Rosetta 3.4
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protocols::enzdes Namespace Reference

Namespaces

namespace  enzutil

Classes

class  AddLigandMotifRotamersOperationCreator
class  AddOrRemoveMatchCsts
 A simple wrapper to get the functionality in EnzConstraintIO into mover format. More...
class  AddOrRemoveMatchCstsCreator
class  AddRigidBodyLigandConfsCreator
class  BackboneSampler
class  BackboneSamplerCreator
class  DesignVsNativeComparison
 class that holds a bunch of native poses and compares them More...
class  DetectProteinLigandInterfaceOperationCreator
class  EnzdesBaseProtocol
class  EnzdesFixBBProtocol
class  EnzdesFlexBBProtocol
class  EnzdesFlexibleRegion
class  EnzdesJobInputter
class  EnzdesJobInputterCreator
class  EnzdesJobOutputter
 for now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb More...
class  EnzdesJobOutputterCreator
class  PredesignPerturbMover
class  RepackLigandSiteWithoutLigandMover
 class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues More...
class  PredesignPerturbMoverCreator
class  SetCatalyticResPackBehavior
 queries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile More...
class  DetectProteinLigandInterface
 Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile. More...
class  ProteinLigandInterfaceUpweighter
 Class to alter a packer task to speficially upweight the protein-ligand interaction energies. More...
class  AddRigidBodyLigandConfs
class  AddLigandMotifRotamers
class  DiffAtomSasaFilterCreator
class  EnzScoreFilterCreator
class  LigBurialFilterCreator
class  LigDSasaFilterCreator
class  LigInterfaceEnergyFilterCreator
class  RepackWithoutLigandFilterCreator
class  EnzdesScorefileFilterCreator
class  LigDSasaFilter
class  LigBurialFilter
class  LigInterfaceEnergyFilter
class  EnzScoreFilter
class  DiffAtomSasaFilter
class  RepackWithoutLigandFilter
struct  ValueEvaluator
 tiny helper struct for EnzdesScoreFileFilter More...
class  EnzdesScorefileFilter
class  EnzRepackMinimize
class  EnzRepackMinimizeCreator
class  ModifyStoredRBConfs
 virtual base class that has some common functionality More...
class  GenerateStoredRBConfs
 generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used More...
class  ApplyRandomStoredRBConf
 for every ligand that has additional stored rb conformations in the enzdes cacheable observer, the one currently in the pose gets exchanged with a random stored one More...
class  MinimizeStoredRBConfs
 rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization More...
class  DiversifyStoredRBConfs
 uses a docking mover to diversiy the stored confs until they're all min_rms_ away from each other note: no scorefunction used here More...
class  ProteinLigandInterfaceUpweighterOperationCreator
class  SecondaryMatchProtocol
class  PoseFoundResiduesCombination
 helper class to process and output the different found poses More...
class  SetCatalyticResPackBehaviorCreator

Typedefs

typedef
utility::pointer::owning_ptr
< DesignVsNativeComparison
DesignVsNativeComparisonOP
typedef
utility::pointer::owning_ptr
< EnzdesBaseProtocol
EnzdesBaseProtocolOP
typedef
utility::pointer::owning_ptr
< EnzdesBaseProtocol const > 
EnzdesBaseProtocolCOP
typedef
utility::pointer::access_ptr
< EnzdesBaseProtocol
EnzdesBaseProtocolAP
typedef
utility::pointer::access_ptr
< EnzdesBaseProtocol const > 
EnzdesBaseProtocolCAP
typedef
utility::pointer::owning_ptr
< EnzdesFixBBProtocol
EnzdesFixBBProtocolOP
typedef
utility::pointer::owning_ptr
< EnzdesFlexBBProtocol
EnzdesFlexBBProtocolOP
typedef
utility::pointer::access_ptr
< EnzdesFlexBBProtocol const > 
EnzdesFlexBBProtocolCAP
typedef
utility::pointer::access_ptr
< EnzdesFlexBBProtocol
EnzdesFlexBBProtocolAP
typedef
utility::pointer::owning_ptr
< EnzdesFlexibleRegion
EnzdesFlexibleRegionOP
typedef
utility::pointer::owning_ptr
< EnzdesFlexibleRegion const > 
EnzdesFlexibleRegionCOP
typedef
utility::pointer::owning_ptr
< EnzdesJobInputter
EnzdesJobInputterOP
typedef
utility::pointer::owning_ptr
< EnzdesJobInputter const > 
EnzdesJobInputterCOP
typedef
utility::pointer::owning_ptr
< EnzdesJobOutputter
EnzdesJobOutputterOP
typedef
utility::pointer::owning_ptr
< PredesignPerturbMover
PredesignPerturbMoverOP
typedef
utility::pointer::owning_ptr
< SetCatalyticResPackBehavior
SetCatalyticResPackBehaviorOP
typedef
utility::pointer::owning_ptr
< SetCatalyticResPackBehavior
const > 
SetCatalyticResPackBehaviorCOP
typedef
utility::pointer::owning_ptr
< DetectProteinLigandInterface
DetectProteinLigandInterfaceOP
typedef
utility::pointer::owning_ptr
< DetectProteinLigandInterface
const > 
DetectProteinLigandInterfaceCOP
typedef
utility::pointer::access_ptr
< DetectProteinLigandInterface
DetectProteinLigandInterfaceAP
typedef
utility::pointer::access_ptr
< DetectProteinLigandInterface
const > 
DetectProteinLigandInterfaceCAP
typedef
utility::pointer::owning_ptr
< ProteinLigandInterfaceUpweighter
ProteinLigandInterfaceUpweighterOP
typedef
utility::pointer::owning_ptr
< ProteinLigandInterfaceUpweighter
const > 
ProteinLigandInterfaceUpweighterCOP
typedef
utility::pointer::owning_ptr
< AddRigidBodyLigandConfs
AddRigidBodyLigandConfsOP
typedef
utility::pointer::owning_ptr
< AddRigidBodyLigandConfs
const > 
AddRigidBodyLigandConfsCOP
typedef
utility::pointer::owning_ptr
< AddLigandMotifRotamers
AddLigandMotifRotamersOP
typedef
utility::pointer::owning_ptr
< AddLigandMotifRotamers const > 
AddLigandMotifRotamersCOP
typedef
utility::pointer::owning_ptr
< EnzdesScorefileFilter
EnzdesScorefileFilterOP
typedef
utility::pointer::owning_ptr
< EnzdesScorefileFilter const > 
EnzdesScorefileFilterCOP
typedef
utility::pointer::owning_ptr
< EnzRepackMinimize
EnzRepackMinimizeOP
typedef
utility::pointer::owning_ptr
< ModifyStoredRBConfs
ModifyStoredRBConfsOP
typedef
utility::pointer::owning_ptr
< ModifyStoredRBConfs const > 
ModifyStoredRBConfsCOP
typedef
utility::pointer::owning_ptr
< GenerateStoredRBConfs
GenerateStoredRBConfsOP
typedef
utility::pointer::owning_ptr
< GenerateStoredRBConfs const > 
GenerateStoredRBConfsCOP
typedef
utility::pointer::owning_ptr
< ApplyRandomStoredRBConf
ApplyRandomStoredRBConfOP
typedef
utility::pointer::owning_ptr
< ApplyRandomStoredRBConf
const > 
ApplyRandomStoredRBConfCOP
typedef
utility::pointer::owning_ptr
< MinimizeStoredRBConfs
MinimizeStoredRBConfsOP
typedef
utility::pointer::owning_ptr
< MinimizeStoredRBConfs const > 
MinimizeStoredRBConfsCOP
typedef
utility::pointer::owning_ptr
< DiversifyStoredRBConfs
DiversifyStoredRBConfsOP
typedef
utility::pointer::owning_ptr
< DiversifyStoredRBConfs const > 
DiversifyStoredRBConfsCOP
typedef
utility::pointer::owning_ptr
< SecondaryMatchProtocol
SecondaryMatchProtocolOP
typedef
utility::pointer::owning_ptr
< SecondaryMatchProtocol const > 
SecondaryMatchProtocolCOP
typedef
utility::pointer::access_ptr
< SecondaryMatchProtocol const > 
SecondaryMatchProtocolCAP
typedef
utility::pointer::owning_ptr
< PoseFoundResiduesCombination
PoseFoundResiduesCombinationOP

Enumerations

enum  CstAction { VOID = 1, ADD_NEW, ADD_PREGENERATED, REMOVE }

Functions

static basic::Tracer tr ("protocols.enzdes.AddorRemoveCsts")
static basic::Tracer TR ("protocols.enzdes.BackboneSampler")
static
numeric::random::RandomGenerator 
RG (6172774)
static basic::Tracer tr ("protocols.enzdes.EnzdesBaseProtocol")
static basic::Tracer tr ("protocols.enzdes.EnzdesFixBBProtocol")
static basic::Tracer tr ("protocols.enzdes.EnzdesFlexBBProtocol")
static basic::Tracer mv_tr ("protocols.enzdes.PredesignPerturbMover")
static basic::Tracer tr ("protocols.enzdes.EnzdesTaskOperations")
static basic::Tracer tr ("protocols.enzdes.ModifyStoredLigandRBConfsMovers")
static basic::Tracer tr ("protocols.enzdes.SecondaryMatchProtocol")

Typedef Documentation


Enumeration Type Documentation

Enumerator:
VOID 
ADD_NEW 
ADD_PREGENERATED 
REMOVE 

Function Documentation

static basic::Tracer protocols::enzdes::mv_tr ( "protocols.enzdes.PredesignPerturbMover"  ) [static]
static numeric::random::RandomGenerator protocols::enzdes::RG ( 6172774  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.ModifyStoredLigandRBConfsMovers"  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesTaskOperations"  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.AddorRemoveCsts"  ) [static]

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::AddOrRemoveMatchCsts::apply(), protocols::enzdes::EnzdesFlexBBProtocol::assemble_next_best_loop_combination(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::SecondaryMatchProtocol::do_matching(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::enzdes::AddOrRemoveMatchCsts::get_const_EnzConstraintIO_for_cstfile(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::enzdes::AddOrRemoveMatchCsts::parse_my_tag(), protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file(), protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position(), protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region(), protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().

static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFlexBBProtocol"  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFixBBProtocol"  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesBaseProtocol"  ) [static]
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.SecondaryMatchProtocol"  ) [static]
static basic::Tracer protocols::enzdes::TR ( "protocols.enzdes.BackboneSampler"  ) [static]
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