protocols::optimize_weights Namespace Reference

Classes
class	DDGBindOptEData
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	ScaleAnnealerTemperatureOperation
class	IterativeOptEDriver
class	NestedEnergyTermPNatAAOptEPositionData
class	NestedEnergyTermDDGMutationOptEData
class	PNatAAOptERotamerData
class	PNatRotOptERotamerData
class	SingleStructureData
class	OptEPositionData
class	PNatAAOptEPositionData
class	PSSMOptEPositionData
class	PNatRotOptEPositionData
class	PNatStructureOptEData
class	DDGMutationOptEData
struct	WeightRangeConstraint
class	ConstraintedOptimizationWeightFunc
class	OptEPositionDataFactory
class	OptEData
class	OptEMultifunc
	OptE mode multifunction class. More...
class	WrapperOptEMultifunc
	OptE mode multifunction class. More...
class	OptEVariableExpression
class	WrappedOptEExpressionCreator
class	PNatLigPoseOptEData

Typedefs
using	AA = core::chemical::AA
typedef utility::pointer::shared_ptr< DDGBindOptEData >	DDGBindOptEDataOP
typedef utility::pointer::shared_ptr< DGBindOptEData >	DGBindOptEDataOP
typedef utility::pointer::shared_ptr< DGBindOptEData const >	DGBindOptEDataCOP
using	Strings = utility::vector1< std::string >
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 basic::Tracer	TR ("DDGBindOptEData")
static basic::Tracer	TR ("protocols.optimize_weights.IterativeOptEDriver")
static 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 basic::Tracer	TR ("NestedEnergyTermOptEData")
static basic::Tracer	TR ("protocols.optimize_weights.OptEData")
std::ostream &	operator<< (std::ostream &os, PNatAAOptERotamerDataOP rd)
static basic::Tracer	TR ("protocols.optimize_weights.OptEMultifunc")

Typedef Documentation

AA

using protocols::optimize_weights::AA = typedef core::chemical::AA

ConstraintedOptimizationWeightFuncOP

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

DDGBindOptEDataOP

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

DDGMutationOptEDataOP

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

DGBindOptEDataCOP

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

DGBindOptEDataOP

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

NestedEnergyTermDDGMutationOptEDataOP

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

NestedEnergyTermPNatAAOptEPositionDataOP

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

Position containers.

OptEDataOP

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

OptEMultifuncAP

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

OptEMultifuncCAP

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

OptEMultifuncCOP

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

OptEMultifuncOP

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

OptEPositionDataOP

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

OptEPositionDataOPs

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

OptEVariableExpressionCOP

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

OptEVariableExpressionOP

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

PNatAAOptEPositionDataOP

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

Position containers.

PNatAAOptERotamerDataOP

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

PNatAAOptERotamerDataOPs

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

PNatLigPoseOptEDataCOP

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

PNatLigPoseOptEDataOP

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

PNatRotOptEPositionDataOP

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

PNatRotOptERotamerDataOP

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

PNatRotOptERotamerDataOPs

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

PNatStructureOptEDataOP

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

PSSMOptEPositionDataOP

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

SingleStructureDataCOP

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

SingleStructureDataOP

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

SingleStructureDataOPs

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

Strings

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

WrapperOptEMultifuncAP

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

WrapperOptEMultifuncCAP

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

WrapperOptEMultifuncCOP

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

WrapperOptEMultifuncOP

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

Enumeration Type Documentation

AddStatus

enum protocols::optimize_weights::AddStatus

Enumerator
ADDED_STRUCTURE_AS_INTENDED
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
DID_NOT_ADD_STRUCTURE

OptEMultifuncMPIMessages

enum protocols::optimize_weights::OptEMultifuncMPIMessages

Enumerator
EVAL_FUNC
EVAL_DFUNC
END_OF_MINIMIZATION

OptEPositionDataType

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

attach_debugger()

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.

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

load_component_weights()

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.

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

References protocols::optimize_weights::OptEPositionDataFactory::is_optE_type_name(), n_optE_data_types, protocols::optimize_weights::OptEPositionDataFactory::optE_type_from_name(), core::id::to_string(), core::pack::task::tokenize_line(), and TR().

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

operator<<()

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

Author

ashworth

TR() [1/5]

static 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::DDGBindOptEData::get_score(), 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::DDGBindOptEData::process_score(), 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().

TR() [2/5]

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

static

TR() [3/5]

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

static

TR() [4/5]

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

static

TR() [5/5]

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

static

TR_VERBOSE()

static 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().