Package rosetta :: Package protocols :: Package optimize_weights :: Module _protocols_optimize_weights_

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Module _protocols_optimize_weights_

Classes

[hide private]

AddStatus
protocols/optimize_weights/IterativeOptEDriver.hh:54

ConstraintedOptimizationWeightFunc
protocols/optimize_weights/OptEData.hh:1057

ConstraintedOptimizationWeightFuncAP

ConstraintedOptimizationWeightFuncCAP

DDGBindOptEData
protocols/optimize_weights/DDGBindOptEData.hh:29

DDGBindOptEDataAP

DDGBindOptEDataCAP

DDGMutationOptEData
protocols/optimize_weights/OptEData.hh:911

DDGMutationOptEDataAP

DDGMutationOptEDataCAP

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.

DGBindOptEDataAP

DGBindOptEDataCAP

IterativeOptEDriver
protocols/optimize_weights/IterativeOptEDriver.hh:61

IterativeOptEDriverAP

IterativeOptEDriverCAP

NestedEnergyTermDDGMutationOptEData
protocols/optimize_weights/NestedEnergyTermOptEData.hh:119

NestedEnergyTermDDGMutationOptEDataAP

NestedEnergyTermDDGMutationOptEDataCAP

NestedEnergyTermPNatAAOptEPositionData
protocols/optimize_weights/NestedEnergyTermOptEData.hh:37

NestedEnergyTermPNatAAOptEPositionDataAP

NestedEnergyTermPNatAAOptEPositionDataCAP

OptEData
////////////////////////////////////////////////////////////////////////////

OptEDataAP

OptEDataCAP

OptEMultifunc
OptE mode multifunction class

OptEMultifuncAP

OptEMultifuncCAP

OptEMultifuncMPIMessages
protocols/optimize_weights/OptEMultifunc.hh:42

OptEPositionData
////////////////////////////////////////////////////////////////////////////

OptEPositionDataAP

OptEPositionDataCAP

OptEPositionDataFactory
protocols/optimize_weights/OptEData.hh:1156

OptEPositionDataFactoryAP

OptEPositionDataFactoryCAP

OptEPositionDataType
protocols/optimize_weights/OptEData.fwd.hh:63

OptEVariableExpression
protocols/optimize_weights/OptEMultifunc.hh:388

OptEVariableExpressionAP

OptEVariableExpressionCAP

PNatAAOptEPositionData
protocols/optimize_weights/OptEData.hh:329

PNatAAOptEPositionDataAP

PNatAAOptEPositionDataCAP

PNatAAOptERotamerData
protocols/optimize_weights/OptEData.hh:44

PNatAAOptERotamerDataAP

PNatAAOptERotamerDataCAP

PNatLigPoseOptEData
protocols/optimize_weights/PNatLigPoseOptEData.hh:34

PNatLigPoseOptEDataAP

PNatLigPoseOptEDataCAP

PNatRotOptEPositionData
protocols/optimize_weights/OptEData.hh:586

PNatRotOptEPositionDataAP

PNatRotOptEPositionDataCAP

PNatRotOptERotamerData
protocols/optimize_weights/OptEData.hh:101

PNatRotOptERotamerDataAP

PNatRotOptERotamerDataCAP

PNatStructureOptEData
protocols/optimize_weights/OptEData.hh:755

PNatStructureOptEDataAP

PNatStructureOptEDataCAP

PSSMOptEPositionData
protocols/optimize_weights/OptEData.hh:502

PSSMOptEPositionDataAP

PSSMOptEPositionDataCAP

SingleStructureData
protocols/optimize_weights/OptEData.hh:159

SingleStructureDataAP

SingleStructureDataCAP

WeightRangeConstraint
protocols/optimize_weights/OptEData.hh:1038

WeightRangeConstraintAP

WeightRangeConstraintCAP

WrappedOptEExpressionCreator
protocols/optimize_weights/OptEMultifunc.hh:403

WrappedOptEExpressionCreatorAP

WrappedOptEExpressionCreatorCAP

WrapperOptEMultifunc
DANGER DANGER DANGER This class must never be allocated on the stack.

WrapperOptEMultifuncAP

WrapperOptEMultifuncCAP

__CPP_ConstraintedOptimizationWeightFunc__

__CPP_DDGBindOptEData__

__CPP_DDGMutationOptEData__

__CPP_DGBindOptEData__

__CPP_NestedEnergyTermDDGMutationOptEData__

__CPP_NestedEnergyTermPNatAAOptEPositionData__

__CPP_OptEMultifunc__

__CPP_OptEPositionData__

__CPP_PNatAAOptEPositionData__

__CPP_PNatLigPoseOptEData__

__CPP_PNatRotOptEPositionData__

__CPP_PNatStructureOptEData__

__CPP_PSSMOptEPositionData__

__CPP_WrappedOptEExpressionCreator__

__CPP_WrapperOptEMultifunc__

Functions

[hide private]

load_component_weights(...)
load_component_weights( (vector1_Real)component_weights) -> None : Read options[ optE::component_weights ] file from input file.

Variables

[hide private]

ADDED_STRUCTURE_AS_INTENDED = rosetta.protocols.optimize_weigh...

ADDED_STRUCTURE_OPPOSITE_AS_INTENDED = rosetta.protocols.optim...

DID_NOT_ADD_STRUCTURE = rosetta.protocols.optimize_weights._pr...

END_OF_MINIMIZATION = rosetta.protocols.optimize_weights._prot...

EVAL_DFUNC = rosetta.protocols.optimize_weights._protocols_opt...

EVAL_FUNC = rosetta.protocols.optimize_weights._protocols_opti...

__package__ = None

constrained_optimization_weight_func = rosetta.protocols.optim...

dG_binding_correlation = rosetta.protocols.optimize_weights._p...

ddG_bind_correlation = rosetta.protocols.optimize_weights._pro...

ddG_mutation_correlation = rosetta.protocols.optimize_weights....

ddG_mutation_correlation_with_unfolded_energy = rosetta.protoc...

n_optE_data_types = rosetta.protocols.optimize_weights._protoc...

prob_native_amino_acid = rosetta.protocols.optimize_weights._p...

prob_native_amino_acid_with_unfolded_energy = rosetta.protocol...

prob_native_ligand_pose = rosetta.protocols.optimize_weights._...

prob_native_rotamer = rosetta.protocols.optimize_weights._prot...

prob_native_structure = rosetta.protocols.optimize_weights._pr...

pssm_data = rosetta.protocols.optimize_weights._protocols_opti...

Function Details

[hide private]

load_component_weights(...)


load_component_weights( (vector1_Real)component_weights) -> None :
    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.
    

    C++ signature :
        void load_component_weights(utility::vector1<double, std::allocator<double> > {lvalue})

Variables Details

[hide private]

ADDED_STRUCTURE_AS_INTENDED

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.AddSta
tus.ADDED_STRUCTURE_AS_INTENDED

ADDED_STRUCTURE_OPPOSITE_AS_INTENDED

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.AddSta
tus.ADDED_STRUCTURE_OPPOSITE_AS_INTENDED

DID_NOT_ADD_STRUCTURE

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.AddSta
tus.DID_NOT_ADD_STRUCTURE

END_OF_MINIMIZATION

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEMu
ltifuncMPIMessages.END_OF_MINIMIZATION

EVAL_DFUNC

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEMu
ltifuncMPIMessages.EVAL_DFUNC

EVAL_FUNC

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEMu
ltifuncMPIMessages.EVAL_FUNC

constrained_optimization_weight_func

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.constrained_optimization_weight_func

dG_binding_correlation

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.dG_binding_correlation

ddG_bind_correlation

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.ddG_bind_correlation

ddG_mutation_correlation

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.ddG_mutation_correlation

ddG_mutation_correlation_with_unfolded_energy

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.ddG_mutation_correlation_with_unfolded_energy

n_optE_data_types

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.n_optE_data_types

prob_native_amino_acid

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.prob_native_amino_acid

prob_native_amino_acid_with_unfolded_energy

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.prob_native_amino_acid_with_unfolded_energy

prob_native_ligand_pose

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.prob_native_ligand_pose

prob_native_rotamer

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.prob_native_rotamer

prob_native_structure

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.prob_native_structure

pssm_data

Value:

rosetta.protocols.optimize_weights._protocols_optimize_weights_.OptEPo
sitionDataType.pssm_data