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 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 thread_local basic::Tracer	tr ("protocols.enzdes.AddorRemoveCsts")
static thread_local basic::Tracer	TR ("protocols.enzdes.BackboneSampler")
static thread_local basic::Tracer	tr ("protocols.enzdes.EnzdesBaseProtocol")
static thread_local basic::Tracer	tr ("protocols.enzdes.EnzdesFixBBProtocol")
static thread_local basic::Tracer	tr ("protocols.enzdes.EnzdesFlexBBProtocol")
static thread_local basic::Tracer	mv_tr ("protocols.enzdes.PredesignPerturbMover")
static thread_local basic::Tracer	tr ("protocols.enzdes.EnzdesTaskOperations")
static thread_local basic::Tracer	tr ("protocols.enzdes.ModifyStoredLigandRBConfsMovers")
static thread_local basic::Tracer	TR ("protocols.enzdes.PackRotamersMoverPartGreedy")
static thread_local basic::Tracer	tr ("protocols.enzdes.SecondaryMatchProtocol")

Typedef Documentation

typedef utility::pointer::shared_ptr< AddLigandMotifRotamers const > protocols::enzdes::AddLigandMotifRotamersCOP

typedef utility::pointer::shared_ptr< AddLigandMotifRotamers > protocols::enzdes::AddLigandMotifRotamersOP

typedef utility::pointer::shared_ptr< AddRigidBodyLigandConfs const > protocols::enzdes::AddRigidBodyLigandConfsCOP

typedef utility::pointer::shared_ptr< AddRigidBodyLigandConfs > protocols::enzdes::AddRigidBodyLigandConfsOP

typedef utility::pointer::shared_ptr< ApplyRandomStoredRBConf const > protocols::enzdes::ApplyRandomStoredRBConfCOP

typedef utility::pointer::shared_ptr< ApplyRandomStoredRBConf > protocols::enzdes::ApplyRandomStoredRBConfOP

typedef utility::pointer::shared_ptr< DesignVsNativeComparison > protocols::enzdes::DesignVsNativeComparisonOP

typedef utility::pointer::weak_ptr< DetectProteinLigandInterface > protocols::enzdes::DetectProteinLigandInterfaceAP

typedef utility::pointer::weak_ptr< DetectProteinLigandInterface const > protocols::enzdes::DetectProteinLigandInterfaceCAP

typedef utility::pointer::shared_ptr< DetectProteinLigandInterface const > protocols::enzdes::DetectProteinLigandInterfaceCOP

typedef utility::pointer::shared_ptr< DetectProteinLigandInterface > protocols::enzdes::DetectProteinLigandInterfaceOP

typedef utility::pointer::shared_ptr< DiversifyStoredRBConfs const > protocols::enzdes::DiversifyStoredRBConfsCOP

typedef utility::pointer::shared_ptr< DiversifyStoredRBConfs > protocols::enzdes::DiversifyStoredRBConfsOP

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< PoseFoundResiduesCombination > protocols::enzdes::PoseFoundResiduesCombinationOP

typedef utility::pointer::shared_ptr< PredesignPerturbMover > protocols::enzdes::PredesignPerturbMoverOP

typedef utility::pointer::shared_ptr< ProteinLigandInterfaceUpweighter const > protocols::enzdes::ProteinLigandInterfaceUpweighterCOP

typedef utility::pointer::shared_ptr< ProteinLigandInterfaceUpweighter > protocols::enzdes::ProteinLigandInterfaceUpweighterOP

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

typedef utility::pointer::shared_ptr< SecondaryMatchProtocol > protocols::enzdes::SecondaryMatchProtocolOP

typedef utility::pointer::shared_ptr< SetCatalyticResPackBehavior const > protocols::enzdes::SetCatalyticResPackBehaviorCOP

typedef utility::pointer::shared_ptr< SetCatalyticResPackBehavior > protocols::enzdes::SetCatalyticResPackBehaviorOP

Enumeration Type Documentation

enum protocols::enzdes::CstAction

Enumerator
VOID
ADD_NEW
ADD_PREGENERATED
REMOVE

Function Documentation

static thread_local basic::Tracer protocols::enzdes::mv_tr ( "protocols.enzdes.PredesignPerturbMover"  )

static

Referenced by protocols::enzdes::EnzdesConstraintReporter::add_constrained_lig_atom(), protocols::enzdes::EnzdesConstraintReporter::add_constrained_nonligand_atom(), protocols::enzdes::PredesignPerturbMover::apply(), and protocols::enzdes::EnzdesConstraintReporter::find_constraints_to_ligand().

static thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFixBBProtocol"  )

static

static thread_local 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::SetCatalyticResPackBehavior::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::enzdes::AddOrRemoveMatchCsts::apply(), protocols::enzdes::EnzdesFlexBBProtocol::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::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::SecondaryMatchProtocol::do_matching(), 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_def(), 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(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().

static thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.ModifyStoredLigandRBConfsMovers"  )

static

static thread_local basic::Tracer protocols::enzdes::TR ( "protocols.enzdes.PackRotamersMoverPartGreedy"  )

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static thread_local 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::RemoveLigandFilter::parse_my_tag(), 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 thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.SecondaryMatchProtocol"  )

static

static thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesTaskOperations"  )

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static thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesBaseProtocol"  )

static

static thread_local basic::Tracer protocols::enzdes::tr ( "protocols.enzdes.EnzdesFlexBBProtocol"  )

static