCOP
typedef utility::pointer::shared_ptr < SymmetricCycpepAlign >	SymmetricCycpepAlignOP
typedef utility::pointer::shared_ptr < SymmetricCycpepAlign const >	SymmetricCycpepAlignCOP
typedef utility::pointer::shared_ptr < TryDisulfPermutations >	TryDisulfPermutationsOP
typedef utility::pointer::shared_ptr < TryDisulfPermutations const >	TryDisulfPermutationsCOP
typedef utility::vector1 < TryDisulfPermutationsOP >	TryDisulfPermutationsOPs
typedef utility::vector1 < TryDisulfPermutationsCOP >	TryDisulfPermutationsCOPs

Enumerations
enum	CrossLinker {   CrossLinker::no_crosslinker = 1, CrossLinker::TBMB, CrossLinker::One_Four_BBMB, CrossLinker::TMA,   CrossLinker::tetrahedral_metal, CrossLinker::octahedral_metal, CrossLinker::trigonal_planar_metal, CrossLinker::trigonal_pyramidal_metal,   CrossLinker::square_planar_metal, CrossLinker::square_pyramidal_metal, CrossLinker::unknown_crosslinker, CrossLinker::end_of_crosslinker_list = unknown_crosslinker }
	Enumeration of allowed crosslinkers. More...
enum	PSM_StubMode { PSM_append, PSM_prepend, PSM_insert }

Functions
std::ostream &	operator<< (std::ostream &os, CrosslinkerMover const &mover)
std::string	subtag_for_cyclize (std::string const &foo)
void	dump_debug_output (core::pose::Pose const &pose)
	if TR.Debug is visible, dump residue information to the console More...
std::ostream &	operator<< (std::ostream &os, SymmetricCycpepAlign const &mover)
	private methods /// More...
static basic::Tracer	TR ("protocols.cyclic_peptide.TryDisulfPermutations")

Variables
constexpr char	DEFAULT_LABEL [] = "PEPTIDE_STUB_EXTENSION"

Typedef Documentation

typedef utility::pointer::shared_ptr< CreateAngleConstraint const > protocols::cyclic_peptide::CreateAngleConstraintCOP

typedef utility::vector1<CreateAngleConstraintCOP> protocols::cyclic_peptide::CreateAngleConstraintCOPs

typedef utility::pointer::shared_ptr< CreateAngleConstraint > protocols::cyclic_peptide::CreateAngleConstraintOP

typedef utility::vector1<CreateAngleConstraintOP> protocols::cyclic_peptide::CreateAngleConstraintOPs

typedef utility::pointer::shared_ptr< CreateDistanceConstraint const > protocols::cyclic_peptide::CreateDistanceConstraintCOP

typedef utility::vector1<CreateDistanceConstraintCOP> protocols::cyclic_peptide::CreateDistanceConstraintCOPs

typedef utility::pointer::shared_ptr< CreateDistanceConstraint > protocols::cyclic_peptide::CreateDistanceConstraintOP

typedef utility::vector1<CreateDistanceConstraintOP> protocols::cyclic_peptide::CreateDistanceConstraintOPs

typedef utility::pointer::shared_ptr< CreateTorsionConstraint const > protocols::cyclic_peptide::CreateTorsionConstraintCOP

typedef utility::vector1<CreateTorsionConstraintCOP> protocols::cyclic_peptide::CreateTorsionConstraintCOPs

typedef utility::pointer::shared_ptr< CreateTorsionConstraint > protocols::cyclic_peptide::CreateTorsionConstraintOP

typedef utility::vector1<CreateTorsionConstraintOP> protocols::cyclic_peptide::CreateTorsionConstraintOPs

typedef utility::pointer::shared_ptr< CrosslinkerMover const > protocols::cyclic_peptide::CrosslinkerMoverCOP

typedef utility::pointer::shared_ptr< CrosslinkerMover > protocols::cyclic_peptide::CrosslinkerMoverOP

typedef utility::pointer::shared_ptr< CycpepSymmetryFilter const > protocols::cyclic_peptide::CycpepSymmetryFilterCOP

typedef utility::pointer::shared_ptr< CycpepSymmetryFilter > protocols::cyclic_peptide::CycpepSymmetryFilterOP

typedef utility::pointer::shared_ptr< DeclareBond const > protocols::cyclic_peptide::DeclareBondCOP

typedef utility::vector1<DeclareBondCOP> protocols::cyclic_peptide::DeclareBondCOPs

typedef utility::pointer::shared_ptr< DeclareBond > protocols::cyclic_peptide::DeclareBondOP

typedef utility::vector1<DeclareBondOP> protocols::cyclic_peptide::DeclareBondOPs

using protocols::cyclic_peptide::FirstResidAdded = typedef core::Size

This type alias is meant to clarify certain return types.

typedef utility::pointer::shared_ptr< FlipChiralityMover const > protocols::cyclic_peptide::FlipChiralityMoverCOP

typedef utility::vector1<FlipChiralityMoverCOP> protocols::cyclic_peptide::FlipChiralityMoverCOPs

typedef utility::pointer::shared_ptr< FlipChiralityMover > protocols::cyclic_peptide::FlipChiralityMoverOP

typedef utility::vector1<FlipChiralityMoverOP> protocols::cyclic_peptide::FlipChiralityMoverOPs

typedef utility::pointer::shared_ptr< OversaturatedHbondAcceptorFilter const > protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCOP

typedef utility::pointer::shared_ptr< OversaturatedHbondAcceptorFilter > protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterOP

typedef utility::pointer::shared_ptr< PeptideCyclizeMover const > protocols::cyclic_peptide::PeptideCyclizeMoverCOP

typedef utility::vector1<PeptideCyclizeMoverCOP> protocols::cyclic_peptide::PeptideCyclizeMoverCOPs

typedef utility::pointer::shared_ptr< PeptideCyclizeMover > protocols::cyclic_peptide::PeptideCyclizeMoverOP

typedef utility::vector1<PeptideCyclizeMoverOP> protocols::cyclic_peptide::PeptideCyclizeMoverOPs

using protocols::cyclic_peptide::PeptideInternalHbondsFilterCOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsFilter const >

using protocols::cyclic_peptide::PeptideInternalHbondsFilterOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsFilter >

using protocols::cyclic_peptide::PeptideInternalHbondsMetricCOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsMetric const >

using protocols::cyclic_peptide::PeptideInternalHbondsMetricOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsMetric >

typedef utility::pointer::shared_ptr< PeptideStubMover const > protocols::cyclic_peptide::PeptideStubMoverCOP

typedef utility::vector1<PeptideStubMoverCOP> protocols::cyclic_peptide::PeptideStubMoverCOPs

typedef utility::pointer::shared_ptr< PeptideStubMover > protocols::cyclic_peptide::PeptideStubMoverOP

typedef utility::vector1<PeptideStubMoverOP> protocols::cyclic_peptide::PeptideStubMoverOPs

typedef utility::pointer::shared_ptr< RamaMutationSelector const > protocols::cyclic_peptide::RamaMutationSelectorCOP

typedef utility::pointer::shared_ptr< RamaMutationSelector > protocols::cyclic_peptide::RamaMutationSelectorOP

typedef utility::pointer::shared_ptr< SymmetricCycpepAlign const > protocols::cyclic_peptide::SymmetricCycpepAlignCOP

typedef utility::pointer::shared_ptr< SymmetricCycpepAlign > protocols::cyclic_peptide::SymmetricCycpepAlignOP

typedef utility::pointer::shared_ptr< TryDisulfPermutations const > protocols::cyclic_peptide::TryDisulfPermutationsCOP

typedef utility::vector1<TryDisulfPermutationsCOP> protocols::cyclic_peptide::TryDisulfPermutationsCOPs

typedef utility::pointer::shared_ptr< TryDisulfPermutations > protocols::cyclic_peptide::TryDisulfPermutationsOP

typedef utility::vector1<TryDisulfPermutationsOP> protocols::cyclic_peptide::TryDisulfPermutationsOPs

Enumeration Type Documentation

enum protocols::cyclic_peptide::CrossLinker

strong

Enumeration of allowed crosslinkers.

Enumerator
no_crosslinker
TBMB
One_Four_BBMB
TMA
tetrahedral_metal
octahedral_metal
trigonal_planar_metal
trigonal_pyramidal_metal
square_planar_metal
square_pyramidal_metal
unknown_crosslinker
end_of_crosslinker_list

enum protocols::cyclic_peptide::PSM_StubMode

Enumerator
PSM_append
PSM_prepend
PSM_insert

Function Documentation

void protocols::cyclic_peptide::dump_debug_output

(

core::pose::Pose const &

pose

)

if TR.Debug is visible, dump residue information to the console

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org) Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om : moved to its own function

References core::pose::Pose::annotated_sequence(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::chemical::ResidueType::n_possible_residue_connections(), core::select::resids(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::show(), and TR().

Referenced by protocols::cyclic_peptide::PeptideStubMover::apply().

std::ostream & protocols::cyclic_peptide::operator<<	(	std::ostream &	os,
		CrosslinkerMover const &	mover
	)

References protocols::cyclic_peptide::CrosslinkerMover::show().

std::ostream & protocols::cyclic_peptide::operator<<	(	std::ostream &	os,
		SymmetricCycpepAlign const &	mover
	)

private methods ///

References protocols::cyclic_peptide::SymmetricCycpepAlign::show().

std::string protocols::cyclic_peptide::subtag_for_cyclize

(

std::string const &

foo

)

Referenced by protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema().

static basic::Tracer protocols::cyclic_peptide::TR ( "protocols.cyclic_peptide.TryDisulfPermutations"  )

static

Referenced by protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::CycpepSymmetryFilter::apply(), protocols::cyclic_peptide::PeptideInternalHbondsFilter::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::cyclic_peptide::CrosslinkerMover::asymmetric_apply(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::calculate(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score(), protocols::cyclic_peptide::TryDisulfPermutations::generate_disulf_permutations(), protocols::cyclic_peptide::PeptideCyclizeMover::get_all(), protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag(), protocols::cyclic_peptide::RamaMutationSelector::set_rama_prepro_multiplier(), protocols::cyclic_peptide::RamaMutationSelector::set_score_threshold(), protocols::cyclic_peptide::RamaMutationSelector::set_target_type(), and protocols::cyclic_peptide::CrosslinkerMover::symmetric_apply().

Variable Documentation

constexpr char protocols::cyclic_peptide::DEFAULT_LABEL[] = "PEPTIDE_STUB_EXTENSION"

Referenced by protocols::cyclic_peptide::PeptideStubMover::default_label().