protocols::pack_daemon Namespace Reference

Classes
class	VectorExpression
class	VariableVectorExpression
class	IterativeVectorExpression
class	VectorFunction
class	VectorFunction2
class	Mean
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	DynamicAggregateFunctionDriver
class	EntityFuncExpressionCreator
class	EntityFunc
class	EntityCorrespondence
class	MultistateAggregateFunction
struct	EntityHistoryLT
class	TopEntitySet
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::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

BasicSimAnnealerRepackerCOP

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

BasicSimAnnealerRepackerOP

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

DaemonSetCOP

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

DaemonSetOP

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

DenseIGRepackerCOP

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

DenseIGRepackerOP

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

DoubleDenseIGRepackerCOP

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

DoubleDenseIGRepackerOP

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

DynamicAggregateFunctionCOP

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

DynamicAggregateFunctionDriverCOP

typedef utility::pointer::shared_ptr< DynamicAggregateFunctionDriver const > protocols::pack_daemon::DynamicAggregateFunctionDriverCOP

DynamicAggregateFunctionDriverOP

typedef utility::pointer::shared_ptr< DynamicAggregateFunctionDriver > protocols::pack_daemon::DynamicAggregateFunctionDriverOP

DynamicAggregateFunctionOP

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

EntityCorrespondenceCOP

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

EntityCorrespondenceOP

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

EntityFuncCOP

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

EntityFuncOP

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

ExpExpressionCOP

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

ExpExpressionOP

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

FileContentsMapCOP

typedef utility::pointer::shared_ptr< FileContentsMap const > protocols::pack_daemon::FileContentsMapCOP

FileContentsMapOP

typedef utility::pointer::shared_ptr< FileContentsMap > protocols::pack_daemon::FileContentsMapOP

InSetExpressionCOP

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

InSetExpressionOP

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

IterativeVectorExpressionCOP

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

IterativeVectorExpressionOP

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

LnExpressionCOP

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

LnExpressionOP

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

MPIMultistateFitnessFunctionCOP

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

MPIMultistateFitnessFunctionOP

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

MultistateAggregateFunctionCOP

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

MultistateAggregateFunctionOP

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

MultistateFitnessFunctionCOP

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

MultistateFitnessFunctionOP

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

NPDPropCalculatorCOP

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

NPDPropCalculatorCreatorCOP

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

NPDPropCalculatorCreatorOP

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

NPDPropCalculatorOP

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

PackDaemonCOP

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

PackDaemonOP

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

PowExpressionCOP

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

PowExpressionOP

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

QuickRepackerCOP

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

QuickRepackerOP

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

SurrogateVariableExpressionCOP

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

SurrogateVariableExpressionOP

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

TopEntitySetCOP

typedef utility::pointer::shared_ptr< TopEntitySet const > protocols::pack_daemon::TopEntitySetCOP

TopEntitySetOP

typedef utility::pointer::shared_ptr< TopEntitySet > protocols::pack_daemon::TopEntitySetOP

VariableVectorExpressionCOP

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

VariableVectorExpressionOP

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

VectorExpressionCOP

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

VectorExpressionCreatorCOP

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

VectorExpressionCreatorOP

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

VectorExpressionOP

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

VectorFunctionCOP

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

VectorFunctionOP

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

VMaxCOP

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

VMaxOP

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

VMinCOP

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

VMinOP

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

Enumeration Type Documentation

DaemonSetMessage

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

ec_funcs

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

Function Documentation

create_entity_resfile_contents()

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

Throws

a 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().

initialize_ga_randomizer_from_entity_task()

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().

initialize_task_from_entity_resfile_and_secondary_resfile()

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
	)

References core::pack::task::ResfileContents::commands_for_residue(), core::pack::task::ResfileContents::default_commands(), core::pose::Pose::size(), and core::pack::task::ResfileContents::specialized_commands_exist_for_residue().

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

TR() [1/2]

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

static

Referenced by protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::pack_daemon::DynamicAggregateFunction::assign_state_energies_to_variables_and_subexpressions(), 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::DynamicAggregateFunction::create_variable_vector_expressions(), protocols::pack_daemon::DynamicAggregateFunctionDriver::distribute_jobs_to_remote_daemons(), protocols::pack_daemon::MultistateFitnessFunction::evaluate(), protocols::pack_daemon::EntityFunc::evaluate(), protocols::pack_daemon::DynamicAggregateFunction::evaluate(), protocols::pack_daemon::DynamicAggregateFunctionDriver::initialize_daemon_with_all_states(), protocols::pack_daemon::DynamicAggregateFunctionDriver::initialize_from_input_file(), protocols::pack_daemon::PackDaemon::print_entity_history(), protocols::pack_daemon::DynamicAggregateFunction::process_FITNESS_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::pack_daemon::DynamicAggregateFunction::process_SCALAR_EXPRESSION_line(), protocols::pack_daemon::EntityFunc::process_SCORE_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_VECTOR_line(), protocols::pack_daemon::EntityFunc::process_SUB_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::read_state_vector_file(), protocols::pack_daemon::PackDaemon::recreate_pose_for_entity(), protocols::pack_daemon::DynamicAggregateFunction::select_relevant_states(), protocols::pack_daemon::PackDaemon::set_dlig_nmeg_limit(), protocols::pack_daemon::PackDaemon::setup(), and protocols::pack_daemon::DynamicAggregateFunction::turn_expression_ASTs_into_expressions().

TR() [2/2]

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

static