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protocols::enzdes Namespace Reference

Namespaces

 enzutil
 

Classes

class  AddLigandMotifRotamers
 
class  AddLigandMotifRotamersOperationCreator
 
class  AddOrRemoveMatchCsts
 A simple wrapper to get the functionality in EnzConstraintIO into mover format. More...
 
class  AddOrRemoveMatchCstsCreator
 
class  AddRigidBodyLigandConfs
 
class  AddRigidBodyLigandConfsCreator
 
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  BackboneSampler
 
class  BackboneSamplerCreator
 
class  DesignVsNativeComparison
 class that holds a bunch of native poses and compares them 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  DetectProteinLigandInterfaceOperationCreator
 
class  DiffAtomSasaFilter
 
class  DiffAtomSasaFilterCreator
 
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  EnzdesBaseProtocol
 
class  EnzdesConstraintReporter
 
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 SML Feb 4 2016 note. I moved most of PDBJobOutputter into an intermediate class wwPDBJobOutputter to share functions with mmCIFJobOutputter. This class is not being modified (doesn't appear to need it). Its use of dump_pdb forces that function to be protected rather than private. More...
 
class  EnzdesJobOutputterCreator
 
class  EnzdesScorefileFilter
 
class  EnzdesScorefileFilterCreator
 
class  EnzRepackMinimize
 
class  EnzRepackMinimizeCreator
 
class  EnzScoreFilter
 
class  EnzScoreFilterCreator
 
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  LigBurialFilter
 
class  LigBurialFilterCreator
 
class  LigDSasaFilter
 
class  LigDSasaFilterCreator
 
class  LigInterfaceEnergyFilter
 
class  LigInterfaceEnergyFilterCreator
 
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  ModifyStoredRBConfs
 virtual base class that has some common functionality More...
 
class  PackRotamersMoverPartGreedy
 a mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer. More...
 
class  PackRotamersMoverPartGreedyCreator
 
class  PoseFoundResiduesCombination
 helper class to process and output the different found poses More...
 
class  PredesignPerturbMover
 
class  PredesignPerturbMoverCreator
 
class  ProteinLigandInterfaceUpweighter
 Class to alter a packer task to speficially upweight the protein-ligand interaction energies. More...
 
class  ProteinLigandInterfaceUpweighterOperationCreator
 
class  RemoveLigandFilter
 
class  RemoveLigandFilterCreator
 
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  RepackWithoutLigandFilter
 
class  RepackWithoutLigandFilterCreator
 
class  ResidueConformerFilter
 filter that figures out which rotamer of a given rotamer lib is in the pose at apply time, and can be used to filter on it. supposed to be used for ligands, and for now only tested for them, but should also work with any other residue. can be used for example in specificity redesign, if one wants to divide up a bunch of designs according to the orientation in which they bind the ligand More...
 
class  ResidueConformerFilterCreator
 
class  SecondaryMatchProtocol
 
class  SetCatalyticResPackBehavior
 queries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile More...
 
class  SetCatalyticResPackBehaviorCreator
 
class  UpdateEnzdesHeaderMover
 mover that updates the enzdes pdb header, for use in cases where catalytic residues may be designed More...
 
class  UpdateEnzdesHeaderMoverCreator
 
struct  ValueEvaluator
 tiny helper struct for EnzdesScoreFileFilter More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< DesignVsNativeComparison
DesignVsNativeComparisonOP
 
typedef
utility::pointer::shared_ptr
< EnzdesBaseProtocol
EnzdesBaseProtocolOP
 
typedef
utility::pointer::shared_ptr
< EnzdesBaseProtocol const > 
EnzdesBaseProtocolCOP
 
typedef
utility::pointer::weak_ptr
< EnzdesBaseProtocol
EnzdesBaseProtocolAP
 
typedef
utility::pointer::weak_ptr
< EnzdesBaseProtocol const > 
EnzdesBaseProtocolCAP
 
typedef
utility::pointer::shared_ptr
< EnzdesFixBBProtocol
EnzdesFixBBProtocolOP
 
typedef
utility::pointer::shared_ptr
< EnzdesFlexBBProtocol
EnzdesFlexBBProtocolOP
 
typedef
utility::pointer::shared_ptr
< EnzdesFlexBBProtocol const > 
EnzdesFlexBBProtocolCOP
 
typedef
utility::pointer::weak_ptr
< EnzdesFlexBBProtocol const > 
EnzdesFlexBBProtocolCAP
 
typedef
utility::pointer::weak_ptr
< EnzdesFlexBBProtocol
EnzdesFlexBBProtocolAP
 
typedef
utility::pointer::shared_ptr
< EnzdesFlexibleRegion
EnzdesFlexibleRegionOP
 
typedef
utility::pointer::shared_ptr
< EnzdesFlexibleRegion const > 
EnzdesFlexibleRegionCOP
 
typedef
utility::pointer::shared_ptr
< EnzdesJobInputter
EnzdesJobInputterOP
 
typedef
utility::pointer::shared_ptr
< EnzdesJobInputter const > 
EnzdesJobInputterCOP
 
typedef
utility::pointer::shared_ptr
< EnzdesJobOutputter
EnzdesJobOutputterOP
 
typedef
utility::pointer::shared_ptr
< PredesignPerturbMover
PredesignPerturbMoverOP
 
typedef
utility::pointer::shared_ptr
< SetCatalyticResPackBehavior
SetCatalyticResPackBehaviorOP
 
typedef
utility::pointer::shared_ptr
< SetCatalyticResPackBehavior
const > 
SetCatalyticResPackBehaviorCOP
 
typedef
utility::pointer::shared_ptr
< DetectProteinLigandInterface
DetectProteinLigandInterfaceOP
 
typedef
utility::pointer::shared_ptr
< DetectProteinLigandInterface
const > 
DetectProteinLigandInterfaceCOP
 
typedef
utility::pointer::weak_ptr
< DetectProteinLigandInterface
DetectProteinLigandInterfaceAP
 
typedef
utility::pointer::weak_ptr
< DetectProteinLigandInterface
const > 
DetectProteinLigandInterfaceCAP
 
typedef
utility::pointer::shared_ptr
< ProteinLigandInterfaceUpweighter
ProteinLigandInterfaceUpweighterOP
 
typedef
utility::pointer::shared_ptr
< ProteinLigandInterfaceUpweighter
const > 
ProteinLigandInterfaceUpweighterCOP
 
typedef
utility::pointer::shared_ptr
< AddRigidBodyLigandConfs
AddRigidBodyLigandConfsOP
 
typedef
utility::pointer::shared_ptr
< AddRigidBodyLigandConfs
const > 
AddRigidBodyLigandConfsCOP
 
typedef
utility::pointer::shared_ptr
< AddLigandMotifRotamers
AddLigandMotifRotamersOP
 
typedef
utility::pointer::shared_ptr
< AddLigandMotifRotamers const > 
AddLigandMotifRotamersCOP
 
typedef
utility::pointer::shared_ptr
< EnzdesScorefileFilter
EnzdesScorefileFilterOP
 
typedef
utility::pointer::shared_ptr
< EnzdesScorefileFilter const > 
EnzdesScorefileFilterCOP
 
typedef
utility::pointer::shared_ptr
< EnzRepackMinimize
EnzRepackMinimizeOP
 
typedef
utility::pointer::shared_ptr
< ModifyStoredRBConfs
ModifyStoredRBConfsOP
 
typedef
utility::pointer::shared_ptr
< ModifyStoredRBConfs const > 
ModifyStoredRBConfsCOP
 
typedef
utility::pointer::shared_ptr
< GenerateStoredRBConfs
GenerateStoredRBConfsOP
 
typedef
utility::pointer::shared_ptr
< GenerateStoredRBConfs const > 
GenerateStoredRBConfsCOP
 
typedef
utility::pointer::shared_ptr
< ApplyRandomStoredRBConf
ApplyRandomStoredRBConfOP
 
typedef
utility::pointer::shared_ptr
< ApplyRandomStoredRBConf
const > 
ApplyRandomStoredRBConfCOP
 
typedef
utility::pointer::shared_ptr
< MinimizeStoredRBConfs
MinimizeStoredRBConfsOP
 
typedef
utility::pointer::shared_ptr
< MinimizeStoredRBConfs const > 
MinimizeStoredRBConfsCOP
 
typedef
utility::pointer::shared_ptr
< DiversifyStoredRBConfs
DiversifyStoredRBConfsOP
 
typedef
utility::pointer::shared_ptr
< DiversifyStoredRBConfs const > 
DiversifyStoredRBConfsCOP
 
typedef
utility::pointer::shared_ptr
< RemoveLigandFilter
RemoveLigandFilterOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatchProtocol
SecondaryMatchProtocolOP
 
typedef
utility::pointer::shared_ptr
< SecondaryMatchProtocol const > 
SecondaryMatchProtocolCOP
 
typedef
utility::pointer::weak_ptr
< SecondaryMatchProtocol const > 
SecondaryMatchProtocolCAP
 
typedef
utility::pointer::shared_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 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.PackRotamersMoverPartGreedy")
 
static basic::Tracer tr ("protocols.enzdes.SecondaryMatchProtocol")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AddLigandMotifRotamers const > protocols::enzdes::AddLigandMotifRotamersCOP
typedef utility::pointer::shared_ptr< AddRigidBodyLigandConfs const > protocols::enzdes::AddRigidBodyLigandConfsCOP
typedef utility::pointer::shared_ptr< ApplyRandomStoredRBConf const > protocols::enzdes::ApplyRandomStoredRBConfCOP
typedef utility::pointer::shared_ptr< DiversifyStoredRBConfs const > protocols::enzdes::DiversifyStoredRBConfsCOP
typedef utility::pointer::weak_ptr< EnzdesBaseProtocol > protocols::enzdes::EnzdesBaseProtocolAP
typedef utility::pointer::weak_ptr< EnzdesBaseProtocol const > protocols::enzdes::EnzdesBaseProtocolCAP
typedef utility::pointer::shared_ptr< EnzdesBaseProtocol const > protocols::enzdes::EnzdesBaseProtocolCOP
typedef utility::pointer::shared_ptr< EnzdesBaseProtocol > protocols::enzdes::EnzdesBaseProtocolOP
typedef utility::pointer::shared_ptr< EnzdesFixBBProtocol > protocols::enzdes::EnzdesFixBBProtocolOP
typedef utility::pointer::weak_ptr< EnzdesFlexBBProtocol > protocols::enzdes::EnzdesFlexBBProtocolAP
typedef utility::pointer::weak_ptr< EnzdesFlexBBProtocol const > protocols::enzdes::EnzdesFlexBBProtocolCAP
typedef utility::pointer::shared_ptr< EnzdesFlexBBProtocol const > protocols::enzdes::EnzdesFlexBBProtocolCOP
typedef utility::pointer::shared_ptr< EnzdesFlexBBProtocol > protocols::enzdes::EnzdesFlexBBProtocolOP
typedef utility::pointer::shared_ptr< EnzdesFlexibleRegion const > protocols::enzdes::EnzdesFlexibleRegionCOP
typedef utility::pointer::shared_ptr< EnzdesFlexibleRegion > protocols::enzdes::EnzdesFlexibleRegionOP
typedef utility::pointer::shared_ptr< EnzdesJobInputter const > protocols::enzdes::EnzdesJobInputterCOP
typedef utility::pointer::shared_ptr< EnzdesJobInputter > protocols::enzdes::EnzdesJobInputterOP
typedef utility::pointer::shared_ptr< EnzdesJobOutputter > protocols::enzdes::EnzdesJobOutputterOP
typedef utility::pointer::shared_ptr< EnzdesScorefileFilter const > protocols::enzdes::EnzdesScorefileFilterCOP
typedef utility::pointer::shared_ptr< EnzdesScorefileFilter > protocols::enzdes::EnzdesScorefileFilterOP
typedef utility::pointer::shared_ptr< EnzRepackMinimize > protocols::enzdes::EnzRepackMinimizeOP
typedef utility::pointer::shared_ptr< GenerateStoredRBConfs const > protocols::enzdes::GenerateStoredRBConfsCOP
typedef utility::pointer::shared_ptr< GenerateStoredRBConfs > protocols::enzdes::GenerateStoredRBConfsOP
typedef utility::pointer::shared_ptr< MinimizeStoredRBConfs const > protocols::enzdes::MinimizeStoredRBConfsCOP
typedef utility::pointer::shared_ptr< MinimizeStoredRBConfs > protocols::enzdes::MinimizeStoredRBConfsOP
typedef utility::pointer::shared_ptr< ModifyStoredRBConfs const > protocols::enzdes::ModifyStoredRBConfsCOP
typedef utility::pointer::shared_ptr< ModifyStoredRBConfs > protocols::enzdes::ModifyStoredRBConfsOP
typedef utility::pointer::shared_ptr< PredesignPerturbMover > protocols::enzdes::PredesignPerturbMoverOP
typedef utility::pointer::shared_ptr< RemoveLigandFilter > protocols::enzdes::RemoveLigandFilterOP
typedef utility::pointer::weak_ptr< SecondaryMatchProtocol const > protocols::enzdes::SecondaryMatchProtocolCAP
typedef utility::pointer::shared_ptr< SecondaryMatchProtocol const > protocols::enzdes::SecondaryMatchProtocolCOP

Enumeration Type Documentation

Enumerator
_VOID 
ADD_NEW 
ADD_PREGENERATED 
REMOVE 

Function Documentation

static basic::Tracer protocols::enzdes::mv_tr ( "protocols.enzdes.PredesignPerturbMover"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFixBBProtocol"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.AddorRemoveCsts"  )
static

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::AddOrRemoveMatchCsts::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::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::EnzdesBaseProtocol::read_ligand_superposition_file(), 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.ModifyStoredLigandRBConfsMovers"  )
static
static basic::Tracer protocols::enzdes::TR ( "protocols.enzdes.BackboneSampler"  )
static

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::enzdes::LigDSasaFilter::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::enzdes::EnzRepackMinimize::apply(), protocols::enzdes::LigBurialFilter::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::enzdes::EnzScoreFilter::apply(), protocols::enzdes::DiffAtomSasaFilter::apply(), protocols::enzdes::EnzdesScorefileFilter::apply(), protocols::enzdes::ResidueConformerFilter::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::enzdes::LigDSasaFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::enzdes::LigInterfaceEnergyFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), protocols::enzdes::EnzRepackMinimize::create_ptask(), protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication(), protocols::enzdes::EnzdesJobInputter::EnzdesJobInputter(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file(), protocols::enzdes::EnzRepackMinimize::minimize_in_stages(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::enzdes::LigDSasaFilter::parse_my_tag(), protocols::enzdes::LigBurialFilter::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::enzdes::DiffAtomSasaFilter::parse_my_tag(), protocols::enzdes::RepackWithoutLigandFilter::parse_my_tag(), protocols::enzdes::EnzdesJobInputter::pose_from_job(), and protocols::enzdes::PackRotamersMoverPartGreedy::update_task_and_neighbors().

static basic::Tracer protocols::enzdes::TR ( "protocols.enzdes.PackRotamersMoverPartGreedy"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.SecondaryMatchProtocol"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesTaskOperations"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesBaseProtocol"  )
static
static basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFlexBBProtocol"  )
static