Rosetta 3.4
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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 std::vector< std::string > Strings
typedef
utility::pointer::owning_ptr
< NestedEnergyTermPNatAAOptEPositionData
NestedEnergyTermPNatAAOptEPositionDataOP
 Position containers.
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
< SingleStructureData const > 
SingleStructureDataCOP
typedef
utility::pointer::owning_ptr
< OptEPositionData
OptEPositionDataOP
typedef
utility::pointer::owning_ptr
< PNatAAOptEPositionData
PNatAAOptEPositionDataOP
 Position containers.
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.
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.
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

Position containers.

Position containers.

typedef std::vector< std::string > protocols::optimize_weights::Strings

Enumeration Type Documentation

Enumerator:
ADDED_STRUCTURE_AS_INTENDED 
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED 
DID_NOT_ADD_STRUCTURE 
Enumerator:
EVAL_FUNC 
EVAL_DFUNC 
END_OF_MINIMIZATION 
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::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.

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

References make_table_of_pilot_apps::d.

static numeric::random::RandomGenerator protocols::optimize_weights::optE_RG ( 10193  ) [static]
static basic::Tracer protocols::optimize_weights::TR ( "NestedEnergyTermOptEData"  ) [static]
static basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.OptEData"  ) [static]
static basic::Tracer protocols::optimize_weights::TR ( "DDGBindOptEData"  ) [static]
basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.IterativeOptEDriver"  )
static basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.OptEMultifunc"  ) [static]
basic::Tracer protocols::optimize_weights::TR_VERBOSE ( "protocols.optimize_weights.IterativeOptEDriver.verbose"  )
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