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protocols::cyclic_peptide Namespace Reference

Namespaces

 crosslinker
 

Classes

class  CrankshaftFlipMover
 This mover performs a cyclic-aware crankshaft flip at a residue position. More...
 
class  CrankshaftFlipMoverCreator
 
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  CycpepRigidBodyPermutationMover
 A mover that takes a cyclic peptide and alters its position (rigid-body transform), superimposing it on a cyclic permutation or reverse cyclic permutation of itself. More...
 
class  CycpepRigidBodyPermutationMoverCreator
 
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  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

using CrankshaftFlipMoverOP = utility::pointer::shared_ptr< CrankshaftFlipMover >
 
using CrankshaftFlipMoverCOP = utility::pointer::shared_ptr< CrankshaftFlipMover const >
 
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
 
using CycpepRigidBodyPermutationMoverOP = utility::pointer::shared_ptr< CycpepRigidBodyPermutationMover >
 
using CycpepRigidBodyPermutationMoverCOP = utility::pointer::shared_ptr< CycpepRigidBodyPermutationMover const >
 
typedef utility::pointer::shared_ptr< CycpepSymmetryFilter > CycpepSymmetryFilterOP
 
typedef utility::pointer::shared_ptr< CycpepSymmetryFilter const > CycpepSymmetryFilterCOP
 
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 class  CrossLinker {
  no_crosslinker = 1 , TBMB , One_Four_BBMB , TMA ,
  thioether , 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 class  CycpepRigidBodyPermutationMoverMode { SET_PERMUTATION = 1 , RANDOM_PERMUTATION , N_MODES =RANDOM_PERMUTATION , UNKNOWN_MODE }
 An enum for the modes for this mover. More...
 
enum  PSM_StubMode { PSM_append , PSM_prepend , PSM_insert }
 

Functions

std::ostream & operator<< (std::ostream &os, CrankshaftFlipMover const &mover)
 private methods /// More...
 
std::ostream & operator<< (std::ostream &os, CrosslinkerMover const &mover)
 
CycpepRigidBodyPermutationMoverMode cycpep_rigid_body_permutation_mover_mode_from_string (std::string const &modestring)
 Given a mover mode string, get the mode enum. More...
 
std::string string_from_cycpep_rigid_body_permutation_mover_mode (CycpepRigidBodyPermutationMoverMode const mode)
 Given a mover mode enum, get the mode string. More...
 
std::string list_cycpep_rigid_body_permutation_mover_modes ()
 Get a comma-separated list of valid mover modes. More...
 
std::ostream & operator<< (std::ostream &os, CycpepRigidBodyPermutationMover 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

◆ CrankshaftFlipMoverCOP

using protocols::cyclic_peptide::CrankshaftFlipMoverCOP = typedef utility::pointer::shared_ptr< CrankshaftFlipMover const >

◆ CrankshaftFlipMoverOP

using protocols::cyclic_peptide::CrankshaftFlipMoverOP = typedef utility::pointer::shared_ptr< CrankshaftFlipMover >

◆ CreateAngleConstraintCOP

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

◆ CreateAngleConstraintCOPs

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

◆ CreateAngleConstraintOP

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

◆ CreateAngleConstraintOPs

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

◆ CreateDistanceConstraintCOP

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

◆ CreateDistanceConstraintCOPs

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

◆ CreateDistanceConstraintOP

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

◆ CreateDistanceConstraintOPs

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

◆ CreateTorsionConstraintCOP

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

◆ CreateTorsionConstraintCOPs

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

◆ CreateTorsionConstraintOP

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

◆ CreateTorsionConstraintOPs

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

◆ CrosslinkerMoverCOP

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

◆ CrosslinkerMoverOP

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

◆ CycpepRigidBodyPermutationMoverCOP

using protocols::cyclic_peptide::CycpepRigidBodyPermutationMoverCOP = typedef utility::pointer::shared_ptr< CycpepRigidBodyPermutationMover const >

◆ CycpepRigidBodyPermutationMoverOP

using protocols::cyclic_peptide::CycpepRigidBodyPermutationMoverOP = typedef utility::pointer::shared_ptr< CycpepRigidBodyPermutationMover >

◆ CycpepSymmetryFilterCOP

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

◆ CycpepSymmetryFilterOP

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

◆ FirstResidAdded

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

This type alias is meant to clarify certain return types.

◆ FlipChiralityMoverCOP

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

◆ FlipChiralityMoverCOPs

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

◆ FlipChiralityMoverOP

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

◆ FlipChiralityMoverOPs

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

◆ OversaturatedHbondAcceptorFilterCOP

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

◆ OversaturatedHbondAcceptorFilterOP

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

◆ PeptideCyclizeMoverCOP

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

◆ PeptideCyclizeMoverCOPs

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

◆ PeptideCyclizeMoverOP

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

◆ PeptideCyclizeMoverOPs

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

◆ PeptideInternalHbondsFilterCOP

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

◆ PeptideInternalHbondsFilterOP

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

◆ PeptideInternalHbondsMetricCOP

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

◆ PeptideInternalHbondsMetricOP

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

◆ PeptideStubMoverCOP

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

◆ PeptideStubMoverCOPs

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

◆ PeptideStubMoverOP

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

◆ PeptideStubMoverOPs

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

◆ RamaMutationSelectorCOP

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

◆ RamaMutationSelectorOP

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

◆ SymmetricCycpepAlignCOP

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

◆ SymmetricCycpepAlignOP

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

◆ TryDisulfPermutationsCOP

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

◆ TryDisulfPermutationsCOPs

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

◆ TryDisulfPermutationsOP

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

◆ TryDisulfPermutationsOPs

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

Enumeration Type Documentation

◆ CrossLinker

enum protocols::cyclic_peptide::CrossLinker
strong

Enumeration of allowed crosslinkers.

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

◆ CycpepRigidBodyPermutationMoverMode

enum protocols::cyclic_peptide::CycpepRigidBodyPermutationMoverMode
strong

An enum for the modes for this mover.

If you add to this list, update the string_from_cycpep_rigid_body_permutation_mover_mode() function.

Enumerator
SET_PERMUTATION 
RANDOM_PERMUTATION 
N_MODES 
UNKNOWN_MODE 

◆ PSM_StubMode

enum protocols::cyclic_peptide::PSM_StubMode
Enumerator
PSM_append 
PSM_prepend 
PSM_insert 

Function Documentation

◆ cycpep_rigid_body_permutation_mover_mode_from_string()

CycpepRigidBodyPermutationMoverMode protocols::cyclic_peptide::cycpep_rigid_body_permutation_mover_mode_from_string ( std::string const &  modestring)

Given a mover mode string, get the mode enum.

Returns CycpepRigidBodyPermutationMoverMode::UNKNOWN_MODE if string not recognized.

References N_MODES, string_from_cycpep_rigid_body_permutation_mover_mode(), and UNKNOWN_MODE.

Referenced by protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode().

◆ dump_debug_output()

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) @modified Jack Maguire : 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().

◆ list_cycpep_rigid_body_permutation_mover_modes()

std::string protocols::cyclic_peptide::list_cycpep_rigid_body_permutation_mover_modes ( )

Get a comma-separated list of valid mover modes.

References N_MODES.

Referenced by protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::provide_xml_schema(), and protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode().

◆ operator<<() [1/4]

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

private methods ///

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

◆ operator<<() [2/4]

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

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

◆ operator<<() [3/4]

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

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

◆ operator<<() [4/4]

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

private methods ///

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

◆ string_from_cycpep_rigid_body_permutation_mover_mode()

std::string protocols::cyclic_peptide::string_from_cycpep_rigid_body_permutation_mover_mode ( CycpepRigidBodyPermutationMoverMode const  mode)

Given a mover mode enum, get the mode string.

References N_MODES, RANDOM_PERMUTATION, and SET_PERMUTATION.

Referenced by cycpep_rigid_body_permutation_mover_mode_from_string(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_residue_index_map(), and protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode().

◆ subtag_for_cyclize()

std::string protocols::cyclic_peptide::subtag_for_cyclize ( std::string const &  foo)

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

◆ TR()

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

Referenced by protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric(), 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::CycpepRigidBodyPermutationMover::align_cycpep_pose_to_original_pose(), protocols::cyclic_peptide::CrankshaftFlipMover::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::cyclic_peptide::CycpepSymmetryFilter::apply(), protocols::cyclic_peptide::PeptideInternalHbondsFilter::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::CycpepRigidBodyPermutationMover::copy_cycpep_pose_coordinates_to_original_pose(), 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::One_Four_BBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_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::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), protocols::cyclic_peptide::TryDisulfPermutations::generate_disulf_permutations(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_residue_index_map(), protocols::cyclic_peptide::PeptideCyclizeMover::get_all(), protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_inversion_random(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_inversion_setting(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_permutation_setting(), protocols::cyclic_peptide::RamaMutationSelector::set_rama_prepro_multiplier(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_residue_selector(), protocols::cyclic_peptide::RamaMutationSelector::set_score_threshold(), protocols::cyclic_peptide::RamaMutationSelector::set_target_type(), protocols::cyclic_peptide::crosslinker::set_up_thioether_bond_mover(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), protocols::cyclic_peptide::crosslinker::set_up_thioether_variants(), protocols::cyclic_peptide::CrosslinkerMover::symmetric_apply(), protocols::cyclic_peptide::CrankshaftFlipMover::try_peptide_flip(), and protocols::cyclic_peptide::CrankshaftFlipMover::try_pre_gly_flip().

Variable Documentation

◆ DEFAULT_LABEL

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

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

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