Namespaces
	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	EnzdesConstraintReporter

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	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	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.PackRotamersMoverPartGreedy")

static numeric::random::RandomGenerator	trg_RG (10805)

static basic::Tracer	tr ("protocols.enzdes.SecondaryMatchProtocol")