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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 {
  no_crosslinker = 1, TBMB, TMA, tetrahedral_metal,
  octahedral_metal, trigonal_planar_metal, trigonal_pyramidal_metal, square_planar_metal,
  square_pyramidal_metal, unknown_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::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< DeclareBond const > protocols::cyclic_peptide::DeclareBondCOP
typedef utility::pointer::shared_ptr< DeclareBond > protocols::cyclic_peptide::DeclareBondOP

This type alias is meant to clarify certain return types.

typedef utility::pointer::shared_ptr< FlipChiralityMover const > protocols::cyclic_peptide::FlipChiralityMoverCOP
typedef utility::pointer::shared_ptr< PeptideCyclizeMover const > protocols::cyclic_peptide::PeptideCyclizeMoverCOP
using protocols::cyclic_peptide::PeptideInternalHbondsFilterCOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsFilter const >
using protocols::cyclic_peptide::PeptideInternalHbondsMetricCOP = typedef utility::pointer::shared_ptr< PeptideInternalHbondsMetric const >
typedef utility::pointer::shared_ptr< PeptideStubMover const > protocols::cyclic_peptide::PeptideStubMoverCOP
typedef utility::pointer::shared_ptr< PeptideStubMover > protocols::cyclic_peptide::PeptideStubMoverOP
typedef utility::pointer::shared_ptr< RamaMutationSelector const > protocols::cyclic_peptide::RamaMutationSelectorCOP
typedef utility::pointer::shared_ptr< SymmetricCycpepAlign const > protocols::cyclic_peptide::SymmetricCycpepAlignCOP
typedef utility::pointer::shared_ptr< TryDisulfPermutations const > protocols::cyclic_peptide::TryDisulfPermutationsCOP

Enumeration Type Documentation

Enumeration of allowed crosslinkers.

Enumerator
no_crosslinker 
TBMB 
TMA 
tetrahedral_metal 
octahedral_metal 
trigonal_planar_metal 
trigonal_pyramidal_metal 
square_planar_metal 
square_pyramidal_metal 
unknown_crosslinker 
end_of_crosslinker_list 
Enumerator
PSM_append 
PSM_prepend 
PSM_insert 

Function Documentation

void protocols::cyclic_peptide::dump_debug_output ( core::pose::Pose const &  pose)
std::ostream & protocols::cyclic_peptide::operator<< ( std::ostream &  os,
CrosslinkerMover const &  mover 
)
std::ostream & protocols::cyclic_peptide::operator<< ( std::ostream &  os,
SymmetricCycpepAlign const &  mover 
)
std::string protocols::cyclic_peptide::subtag_for_cyclize ( std::string const &  foo)
static basic::Tracer protocols::cyclic_peptide::TR ( "protocols.cyclic_peptide.TryDisulfPermutations"  )
static

Referenced by protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(), 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::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"