protocols::optimize_weights Namespace Reference

Classes
class	ConstraintedOptimizationWeightFunc
class	DDGBindOptEData
class	DDGMutationOptEData
class	DGBindOptEData
	Score a "bound" and an "unbound" structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding. More...
class	IterativeOptEDriver
class	NestedEnergyTermDDGMutationOptEData
class	NestedEnergyTermPNatAAOptEPositionData
class	OptEData
class	OptEMultifunc
	OptE mode multifunction class. More...
class	OptEPositionData
class	OptEPositionDataFactory
class	OptEVariableExpression
class	PNatAAOptEPositionData
class	PNatAAOptERotamerData
class	PNatLigPoseOptEData
class	PNatRotOptEPositionData
class	PNatRotOptERotamerData
class	PNatStructureOptEData
class	PSSMOptEPositionData
class	ScaleAnnealerTemperatureOperation
class	SingleStructureData
struct	WeightRangeConstraint
class	WrappedOptEExpressionCreator
class	WrapperOptEMultifunc
	OptE mode multifunction class. More...

Typedefs
typedef core::chemical::AA	AA
typedef utility::pointer::shared_ptr < DDGBindOptEData >	DDGBindOptEDataOP
typedef utility::pointer::shared_ptr < DGBindOptEData >	DGBindOptEDataOP
typedef utility::pointer::shared_ptr < DGBindOptEData const >	DGBindOptEDataCOP
typedef utility::vector1 < std::string >	Strings
typedef utility::pointer::shared_ptr < NestedEnergyTermPNatAAOptEPositionData >	NestedEnergyTermPNatAAOptEPositionDataOP
	Position containers. More...
typedef utility::pointer::shared_ptr < NestedEnergyTermDDGMutationOptEData >	NestedEnergyTermDDGMutationOptEDataOP
typedef utility::pointer::shared_ptr < PNatAAOptERotamerData >	PNatAAOptERotamerDataOP
typedef utility::pointer::shared_ptr < PNatRotOptERotamerData >	PNatRotOptERotamerDataOP
typedef utility::pointer::shared_ptr < SingleStructureData >	SingleStructureDataOP
typedef utility::pointer::shared_ptr < ConstraintedOptimizationWeightFunc >	ConstraintedOptimizationWeightFuncOP
typedef utility::pointer::shared_ptr < SingleStructureData const >	SingleStructureDataCOP
typedef utility::pointer::shared_ptr < OptEPositionData >	OptEPositionDataOP
typedef utility::pointer::shared_ptr < PNatAAOptEPositionData >	PNatAAOptEPositionDataOP
	Position containers. More...
typedef utility::pointer::shared_ptr < PSSMOptEPositionData >	PSSMOptEPositionDataOP
typedef utility::pointer::shared_ptr < PNatRotOptEPositionData >	PNatRotOptEPositionDataOP
typedef utility::pointer::shared_ptr < PNatStructureOptEData >	PNatStructureOptEDataOP
typedef utility::pointer::shared_ptr < DDGMutationOptEData >	DDGMutationOptEDataOP
typedef utility::pointer::shared_ptr < OptEData >	OptEDataOP
typedef utility::vector1 < PNatAAOptERotamerDataOP >	PNatAAOptERotamerDataOPs
typedef utility::vector1 < PNatRotOptERotamerDataOP >	PNatRotOptERotamerDataOPs
typedef utility::vector1 < SingleStructureDataOP >	SingleStructureDataOPs
typedef utility::vector1 < OptEPositionDataOP >	OptEPositionDataOPs
typedef utility::pointer::shared_ptr < OptEMultifunc >	OptEMultifuncOP
typedef utility::pointer::shared_ptr < OptEMultifunc const >	OptEMultifuncCOP
typedef utility::pointer::weak_ptr < OptEMultifunc >	OptEMultifuncAP
typedef utility::pointer::weak_ptr < OptEMultifunc const >	OptEMultifuncCAP
typedef utility::pointer::shared_ptr < WrapperOptEMultifunc >	WrapperOptEMultifuncOP
typedef utility::pointer::shared_ptr < WrapperOptEMultifunc const >	WrapperOptEMultifuncCOP
typedef utility::pointer::weak_ptr < WrapperOptEMultifunc >	WrapperOptEMultifuncAP
typedef utility::pointer::weak_ptr < WrapperOptEMultifunc const >	WrapperOptEMultifuncCAP
typedef utility::pointer::shared_ptr < OptEVariableExpression >	OptEVariableExpressionOP
typedef utility::pointer::shared_ptr < OptEVariableExpression const >	OptEVariableExpressionCOP
typedef utility::pointer::shared_ptr < PNatLigPoseOptEData >	PNatLigPoseOptEDataOP
typedef utility::pointer::shared_ptr < PNatLigPoseOptEData const >	PNatLigPoseOptEDataCOP

Enumerations
enum	AddStatus { ADDED_STRUCTURE_AS_INTENDED, ADDED_STRUCTURE_OPPOSITE_AS_INTENDED, DID_NOT_ADD_STRUCTURE }
enum	OptEPositionDataType {   prob_native_amino_acid = 1, pssm_data, prob_native_rotamer, prob_native_structure,   prob_native_ligand_pose, dG_binding_correlation, ddG_mutation_correlation, constrained_optimization_weight_func,   prob_native_amino_acid_with_unfolded_energy, ddG_mutation_correlation_with_unfolded_energy, ddG_bind_correlation, n_optE_data_types = ddG_bind_correlation }
enum	OptEMultifuncMPIMessages { EVAL_FUNC, EVAL_DFUNC, END_OF_MINIMIZATION }

Functions
static thread_local basic::Tracer	TR ("DDGBindOptEData")
static thread_local basic::Tracer	TR ("protocols.optimize_weights.IterativeOptEDriver")
static thread_local basic::Tracer	TR_VERBOSE ("protocols.optimize_weights.IterativeOptEDriver.verbose")
void	attach_debugger ()
	for parallel applications. Wait at a specific point and stay there until you can attach a gdb process (with the –pid <ID> flag in gdb) and internally modify the variable "i" to some non-zero value with a "set var i = 7" command. More...
void	load_component_weights (utility::vector1< core::Real > &component_weights)
	Read options[ optE::component_weights ] file from input file. Not a member of the above driver class since its independent of the driver; possibly belongs in a separate source file. Any component specified in the weights file is set to the corresponding weight. Any component not specified in the weights file is set to 1. More...
static thread_local basic::Tracer	TR ("NestedEnergyTermOptEData")
static thread_local basic::Tracer	TR ("protocols.optimize_weights.OptEData")
std::ostream &	operator<< (std::ostream &os, PNatAAOptERotamerDataOP rd)
static thread_local basic::Tracer	TR ("protocols.optimize_weights.OptEMultifunc")

Typedef Documentation

typedef core::chemical::AA protocols::optimize_weights::AA

typedef utility::pointer::shared_ptr< ConstraintedOptimizationWeightFunc > protocols::optimize_weights::ConstraintedOptimizationWeightFuncOP

typedef utility::pointer::shared_ptr< DDGBindOptEData > protocols::optimize_weights::DDGBindOptEDataOP

typedef utility::pointer::shared_ptr< DDGMutationOptEData > protocols::optimize_weights::DDGMutationOptEDataOP

typedef utility::pointer::shared_ptr< DGBindOptEData const > protocols::optimize_weights::DGBindOptEDataCOP

typedef utility::pointer::shared_ptr< DGBindOptEData > protocols::optimize_weights::DGBindOptEDataOP

typedef utility::pointer::shared_ptr< NestedEnergyTermDDGMutationOptEData > protocols::optimize_weights::NestedEnergyTermDDGMutationOptEDataOP

typedef utility::pointer::shared_ptr< NestedEnergyTermPNatAAOptEPositionData > protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionDataOP

Position containers.

typedef utility::pointer::shared_ptr< OptEData > protocols::optimize_weights::OptEDataOP

typedef utility::pointer::weak_ptr< OptEMultifunc > protocols::optimize_weights::OptEMultifuncAP

typedef utility::pointer::weak_ptr< OptEMultifunc const > protocols::optimize_weights::OptEMultifuncCAP

typedef utility::pointer::shared_ptr< OptEMultifunc const > protocols::optimize_weights::OptEMultifuncCOP

typedef utility::pointer::shared_ptr< OptEMultifunc > protocols::optimize_weights::OptEMultifuncOP

typedef utility::pointer::shared_ptr< OptEPositionData > protocols::optimize_weights::OptEPositionDataOP

typedef utility::vector1< OptEPositionDataOP > protocols::optimize_weights::OptEPositionDataOPs

typedef utility::pointer::shared_ptr< OptEVariableExpression const > protocols::optimize_weights::OptEVariableExpressionCOP

typedef utility::pointer::shared_ptr< OptEVariableExpression > protocols::optimize_weights::OptEVariableExpressionOP

typedef utility::pointer::shared_ptr< PNatAAOptEPositionData > protocols::optimize_weights::PNatAAOptEPositionDataOP

Position containers.

typedef utility::pointer::shared_ptr< PNatAAOptERotamerData > protocols::optimize_weights::PNatAAOptERotamerDataOP

typedef utility::vector1< PNatAAOptERotamerDataOP > protocols::optimize_weights::PNatAAOptERotamerDataOPs

typedef utility::pointer::shared_ptr< PNatLigPoseOptEData const > protocols::optimize_weights::PNatLigPoseOptEDataCOP

typedef utility::pointer::shared_ptr< PNatLigPoseOptEData > protocols::optimize_weights::PNatLigPoseOptEDataOP

typedef utility::pointer::shared_ptr< PNatRotOptEPositionData > protocols::optimize_weights::PNatRotOptEPositionDataOP

typedef utility::pointer::shared_ptr< PNatRotOptERotamerData > protocols::optimize_weights::PNatRotOptERotamerDataOP

typedef utility::vector1< PNatRotOptERotamerDataOP > protocols::optimize_weights::PNatRotOptERotamerDataOPs

typedef utility::pointer::shared_ptr< PNatStructureOptEData > protocols::optimize_weights::PNatStructureOptEDataOP

typedef utility::pointer::shared_ptr< PSSMOptEPositionData > protocols::optimize_weights::PSSMOptEPositionDataOP

typedef utility::pointer::shared_ptr< SingleStructureData const > protocols::optimize_weights::SingleStructureDataCOP

typedef utility::pointer::shared_ptr< SingleStructureData > protocols::optimize_weights::SingleStructureDataOP

typedef utility::vector1< SingleStructureDataOP > protocols::optimize_weights::SingleStructureDataOPs

typedef utility::vector1< std::string > protocols::optimize_weights::Strings

typedef utility::pointer::weak_ptr< WrapperOptEMultifunc > protocols::optimize_weights::WrapperOptEMultifuncAP

typedef utility::pointer::weak_ptr< WrapperOptEMultifunc const > protocols::optimize_weights::WrapperOptEMultifuncCAP

typedef utility::pointer::shared_ptr< WrapperOptEMultifunc const > protocols::optimize_weights::WrapperOptEMultifuncCOP

typedef utility::pointer::shared_ptr< WrapperOptEMultifunc > protocols::optimize_weights::WrapperOptEMultifuncOP

Enumeration Type Documentation

enum protocols::optimize_weights::AddStatus

Enumerator
ADDED_STRUCTURE_AS_INTENDED
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
DID_NOT_ADD_STRUCTURE

enum protocols::optimize_weights::OptEMultifuncMPIMessages

Enumerator
EVAL_FUNC
EVAL_DFUNC
END_OF_MINIMIZATION

enum protocols::optimize_weights::OptEPositionDataType

Enumerator
prob_native_amino_acid
pssm_data
prob_native_rotamer
prob_native_structure
prob_native_ligand_pose
dG_binding_correlation
ddG_mutation_correlation
constrained_optimization_weight_func
prob_native_amino_acid_with_unfolded_energy
ddG_mutation_correlation_with_unfolded_energy
ddG_bind_correlation
n_optE_data_types

Function Documentation

void protocols::optimize_weights::attach_debugger

(

)

for parallel applications. Wait at a specific point and stay there until you can attach a gdb process (with the –pid <ID> flag in gdb) and internally modify the variable "i" to some non-zero value with a "set var i = 7" command.

attach_debugger

References protocols::stepwise::modeler::rna::sleep().

void protocols::optimize_weights::load_component_weights

(

utility::vector1< core::Real > &

component_weights

)

Read options[ optE::component_weights ] file from input file. Not a member of the above driver class since its independent of the driver; possibly belongs in a separate source file. Any component specified in the weights file is set to the corresponding weight. Any component not specified in the weights file is set to 1.

IterativeOptEDriver::load_component_weights()

input file should be white-space delimited component-name/weight pairs.

References utility::from_string(), protocols::optimize_weights::OptEPositionDataFactory::is_optE_type_name(), n_optE_data_types, protocols::optimize_weights::OptEPositionDataFactory::optE_type_from_name(), option, utility::to_string(), core::pack::task::tokenize_line(), TR(), user, utility_exit, and utility_exit_with_message.

Referenced by protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver().

std::ostream & protocols::optimize_weights::operator<<	(	std::ostream &	os,
		PNatAAOptERotamerDataOP	rd
	)

(ostream operator for OptERotamerDataOP)

Author

ashworth

static thread_local basic::Tracer protocols::optimize_weights::TR ( "DDGBindOptEData"  )

static

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ligand_discrimination_data(), protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_energies_from_slave_cpus(), protocols::optimize_weights::IterativeOptEDriver::collect_rotamer_recovery_data_from_slave_cpus(), protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::converged(), protocols::optimize_weights::IterativeOptEDriver::decide_if_sequence_recovery_improved(), protocols::optimize_weights::OptEMultifunc::dfunc(), protocols::optimize_weights::WrapperOptEMultifunc::dfunc(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::optimize_weights::PNatRotOptEPositionData::get_score(), protocols::optimize_weights::PNatStructureOptEData::get_score(), protocols::optimize_weights::DDGMutationOptEData::get_score(), protocols::optimize_weights::IterativeOptEDriver::go(), protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver(), load_component_weights(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::optimize_weights::OptEMultifunc::operator()(), protocols::optimize_weights::WrapperOptEMultifunc::operator()(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::optimize_weights::OptEData::read_from_binary_file(), protocols::optimize_weights::OptEData::read_from_file(), protocols::optimize_weights::IterativeOptEDriver::score_position_data(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::optimize_weights::IterativeOptEDriver::write_parameters_to_std_out(), protocols::optimize_weights::OptEData::write_to_binary_file(), and protocols::optimize_weights::OptEData::write_to_file().

static thread_local basic::Tracer protocols::optimize_weights::TR ( "NestedEnergyTermOptEData"  )

static

static thread_local basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.OptEMultifunc"  )

static

static thread_local basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.OptEData"  )

static

static thread_local basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.IterativeOptEDriver"  )

static

static thread_local basic::Tracer protocols::optimize_weights::TR_VERBOSE ( "protocols.optimize_weights.IterativeOptEDriver.verbose"  )

static

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::divide_up_pdbs(), protocols::optimize_weights::IterativeOptEDriver::initialize_free_and_fixed(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::optimize_weights::IterativeOptEDriver::run_design_on_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::score_position_data(), and protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile().