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protocols::pack_daemon Namespace Reference

Classes

class  VectorExpression
 
class  VariableVectorExpression
 
class  IterativeVectorExpression
 
class  VectorFunction
 
class  VectorFunction2
 
class  VMax
 
class  VMin
 
class  VMaxBy
 Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1. More...
 
class  VMinBy
 Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1. More...
 
class  PowExpression
 
class  ExpExpression
 
class  LnExpression
 
class  InSetExpression
 Returns "true" if the expression ex evaluates to one of a set of indicated values. More...
 
class  SurrogateVariableExpression
 Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable). More...
 
class  VectorExpressionCreator
 
class  StructureFileNames
 
class  DynamicAggregateFunction
 
class  EntityFuncExpressionCreator
 
class  EntityFunc
 
class  EntityCorrespondence
 
class  MultistateAggregateFunction
 
struct  EntityHistoryLT
 
class  MultistateFitnessFunction
 
class  MPIMultistateFitnessFunction
 
class  PackDaemon
 
class  DaemonSet
 
class  NPDPropCalculator
 
class  NPDPropCalculatorCreator
 
class  QuickRepacker
 
class  BasicSimAnnealerRepacker
 
class  RotamerSubsetRepacker
 
class  DenseIGRepacker
 
class  DoubleDenseIGRepacker
 
class  FASTER_IG_Repacker
 

Typedefs

typedef
utility::pointer::owning_ptr
< VectorExpression > 		VectorExpressionOP
 
typedef
utility::pointer::owning_ptr
< VectorExpression const > 		VectorExpressionCOP
 
typedef
utility::pointer::owning_ptr
< VariableVectorExpression > 		VariableVectorExpressionOP
 
typedef
utility::pointer::owning_ptr
< VariableVectorExpression
const > 		VariableVectorExpressionCOP
 
typedef
utility::pointer::owning_ptr
< IterativeVectorExpression > 		IterativeVectorExpressionOP
 
typedef
utility::pointer::owning_ptr
< IterativeVectorExpression
const > 		IterativeVectorExpressionCOP
 
typedef
utility::pointer::owning_ptr
< VectorFunction > 		VectorFunctionOP
 
typedef
utility::pointer::owning_ptr
< VectorFunction const > 		VectorFunctionCOP
 
typedef
utility::pointer::owning_ptr
< VMax > 		VMaxOP
 
typedef
utility::pointer::owning_ptr
< VMax const > 		VMaxCOP
 
typedef
utility::pointer::owning_ptr
< VMin > 		VMinOP
 
typedef
utility::pointer::owning_ptr
< VMin const > 		VMinCOP
 
typedef
utility::pointer::owning_ptr
< PowExpression > 		PowExpressionOP
 
typedef
utility::pointer::owning_ptr
< PowExpression const > 		PowExpressionCOP
 
typedef
utility::pointer::owning_ptr
< ExpExpression > 		ExpExpressionOP
 
typedef
utility::pointer::owning_ptr
< ExpExpression const > 		ExpExpressionCOP
 
typedef
utility::pointer::owning_ptr
< LnExpression > 		LnExpressionOP
 
typedef
utility::pointer::owning_ptr
< LnExpression const > 		LnExpressionCOP
 
typedef
utility::pointer::owning_ptr
< InSetExpression > 		InSetExpressionOP
 
typedef
utility::pointer::owning_ptr
< InSetExpression const > 		InSetExpressionCOP
 
typedef
utility::pointer::owning_ptr
< VectorExpressionCreator > 		VectorExpressionCreatorOP
 
typedef
utility::pointer::owning_ptr
< VectorExpressionCreator
const > 		VectorExpressionCreatorCOP
 
typedef
utility::pointer::owning_ptr
< SurrogateVariableExpression > 		SurrogateVariableExpressionOP
 
typedef
utility::pointer::owning_ptr
< SurrogateVariableExpression
const > 		SurrogateVariableExpressionCOP
 
typedef
utility::pointer::owning_ptr
< DynamicAggregateFunction > 		DynamicAggregateFunctionOP
 
typedef
utility::pointer::owning_ptr
< DynamicAggregateFunction
const > 		DynamicAggregateFunctionCOP
 
typedef
utility::pointer::owning_ptr
< EntityFunc > 		EntityFuncOP
 
typedef
utility::pointer::owning_ptr
< EntityFunc const > 		EntityFuncCOP
 
typedef
utility::pointer::owning_ptr
< EntityCorrespondence > 		EntityCorrespondenceOP
 
typedef
utility::pointer::owning_ptr
< EntityCorrespondence const > 		EntityCorrespondenceCOP
 
typedef
utility::pointer::owning_ptr
< MultistateAggregateFunction > 		MultistateAggregateFunctionOP
 
typedef
utility::pointer::owning_ptr
< MultistateAggregateFunction
const > 		MultistateAggregateFunctionCOP
 
typedef
utility::pointer::owning_ptr
< MultistateFitnessFunction > 		MultistateFitnessFunctionOP
 
typedef
utility::pointer::owning_ptr
< MultistateFitnessFunction
const > 		MultistateFitnessFunctionCOP
 
typedef
utility::pointer::owning_ptr
< MPIMultistateFitnessFunction > 		MPIMultistateFitnessFunctionOP
 
typedef
utility::pointer::owning_ptr
< MPIMultistateFitnessFunction
const > 		MPIMultistateFitnessFunctionCOP
 
typedef
utility::pointer::owning_ptr
< PackDaemon > 		PackDaemonOP
 
typedef
utility::pointer::owning_ptr
< PackDaemon const > 		PackDaemonCOP
 
typedef
utility::pointer::owning_ptr
< DaemonSet > 		DaemonSetOP
 
typedef
utility::pointer::owning_ptr
< DaemonSet const > 		DaemonSetCOP
 
typedef
utility::pointer::owning_ptr
< NPDPropCalculator > 		NPDPropCalculatorOP
 
typedef
utility::pointer::owning_ptr
< NPDPropCalculator const > 		NPDPropCalculatorCOP
 
typedef
utility::pointer::owning_ptr
< NPDPropCalculatorCreator > 		NPDPropCalculatorCreatorOP
 
typedef
utility::pointer::owning_ptr
< NPDPropCalculatorCreator
const > 		NPDPropCalculatorCreatorCOP
 
typedef
utility::pointer::owning_ptr
< QuickRepacker > 		QuickRepackerOP
 
typedef
utility::pointer::owning_ptr
< QuickRepacker const > 		QuickRepackerCOP
 
typedef
utility::pointer::owning_ptr
< BasicSimAnnealerRepacker > 		BasicSimAnnealerRepackerOP
 
typedef
utility::pointer::owning_ptr
< BasicSimAnnealerRepacker
const > 		BasicSimAnnealerRepackerCOP
 
typedef
utility::pointer::owning_ptr
< DenseIGRepacker > 		DenseIGRepackerOP
 
typedef
utility::pointer::owning_ptr
< DenseIGRepacker const > 		DenseIGRepackerCOP
 
typedef
utility::pointer::owning_ptr
< DoubleDenseIGRepacker > 		DoubleDenseIGRepackerOP
 
typedef
utility::pointer::owning_ptr
< DoubleDenseIGRepacker const > 		DoubleDenseIGRepackerCOP
 

Enumerations

enum  ec_funcs {
  func_add_resid_to_entity_list = 1, func_entity_for_residue, func_n_residues_for_entity, func_residues_for_entity_begin,
  func_residues_for_entity_end
}
 
enum  DaemonSetMessage {
  error_message = 0, success_message, add_daemon, evaluate_entity,
  keep_rotamer_assignment_for_last_entity, discard_old_entity, geneate_pose_from_old_state, spin_down,
  n_daemon_set_messages
}
 

Functions

static basic::Tracer TR ("protocols.pack_daemon.DynamicAggregateFunction")
 
static basic::Tracer TR ("protocols.pack_daemon.PackDaemon")
 

Typedef Documentation

typedef utility::pointer::owning_ptr< BasicSimAnnealerRepacker const > protocols::pack_daemon::BasicSimAnnealerRepackerCOP

Definition at line 51 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< BasicSimAnnealerRepacker > protocols::pack_daemon::BasicSimAnnealerRepackerOP

Definition at line 48 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DaemonSet const > protocols::pack_daemon::DaemonSetCOP

Definition at line 33 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DaemonSet > protocols::pack_daemon::DaemonSetOP

Definition at line 30 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DenseIGRepacker const > protocols::pack_daemon::DenseIGRepackerCOP

Definition at line 56 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DenseIGRepacker > protocols::pack_daemon::DenseIGRepackerOP

Definition at line 53 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DoubleDenseIGRepacker const > protocols::pack_daemon::DoubleDenseIGRepackerCOP

Definition at line 61 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DoubleDenseIGRepacker > protocols::pack_daemon::DoubleDenseIGRepackerOP

Definition at line 58 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< DynamicAggregateFunction const > protocols::pack_daemon::DynamicAggregateFunctionCOP

Definition at line 74 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< DynamicAggregateFunction > protocols::pack_daemon::DynamicAggregateFunctionOP

Definition at line 71 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< EntityCorrespondence const > protocols::pack_daemon::EntityCorrespondenceCOP

Definition at line 26 of file EntityCorrespondence.fwd.hh.

typedef utility::pointer::owning_ptr< EntityCorrespondence > protocols::pack_daemon::EntityCorrespondenceOP

Definition at line 24 of file EntityCorrespondence.fwd.hh.

typedef utility::pointer::owning_ptr< EntityFunc const > protocols::pack_daemon::EntityFuncCOP

Definition at line 82 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< EntityFunc > protocols::pack_daemon::EntityFuncOP

Definition at line 80 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< ExpExpression const > protocols::pack_daemon::ExpExpressionCOP

Definition at line 53 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< ExpExpression > protocols::pack_daemon::ExpExpressionOP

Definition at line 51 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< InSetExpression const > protocols::pack_daemon::InSetExpressionCOP

Definition at line 61 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< InSetExpression > protocols::pack_daemon::InSetExpressionOP

Definition at line 59 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< IterativeVectorExpression const > protocols::pack_daemon::IterativeVectorExpressionCOP

Definition at line 33 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< IterativeVectorExpression > protocols::pack_daemon::IterativeVectorExpressionOP

Definition at line 31 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< LnExpression const > protocols::pack_daemon::LnExpressionCOP

Definition at line 57 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< LnExpression > protocols::pack_daemon::LnExpressionOP

Definition at line 55 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MPIMultistateFitnessFunction const > protocols::pack_daemon::MPIMultistateFitnessFunctionCOP

Definition at line 31 of file MultistateFitnessFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MPIMultistateFitnessFunction > protocols::pack_daemon::MPIMultistateFitnessFunctionOP

Definition at line 28 of file MultistateFitnessFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MultistateAggregateFunction const > protocols::pack_daemon::MultistateAggregateFunctionCOP

Definition at line 26 of file MultistateAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MultistateAggregateFunction > protocols::pack_daemon::MultistateAggregateFunctionOP

Definition at line 23 of file MultistateAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MultistateFitnessFunction const > protocols::pack_daemon::MultistateFitnessFunctionCOP

Definition at line 26 of file MultistateFitnessFunction.fwd.hh.

typedef utility::pointer::owning_ptr< MultistateFitnessFunction > protocols::pack_daemon::MultistateFitnessFunctionOP

Definition at line 23 of file MultistateFitnessFunction.fwd.hh.

typedef utility::pointer::owning_ptr< NPDPropCalculator const > protocols::pack_daemon::NPDPropCalculatorCOP

Definition at line 37 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< NPDPropCalculatorCreator const > protocols::pack_daemon::NPDPropCalculatorCreatorCOP

Definition at line 41 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< NPDPropCalculatorCreator > protocols::pack_daemon::NPDPropCalculatorCreatorOP

Definition at line 39 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< NPDPropCalculator > protocols::pack_daemon::NPDPropCalculatorOP

Definition at line 35 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< PackDaemon const > protocols::pack_daemon::PackDaemonCOP

Definition at line 28 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< PackDaemon > protocols::pack_daemon::PackDaemonOP

Definition at line 25 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< PowExpression const > protocols::pack_daemon::PowExpressionCOP

Definition at line 49 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< PowExpression > protocols::pack_daemon::PowExpressionOP

Definition at line 47 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< QuickRepacker const > protocols::pack_daemon::QuickRepackerCOP

Definition at line 46 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< QuickRepacker > protocols::pack_daemon::QuickRepackerOP

Definition at line 43 of file PackDaemon.fwd.hh.

typedef utility::pointer::owning_ptr< SurrogateVariableExpression const > protocols::pack_daemon::SurrogateVariableExpressionCOP

Definition at line 69 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< SurrogateVariableExpression > protocols::pack_daemon::SurrogateVariableExpressionOP

Definition at line 67 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VariableVectorExpression const > protocols::pack_daemon::VariableVectorExpressionCOP

Definition at line 29 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VariableVectorExpression > protocols::pack_daemon::VariableVectorExpressionOP

Definition at line 27 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorExpression const > protocols::pack_daemon::VectorExpressionCOP

Definition at line 25 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorExpressionCreator const > protocols::pack_daemon::VectorExpressionCreatorCOP

Definition at line 65 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorExpressionCreator > protocols::pack_daemon::VectorExpressionCreatorOP

Definition at line 63 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorExpression > protocols::pack_daemon::VectorExpressionOP

Definition at line 23 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorFunction const > protocols::pack_daemon::VectorFunctionCOP

Definition at line 37 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VectorFunction > protocols::pack_daemon::VectorFunctionOP

Definition at line 35 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VMax const > protocols::pack_daemon::VMaxCOP

Definition at line 41 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VMax > protocols::pack_daemon::VMaxOP

Definition at line 39 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VMin const > protocols::pack_daemon::VMinCOP

Definition at line 45 of file DynamicAggregateFunction.fwd.hh.

typedef utility::pointer::owning_ptr< VMin > protocols::pack_daemon::VMinOP

Definition at line 43 of file DynamicAggregateFunction.fwd.hh.

Enumeration Type Documentation

enum protocols::pack_daemon::DaemonSetMessage
Enumerator
error_message 
success_message 
add_daemon 
evaluate_entity 
keep_rotamer_assignment_for_last_entity 
discard_old_entity 
geneate_pose_from_old_state 
spin_down 
n_daemon_set_messages 

Definition at line 184 of file PackDaemon.hh.

enum protocols::pack_daemon::ec_funcs
Enumerator
func_add_resid_to_entity_list 
func_entity_for_residue 
func_n_residues_for_entity 
func_residues_for_entity_begin 
func_residues_for_entity_end 

Definition at line 35 of file EntityCorrespondence.cc.

Function Documentation

static basic::Tracer protocols::pack_daemon::TR ( "protocols.pack_daemon.DynamicAggregateFunction"  )
static

Referenced by protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::pack_daemon::DenseIGRepacker::create_dense_pdig_from_rot_to_pack(), protocols::pack_daemon::FASTER_IG_Repacker::create_faster_ig_from_rot_to_pack(), protocols::pack_daemon::MultistateFitnessFunction::evaluate(), protocols::pack_daemon::PackDaemon::print_entity_history(), protocols::pack_daemon::PackDaemon::recreate_pose_for_entity(), protocols::pack_daemon::PackDaemon::set_dlig_nmeg_limit(), and protocols::pack_daemon::PackDaemon::setup().

static basic::Tracer protocols::pack_daemon::TR ( "protocols.pack_daemon.PackDaemon"  )
static
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