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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

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

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

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

Position containers.

typedef utility::pointer::shared_ptr< PNatLigPoseOptEData const > protocols::optimize_weights::PNatLigPoseOptEDataCOP
typedef utility::pointer::shared_ptr< SingleStructureData const > protocols::optimize_weights::SingleStructureDataCOP
using protocols::optimize_weights::Strings = typedef utility::vector1<std::string>
typedef utility::pointer::shared_ptr< WrapperOptEMultifunc const > protocols::optimize_weights::WrapperOptEMultifuncCOP

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.

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.

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().

std::ostream & protocols::optimize_weights::operator<< ( std::ostream &  os,
PNatAAOptERotamerDataOP  rd 
)
Author
ashworth
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
static basic::Tracer protocols::optimize_weights::TR ( "protocols.optimize_weights.IterativeOptEDriver"  )
static
static basic::Tracer protocols::optimize_weights::TR_VERBOSE ( "protocols.optimize_weights.IterativeOptEDriver.verbose"  )
static