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protocols::pack_daemon Namespace Reference

Classes

class  BasicSimAnnealerRepacker
 
class  DaemonSet
 
class  DenseIGRepacker
 
class  DoubleDenseIGRepacker
 
class  DynamicAggregateFunction
 
class  DynamicAggregateFunctionDriver
 
class  EntityCorrespondence
 
class  EntityFunc
 
class  EntityFuncExpressionCreator
 
struct  EntityHistoryLT
 
class  ExpExpression
 
class  FASTER_IG_Repacker
 
class  InSetExpression
 Returns "true" if the expression ex evaluates to one of a set of indicated values. More...
 
class  IterativeVectorExpression
 
class  LnExpression
 
class  Mean
 
class  MPIMultistateFitnessFunction
 
class  MultistateAggregateFunction
 
class  MultistateFitnessFunction
 
class  NPDPropCalculator
 
class  NPDPropCalculatorCreator
 
class  PackDaemon
 
class  PowExpression
 
class  QuickRepacker
 
class  RotamerSubsetRepacker
 
class  StructureFileNames
 
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  TopEntitySet
 
class  VariableVectorExpression
 
class  VectorExpression
 
class  VectorExpressionCreator
 
class  VectorFunction
 
class  VectorFunction2
 
class  VMax
 
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  VMin
 
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...
 

Typedefs

typedef
utility::pointer::shared_ptr
< VectorExpression
VectorExpressionOP
 
typedef
utility::pointer::shared_ptr
< VectorExpression const > 
VectorExpressionCOP
 
typedef
utility::pointer::shared_ptr
< VariableVectorExpression
VariableVectorExpressionOP
 
typedef
utility::pointer::shared_ptr
< VariableVectorExpression
const > 
VariableVectorExpressionCOP
 
typedef
utility::pointer::shared_ptr
< IterativeVectorExpression
IterativeVectorExpressionOP
 
typedef
utility::pointer::shared_ptr
< IterativeVectorExpression
const > 
IterativeVectorExpressionCOP
 
typedef
utility::pointer::shared_ptr
< VectorFunction
VectorFunctionOP
 
typedef
utility::pointer::shared_ptr
< VectorFunction const > 
VectorFunctionCOP
 
typedef
utility::pointer::shared_ptr
< VMax
VMaxOP
 
typedef
utility::pointer::shared_ptr
< VMax const > 
VMaxCOP
 
typedef
utility::pointer::shared_ptr
< VMin
VMinOP
 
typedef
utility::pointer::shared_ptr
< VMin const > 
VMinCOP
 
typedef
utility::pointer::shared_ptr
< PowExpression
PowExpressionOP
 
typedef
utility::pointer::shared_ptr
< PowExpression const > 
PowExpressionCOP
 
typedef
utility::pointer::shared_ptr
< ExpExpression
ExpExpressionOP
 
typedef
utility::pointer::shared_ptr
< ExpExpression const > 
ExpExpressionCOP
 
typedef
utility::pointer::shared_ptr
< LnExpression
LnExpressionOP
 
typedef
utility::pointer::shared_ptr
< LnExpression const > 
LnExpressionCOP
 
typedef
utility::pointer::shared_ptr
< InSetExpression
InSetExpressionOP
 
typedef
utility::pointer::shared_ptr
< InSetExpression const > 
InSetExpressionCOP
 
typedef
utility::pointer::shared_ptr
< VectorExpressionCreator
VectorExpressionCreatorOP
 
typedef
utility::pointer::shared_ptr
< VectorExpressionCreator
const > 
VectorExpressionCreatorCOP
 
typedef
utility::pointer::shared_ptr
< SurrogateVariableExpression
SurrogateVariableExpressionOP
 
typedef
utility::pointer::shared_ptr
< SurrogateVariableExpression
const > 
SurrogateVariableExpressionCOP
 
typedef
utility::pointer::shared_ptr
< FileContentsMap > 
FileContentsMapOP
 
typedef
utility::pointer::shared_ptr
< FileContentsMap const > 
FileContentsMapCOP
 
typedef
utility::pointer::shared_ptr
< DynamicAggregateFunction
DynamicAggregateFunctionOP
 
typedef
utility::pointer::shared_ptr
< DynamicAggregateFunction
const > 
DynamicAggregateFunctionCOP
 
typedef
utility::pointer::shared_ptr
< DynamicAggregateFunctionDriver
DynamicAggregateFunctionDriverOP
 
typedef
utility::pointer::shared_ptr
< DynamicAggregateFunctionDriver
const > 
DynamicAggregateFunctionDriverCOP
 
typedef
utility::pointer::shared_ptr
< EntityFunc
EntityFuncOP
 
typedef
utility::pointer::shared_ptr
< EntityFunc const > 
EntityFuncCOP
 
typedef
utility::pointer::shared_ptr
< EntityCorrespondence
EntityCorrespondenceOP
 
typedef
utility::pointer::shared_ptr
< EntityCorrespondence const > 
EntityCorrespondenceCOP
 
typedef
utility::pointer::shared_ptr
< MultistateAggregateFunction
MultistateAggregateFunctionOP
 
typedef
utility::pointer::shared_ptr
< MultistateAggregateFunction
const > 
MultistateAggregateFunctionCOP
 
typedef
utility::pointer::shared_ptr
< TopEntitySet
TopEntitySetOP
 
typedef
utility::pointer::shared_ptr
< TopEntitySet const > 
TopEntitySetCOP
 
typedef
utility::pointer::shared_ptr
< MultistateFitnessFunction
MultistateFitnessFunctionOP
 
typedef
utility::pointer::shared_ptr
< MultistateFitnessFunction
const > 
MultistateFitnessFunctionCOP
 
typedef
utility::pointer::shared_ptr
< MPIMultistateFitnessFunction
MPIMultistateFitnessFunctionOP
 
typedef
utility::pointer::shared_ptr
< MPIMultistateFitnessFunction
const > 
MPIMultistateFitnessFunctionCOP
 
typedef
utility::pointer::shared_ptr
< PackDaemon
PackDaemonOP
 
typedef
utility::pointer::shared_ptr
< PackDaemon const > 
PackDaemonCOP
 
typedef
utility::pointer::shared_ptr
< DaemonSet
DaemonSetOP
 
typedef
utility::pointer::shared_ptr
< DaemonSet const > 
DaemonSetCOP
 
typedef
utility::pointer::shared_ptr
< NPDPropCalculator
NPDPropCalculatorOP
 
typedef
utility::pointer::shared_ptr
< NPDPropCalculator const > 
NPDPropCalculatorCOP
 
typedef
utility::pointer::shared_ptr
< NPDPropCalculatorCreator
NPDPropCalculatorCreatorOP
 
typedef
utility::pointer::shared_ptr
< NPDPropCalculatorCreator
const > 
NPDPropCalculatorCreatorCOP
 
typedef
utility::pointer::shared_ptr
< QuickRepacker
QuickRepackerOP
 
typedef
utility::pointer::shared_ptr
< QuickRepacker const > 
QuickRepackerCOP
 
typedef
utility::pointer::shared_ptr
< BasicSimAnnealerRepacker
BasicSimAnnealerRepackerOP
 
typedef
utility::pointer::shared_ptr
< BasicSimAnnealerRepacker
const > 
BasicSimAnnealerRepackerCOP
 
typedef
utility::pointer::shared_ptr
< DenseIGRepacker
DenseIGRepackerOP
 
typedef
utility::pointer::shared_ptr
< DenseIGRepacker const > 
DenseIGRepackerCOP
 
typedef
utility::pointer::shared_ptr
< DoubleDenseIGRepacker
DoubleDenseIGRepackerOP
 
typedef
utility::pointer::shared_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")
 
void create_entity_resfile_contents (std::istream &resfile, std::string const &resfile_name, core::pack::task::ResfileContentsOP &entity_resfile_contents, core::pack::task::PackerTaskOP &entity_task, core::Size &num_entities)
 
void initialize_task_from_entity_resfile_and_secondary_resfile (core::pose::Pose const &pose, EntityCorrespondenceCOP ec, core::pack::task::ResfileContents const &entity_resfile_contents, core::pack::task::ResfileContents const &secondary_resfile_contents, core::pack::task::PackerTaskOP task)
 
void initialize_ga_randomizer_from_entity_task (protocols::genetic_algorithm::PositionSpecificRandomizerOP rand, core::pack::task::PackerTaskOP entity_task)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< DaemonSet const > protocols::pack_daemon::DaemonSetCOP
typedef utility::pointer::shared_ptr< DaemonSet > protocols::pack_daemon::DaemonSetOP
typedef utility::pointer::shared_ptr< DenseIGRepacker const > protocols::pack_daemon::DenseIGRepackerCOP
typedef utility::pointer::shared_ptr< DenseIGRepacker > protocols::pack_daemon::DenseIGRepackerOP
typedef utility::pointer::shared_ptr< DoubleDenseIGRepacker const > protocols::pack_daemon::DoubleDenseIGRepackerCOP
typedef utility::pointer::shared_ptr< EntityCorrespondence const > protocols::pack_daemon::EntityCorrespondenceCOP
typedef utility::pointer::shared_ptr< EntityFunc const > protocols::pack_daemon::EntityFuncCOP
typedef utility::pointer::shared_ptr< EntityFunc > protocols::pack_daemon::EntityFuncOP
typedef utility::pointer::shared_ptr< ExpExpression const > protocols::pack_daemon::ExpExpressionCOP
typedef utility::pointer::shared_ptr< ExpExpression > protocols::pack_daemon::ExpExpressionOP
typedef utility::pointer::shared_ptr< FileContentsMap const > protocols::pack_daemon::FileContentsMapCOP
typedef utility::pointer::shared_ptr< FileContentsMap > protocols::pack_daemon::FileContentsMapOP
typedef utility::pointer::shared_ptr< InSetExpression const > protocols::pack_daemon::InSetExpressionCOP
typedef utility::pointer::shared_ptr< InSetExpression > protocols::pack_daemon::InSetExpressionOP
typedef utility::pointer::shared_ptr< LnExpression const > protocols::pack_daemon::LnExpressionCOP
typedef utility::pointer::shared_ptr< LnExpression > protocols::pack_daemon::LnExpressionOP
typedef utility::pointer::shared_ptr< NPDPropCalculator const > protocols::pack_daemon::NPDPropCalculatorCOP
typedef utility::pointer::shared_ptr< NPDPropCalculator > protocols::pack_daemon::NPDPropCalculatorOP
typedef utility::pointer::shared_ptr< PackDaemon const > protocols::pack_daemon::PackDaemonCOP
typedef utility::pointer::shared_ptr< PackDaemon > protocols::pack_daemon::PackDaemonOP
typedef utility::pointer::shared_ptr< PowExpression const > protocols::pack_daemon::PowExpressionCOP
typedef utility::pointer::shared_ptr< PowExpression > protocols::pack_daemon::PowExpressionOP
typedef utility::pointer::shared_ptr< QuickRepacker const > protocols::pack_daemon::QuickRepackerCOP
typedef utility::pointer::shared_ptr< QuickRepacker > protocols::pack_daemon::QuickRepackerOP
typedef utility::pointer::shared_ptr< TopEntitySet const > protocols::pack_daemon::TopEntitySetCOP
typedef utility::pointer::shared_ptr< TopEntitySet > protocols::pack_daemon::TopEntitySetOP
typedef utility::pointer::shared_ptr< VectorExpression const > protocols::pack_daemon::VectorExpressionCOP
typedef utility::pointer::shared_ptr< VectorExpressionCreator const > protocols::pack_daemon::VectorExpressionCreatorCOP
typedef utility::pointer::shared_ptr< VectorExpression > protocols::pack_daemon::VectorExpressionOP
typedef utility::pointer::shared_ptr< VectorFunction const > protocols::pack_daemon::VectorFunctionCOP
typedef utility::pointer::shared_ptr< VectorFunction > protocols::pack_daemon::VectorFunctionOP
typedef utility::pointer::shared_ptr< VMax const > protocols::pack_daemon::VMaxCOP
typedef utility::pointer::shared_ptr< VMax > protocols::pack_daemon::VMaxOP
typedef utility::pointer::shared_ptr< VMin const > protocols::pack_daemon::VMinCOP
typedef utility::pointer::shared_ptr< VMin > protocols::pack_daemon::VMinOP

Enumeration Type Documentation

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 
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 

Function Documentation

void protocols::pack_daemon::create_entity_resfile_contents ( std::istream &  resfile,
std::string const &  resfile_name,
core::pack::task::ResfileContentsOP entity_resfile_contents,
core::pack::task::PackerTaskOP entity_task,
core::Size num_entities 
)
Exceptions
Throwsa utility::excn::EXCN_Msg_Exception if the input entity resfile does not does not conform to the entity resfile format.

References core::chemical::FA_STANDARD, and core::pose::make_pose_from_sequence().

Referenced by protocols::pack_daemon::DaemonSet::set_entity_resfile().

void protocols::pack_daemon::initialize_ga_randomizer_from_entity_task ( protocols::genetic_algorithm::PositionSpecificRandomizerOP  rand,
core::pack::task::PackerTaskOP  entity_task 
)

Create the list of available entity elements from the set of available residue types in the "entity_task", the PackerTask that has been created from an entity resfile, which defines a hypothetical pose and places restrictions on the amino acids this pose can adopt. These restrictions in turn must be translated into the available search space that the genetic algorithm can explore.

References protocols::multistate_design::list_amino_acid_options().

void protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile ( core::pose::Pose const &  pose,
EntityCorrespondenceCOP  ec,
core::pack::task::ResfileContents const &  entity_resfile_contents,
core::pack::task::ResfileContents const &  secondary_resfile_contents,
core::pack::task::PackerTaskOP  task 
)
static basic::Tracer protocols::pack_daemon::TR ( "protocols.pack_daemon.DynamicAggregateFunction"  )
static
static basic::Tracer protocols::pack_daemon::TR ( "protocols.pack_daemon.PackDaemon"  )
static