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
typedef core::chemical::AA	AA
typedef utility::pointer::owning_ptr < DDGBindOptEData >	DDGBindOptEDataOP
typedef utility::pointer::owning_ptr < DGBindOptEData >	DGBindOptEDataOP
typedef utility::pointer::owning_ptr < DGBindOptEData const >	DGBindOptEDataCOP
typedef utility::vector1 < std::string >	Strings
typedef utility::pointer::owning_ptr < NestedEnergyTermPNatAAOptEPositionData >	NestedEnergyTermPNatAAOptEPositionDataOP
	Position containers. More...
typedef utility::pointer::owning_ptr < NestedEnergyTermDDGMutationOptEData >	NestedEnergyTermDDGMutationOptEDataOP
typedef utility::pointer::owning_ptr < PNatAAOptERotamerData >	PNatAAOptERotamerDataOP
typedef utility::pointer::owning_ptr < PNatRotOptERotamerData >	PNatRotOptERotamerDataOP
typedef utility::pointer::owning_ptr < SingleStructureData >	SingleStructureDataOP
typedef utility::pointer::owning_ptr < ConstraintedOptimizationWeightFunc >	ConstraintedOptimizationWeightFuncOP
typedef utility::pointer::owning_ptr < SingleStructureData const >	SingleStructureDataCOP
typedef utility::pointer::owning_ptr < OptEPositionData >	OptEPositionDataOP
typedef utility::pointer::owning_ptr < PNatAAOptEPositionData >	PNatAAOptEPositionDataOP
	Position containers. More...
typedef utility::pointer::owning_ptr < PSSMOptEPositionData >	PSSMOptEPositionDataOP
typedef utility::pointer::owning_ptr < PNatRotOptEPositionData >	PNatRotOptEPositionDataOP
typedef utility::pointer::owning_ptr < PNatStructureOptEData >	PNatStructureOptEDataOP
typedef utility::pointer::owning_ptr < DDGMutationOptEData >	DDGMutationOptEDataOP
typedef utility::pointer::owning_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::owning_ptr < OptEMultifunc >	OptEMultifuncOP
typedef utility::pointer::owning_ptr < OptEMultifunc const >	OptEMultifuncCOP
typedef utility::pointer::owning_ptr < WrapperOptEMultifunc >	WrapperOptEMultifuncOP
typedef utility::pointer::owning_ptr < WrapperOptEMultifunc const >	WrapperOptEMultifuncCOP
typedef utility::pointer::access_ptr < WrapperOptEMultifunc >	WrapperOptEMultifuncAP
typedef utility::pointer::access_ptr < WrapperOptEMultifunc const >	WrapperOptEMultifuncCAP
typedef utility::pointer::owning_ptr < OptEVariableExpression >	OptEVariableExpressionOP
typedef utility::pointer::owning_ptr < OptEVariableExpression const >	OptEVariableExpressionCOP
typedef utility::pointer::owning_ptr < PNatLigPoseOptEData >	PNatLigPoseOptEDataOP
typedef utility::pointer::owning_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")
basic::Tracer	TR ("protocols.optimize_weights.IterativeOptEDriver")
basic::Tracer	TR_VERBOSE ("protocols.optimize_weights.IterativeOptEDriver.verbose")
static numeric::random::RandomGenerator	optE_RG (10193)
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

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

Definition at line 42 of file DDGBindOptEData.cc.

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

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

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

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

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

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

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

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

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

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

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

Definition at line 32 of file NestedEnergyTermOptEData.fwd.hh.

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

Position containers.

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

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

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

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

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

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

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

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

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

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

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

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

Definition at line 36 of file OptEMultifunc.fwd.hh.

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

Definition at line 34 of file OptEMultifunc.fwd.hh.

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

Position containers.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Definition at line 52 of file OptEData.fwd.hh.

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

Definition at line 50 of file OptEData.fwd.hh.

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

Definition at line 44 of file OptEData.fwd.hh.

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

Definition at line 42 of file OptEData.fwd.hh.

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

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

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

Definition at line 57 of file NestedEnergyTermOptEData.cc.

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

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

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

Definition at line 32 of file OptEMultifunc.fwd.hh.

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

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

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

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

Enumeration Type Documentation

enum protocols::optimize_weights::AddStatus

Enumerator
ADDED_STRUCTURE_AS_INTENDED
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
DID_NOT_ADD_STRUCTURE

Definition at line 58 of file IterativeOptEDriver.hh.

enum protocols::optimize_weights::OptEMultifuncMPIMessages

Enumerator
EVAL_FUNC
EVAL_DFUNC
END_OF_MINIMIZATION

Definition at line 47 of file OptEMultifunc.hh.

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

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

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

Definition at line 5449 of file IterativeOptEDriver.cc.

References protocols::swa::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.

Definition at line 5373 of file IterativeOptEDriver.cc.

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

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

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

(ostream operator for OptERotamerDataOP)

Author

ashworth

Definition at line 87 of file OptEData.cc.

static numeric::random::RandomGenerator protocols::optimize_weights::optE_RG ( 10193  )

static

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

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

static

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

static

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

static

basic::Tracer protocols::optimize_weights::TR

(

"protocols.optimize_weights.IterativeOptEDriver"

)

basic::Tracer protocols::optimize_weights::TR_VERBOSE

(

"protocols.optimize_weights.IterativeOptEDriver.verbose"

)

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().