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protocols::carbohydrates Namespace Reference

Classes

class  CreateGlycanSequonMover
 Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry. More...
 
class  CreateGlycanSequonMoverCreator
 
class  GlycanSampler
 Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling. More...
 
class  GlycanSamplerCreator
 
class  GlycanTreeMinMover
 A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector. More...
 
class  GlycanTreeMinMoverCreator
 
class  GlycanTreeModeler
 A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves. More...
 
class  GlycanTreeModelerCreator
 
class  IdealizeAnomericHydrogens
 This code sets all the anomeric hydrogen positions based on the input structure. More...
 
class  IdealizeAnomericHydrogensCreator
 
class  LinkageConformerMover
 This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues. Randomly samples on any set selector at each apply or (default) samples a linkage conformer for each residue set. More...
 
class  LinkageConformerMoverCreator
 
class  RingPlaneFlipMover
 A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond. More...
 
class  RingPlaneFlipMoverCreator
 MoverCreator allowing the MoverFactory to create a RingConformationMover. More...
 
class  SimpleGlycosylateMover
 A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use the GlycanSampler to model the resulting glycosylation!. More...
 
class  SimpleGlycosylateMoverCreator
 
class  TautomerizeAnomerMover
 A Mover class for tautomerizing from one anomer to another at a reducing end. More...
 
class  TautomerizeAnomerMoverCreator
 MoverCreator allowing the MoverFactory to create a TautomerizeAnomerMover. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< CreateGlycanSequonMover
CreateGlycanSequonMoverOP
 
typedef
utility::pointer::shared_ptr
< CreateGlycanSequonMover
const > 
CreateGlycanSequonMoverCOP
 
typedef
utility::pointer::shared_ptr
< GlycanSampler
GlycanSamplerOP
 
typedef
utility::pointer::shared_ptr
< GlycanSampler const > 
GlycanSamplerCOP
 
typedef
utility::pointer::shared_ptr
< GlycanTreeMinMover
GlycanTreeMinMoverOP
 
typedef
utility::pointer::shared_ptr
< GlycanTreeMinMover const > 
GlycanTreeMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< GlycanTreeModeler
GlycanTreeModelerOP
 
typedef
utility::pointer::shared_ptr
< GlycanTreeModeler const > 
GlycanTreeModelerCOP
 
typedef
utility::pointer::shared_ptr
< IdealizeAnomericHydrogensMover > 
IdealizeAnomericHydrogensMoverOP
 
typedef
utility::pointer::shared_ptr
< IdealizeAnomericHydrogensMover
const > 
IdealizeAnomericHydrogensMoverCOP
 
typedef
utility::pointer::shared_ptr
< LinkageConformerMover
LinkageConformerMoverOP
 
typedef
utility::pointer::shared_ptr
< LinkageConformerMover const > 
LinkageConformerMoverCOP
 
typedef
utility::pointer::shared_ptr
< RingPlaneFlipMover
RingPlaneFlipMoverOP
 
typedef
utility::pointer::shared_ptr
< RingPlaneFlipMover const > 
RingPlaneFlipMoverCOP
 
typedef
utility::pointer::shared_ptr
< SimpleGlycosylateMover
SimpleGlycosylateMoverOP
 
typedef
utility::pointer::shared_ptr
< SimpleGlycosylateMover const > 
SimpleGlycosylateMoverCOP
 
typedef
utility::pointer::shared_ptr
< TautomerizeAnomerMover
TautomerizeAnomerMoverOP
 
typedef
utility::pointer::shared_ptr
< TautomerizeAnomerMover const > 
TautomerizeAnomerMoverCOP
 

Enumerations

enum  GlycanSequon {
  n_linked_typical = 1, n_linked_basic_enhanced, n_linked_best_enhanced, c_linked_NxC,
  c_linked_WxxW, c_linked_WSTxC
}
 
enum  QuenchDirection { forward = 1, backward }
 

Functions

std::map< GlycanSequon,
std::string > 
create_sequons ()
 Create a map of the name and full sequon. More...
 
std::ostream & operator<< (std::ostream &os, CreateGlycanSequonMover const &mover)
 private methods /// More...
 
std::ostream & operator<< (std::ostream &os, GlycanSampler const &mover)
 
std::ostream & operator<< (std::ostream &os, GlycanTreeModeler const &mover)
 private methods /// More...
 
std::ostream & operator<< (std::ostream &os, LinkageConformerMover const &mover)
 
std::ostream & operator<< (std::ostream &output, RingPlaneFlipMover const &object_to_output)
 
std::ostream & operator<< (std::ostream &os, SimpleGlycosylateMover const &mover)
 
std::ostream & operator<< (std::ostream &output, TautomerizeAnomerMover const &object_to_output)
 
core::pack::task::TaskFactoryOP get_all_glycans_and_neighbor_res_task_factory (utility::vector1< bool > const &subset, core::Real pack_distance=6.0, bool read_resfile=true)
 Get a TaskFactory of all residues in the subset and neighboring residues. More...
 
void run_shear_min_pack (protocols::minimization_packing::MinMover &min_mover, protocols::minimization_packing::PackRotamersMover &packer, protocols::simple_moves::ShearMover &shear, protocols::moves::MonteCarlo &mc, core::Size n_glycan_residues, core::pose::Pose &pose, bool use_shear=true)
 Run a shear/min/pack on all residues set to move. More...
 
core::Size get_total_rounds_for_overlap_one_layer_two (core::pose::Pose const &pose, utility::vector1< bool > const &residue_subset, core::Size sampler_rounds)
 Used for benchmarking to test even sampling of different kinematic protocols Get the total number of sampling rounds for the GlycanTreeModeler protocol with previous default settings. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< GlycanSampler const > protocols::carbohydrates::GlycanSamplerCOP
typedef utility::pointer::shared_ptr< GlycanSampler > protocols::carbohydrates::GlycanSamplerOP
typedef utility::pointer::shared_ptr< GlycanTreeMinMover const > protocols::carbohydrates::GlycanTreeMinMoverCOP
typedef utility::pointer::shared_ptr< GlycanTreeMinMover > protocols::carbohydrates::GlycanTreeMinMoverOP
typedef utility::pointer::shared_ptr< GlycanTreeModeler const > protocols::carbohydrates::GlycanTreeModelerCOP
typedef utility::pointer::shared_ptr< GlycanTreeModeler > protocols::carbohydrates::GlycanTreeModelerOP
typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover const > protocols::carbohydrates::IdealizeAnomericHydrogensMoverCOP
typedef utility::pointer::shared_ptr< IdealizeAnomericHydrogensMover > protocols::carbohydrates::IdealizeAnomericHydrogensMoverOP
typedef utility::pointer::shared_ptr< LinkageConformerMover const > protocols::carbohydrates::LinkageConformerMoverCOP
typedef utility::pointer::shared_ptr< RingPlaneFlipMover const > protocols::carbohydrates::RingPlaneFlipMoverCOP
typedef utility::pointer::shared_ptr< RingPlaneFlipMover > protocols::carbohydrates::RingPlaneFlipMoverOP
typedef utility::pointer::shared_ptr< SimpleGlycosylateMover const > protocols::carbohydrates::SimpleGlycosylateMoverCOP
typedef utility::pointer::shared_ptr< TautomerizeAnomerMover const > protocols::carbohydrates::TautomerizeAnomerMoverCOP

Enumeration Type Documentation

Enumerator
n_linked_typical 
n_linked_basic_enhanced 
n_linked_best_enhanced 
c_linked_NxC 
c_linked_WxxW 
c_linked_WSTxC 
Enumerator
forward 
backward 

Function Documentation

std::map< GlycanSequon, std::string > protocols::carbohydrates::create_sequons ( )
core::pack::task::TaskFactoryOP protocols::carbohydrates::get_all_glycans_and_neighbor_res_task_factory ( utility::vector1< bool > const &  subset,
core::Real  pack_distance = 6.0,
bool  read_resfile = true 
)

Get a TaskFactory of all residues in the subset and neighboring residues.

Operations: InitializeFromCommandline ReadResFile? If option given on cmd-line, returns TF up to this. NeighborhoodResidueSelector/OperateOnResidueSubset RestrictRepacking/PreventRepacking

References core::chemical::VIRTUAL_RESIDUE.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::carbohydrates::GlycanSampler::setup_default_task_factory(), and protocols::carbohydrates::GlycanSampler::setup_packer().

core::Size protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  residue_subset,
core::Size  sampler_rounds 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  os,
SimpleGlycosylateMover const &  mover 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  os,
LinkageConformerMover const &  mover 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  output,
TautomerizeAnomerMover const &  object_to_output 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  os,
GlycanSampler const &  mover 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  os,
CreateGlycanSequonMover const &  mover 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  output,
RingPlaneFlipMover const &  object_to_output 
)
std::ostream & protocols::carbohydrates::operator<< ( std::ostream &  os,
GlycanTreeModeler const &  mover 
)

private methods ///

References protocols::carbohydrates::GlycanTreeModeler::show().

void protocols::carbohydrates::run_shear_min_pack ( minimization_packing::MinMover &  min_mover,
minimization_packing::PackRotamersMover &  packer,
simple_moves::ShearMover &  shear,
moves::MonteCarlo &  mc,
core::Size  n_glycan_residues,
core::pose::Pose pose,
bool  use_shear 
)