Python: module rosetta.protocols.optimize

rosetta.protocols.optimize_weights

index
(built-in)

Bindings for protocols::optimize_weights namespace

Classes



builtins.object

AddStatus
IterativeOptEDriver
OptEData
OptEMultifuncMPIMessages
OptEPositionData

ConstraintedOptimizationWeightFunc
DDGBindOptEData
DDGMutationOptEData

NestedEnergyTermDDGMutationOptEData

DGBindOptEData
PNatAAOptEPositionData

NestedEnergyTermPNatAAOptEPositionData
PSSMOptEPositionData

PNatRotOptEPositionData
PNatStructureOptEData

PNatLigPoseOptEData

OptEPositionDataFactory
OptEPositionDataType
PNatAAOptERotamerData
PNatRotOptERotamerData
SingleStructureData
WeightRangeConstraint

rosetta.core.optimization.Multifunc(builtins.object)

OptEMultifunc
WrapperOptEMultifunc

rosetta.numeric.expression_parser.ExpressionCreator(rosetta.numeric.expression_parser.ASTVisitor)

WrappedOptEExpressionCreator

rosetta.numeric.expression_parser.VariableExpression(rosetta.numeric.expression_parser.Expression)

OptEVariableExpression

class AddStatus(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.optimize_weights.AddStatus, rosetta.protocols.optimize_weights.AddStatus) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.optimize_weights.AddStatus) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.optimize_weights.AddStatus, int) -> NoneType 2. __init__(rosetta.protocols.optimize_weights.AddStatus, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.optimize_weights.AddStatus) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.optimize_weights.AddStatus, rosetta.protocols.optimize_weights.AddStatus) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.optimize_weights.AddStatus) -> str

Data and other attributes defined here:

ADDED_STRUCTURE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_AS_INTENDED

ADDED_STRUCTURE_OPPOSITE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_OPPOSITE_AS_INTENDED

DID_NOT_ADD_STRUCTURE = AddStatus.DID_NOT_ADD_STRUCTURE

class ConstraintedOptimizationWeightFunc(OptEPositionData)


Method resolution order:

ConstraintedOptimizationWeightFunc

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(self : handle, score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType 3. __init__(handle, rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc,  : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) -> rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

initialize_constraints_from_file(...) from builtins.PyCapsule
initialize_constraints_from_file(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class DDGBindOptEData(OptEPositionData)


Method resolution order:

DDGBindOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.DDGBindOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

add_mutant_complex(...) from builtins.PyCapsule
add_mutant_complex(self : rosetta.protocols.optimize_weights.DDGBindOptEData, mut : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_mutant_unbounds(...) from builtins.PyCapsule
add_mutant_unbounds(self : rosetta.protocols.optimize_weights.DDGBindOptEData, mut : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_mutation(...) from builtins.PyCapsule
add_mutation(self : rosetta.protocols.optimize_weights.DDGBindOptEData, mutation : (int, (rosetta.core.chemical.AA, rosetta.core.chemical.AA))) -> NoneType

add_wt_complex(...) from builtins.PyCapsule
add_wt_complex(self : rosetta.protocols.optimize_weights.DDGBindOptEData, wt : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_wt_unbounds(...) from builtins.PyCapsule
add_wt_unbounds(self : rosetta.protocols.optimize_weights.DDGBindOptEData, wt : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.DDGBindOptEData,  : rosetta.protocols.optimize_weights.DDGBindOptEData) -> rosetta.protocols.optimize_weights.DDGBindOptEData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.DDGBindOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.DDGBindOptEData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.DDGBindOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.DDGBindOptEData,  : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.DDGBindOptEData,  : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_experimental_ddg_bind(...) from builtins.PyCapsule
set_experimental_ddg_bind(self : rosetta.protocols.optimize_weights.DDGBindOptEData, exp_ddg_bind : float) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.DDGBindOptEData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.DDGBindOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.DDGBindOptEData,  : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.DDGBindOptEData,  : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Data and other attributes defined here:

DDG_Bind_File_Index = <class 'rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index'>

MUT_COMPLEXES_LIST_FILE = DDG_Bind_File_Index.MUT_COMPLEXES_LIST_FILE

MUT_UNBOUNDS_LIST_FILE = DDG_Bind_File_Index.MUT_UNBOUNDS_LIST_FILE

WT_COMPLEXES_LIST_FILE = DDG_Bind_File_Index.WT_COMPLEXES_LIST_FILE

WT_UNBOUNDS_LIST_FILE = DDG_Bind_File_Index.WT_UNBOUNDS_LIST_FILE

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class DDGMutationOptEData(OptEPositionData)


Method resolution order:

DDGMutationOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.DDGMutationOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

add_mutant(...) from builtins.PyCapsule
add_mutant(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, mut : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_wt(...) from builtins.PyCapsule
add_wt(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, wt : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.DDGMutationOptEData,  : rosetta.protocols.optimize_weights.DDGMutationOptEData) -> rosetta.protocols.optimize_weights.DDGMutationOptEData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.DDGMutationOptEData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_experimental_ddg(...) from builtins.PyCapsule
set_experimental_ddg(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, ddg : float) -> NoneType

set_mut_aa(...) from builtins.PyCapsule
set_mut_aa(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, mut_aa : rosetta.core.chemical.AA) -> NoneType

set_wt_aa(...) from builtins.PyCapsule
set_wt_aa(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, wt_aa : rosetta.core.chemical.AA) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.DDGMutationOptEData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.DDGMutationOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class DGBindOptEData(OptEPositionData)

    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.

Method resolution order:

DGBindOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.DGBindOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.DGBindOptEData,  : rosetta.protocols.optimize_weights.DGBindOptEData) -> rosetta.protocols.optimize_weights.DGBindOptEData

bound_struct(...) from builtins.PyCapsule
bound_struct(self : rosetta.protocols.optimize_weights.DGBindOptEData, x : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

deltaG_bind(...) from builtins.PyCapsule
deltaG_bind(self : rosetta.protocols.optimize_weights.DGBindOptEData, x : float) -> NoneType

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.DGBindOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.DGBindOptEData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.DGBindOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.DGBindOptEData,  : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.DGBindOptEData,  : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.DGBindOptEData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.DGBindOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

unbound_struct(...) from builtins.PyCapsule
unbound_struct(self : rosetta.protocols.optimize_weights.DGBindOptEData, x : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.DGBindOptEData,  : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.DGBindOptEData,  : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class IterativeOptEDriver(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(rosetta.protocols.optimize_weights.IterativeOptEDriver) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

go(...) from builtins.PyCapsule
go(rosetta.protocols.optimize_weights.IterativeOptEDriver) -> NoneType

task_factory(...) from builtins.PyCapsule
task_factory(self : rosetta.protocols.optimize_weights.IterativeOptEDriver,  : rosetta.core.pack.task.TaskFactory) -> NoneType take care when using a custom TaskFactory: TaskOperations must not 'accumulate state' as they will be reused repeatedly

class NestedEnergyTermDDGMutationOptEData(DDGMutationOptEData)


Method resolution order:

NestedEnergyTermDDGMutationOptEData

DDGMutationOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData,  : rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) -> rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) -> int

set_mut_unfolded_energies_emap(...) from builtins.PyCapsule
set_mut_unfolded_energies_emap(self : rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, e : rosetta.core.scoring.EMapVector) -> NoneType

set_wt_unfolded_energies_emap(...) from builtins.PyCapsule
set_wt_unfolded_energies_emap(self : rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, e : rosetta.core.scoring.EMapVector) -> NoneType

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

Methods inherited from DDGMutationOptEData:

add_mutant(...) from builtins.PyCapsule
add_mutant(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, mut : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_wt(...) from builtins.PyCapsule
add_wt(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, wt : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_experimental_ddg(...) from builtins.PyCapsule
set_experimental_ddg(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, ddg : float) -> NoneType

set_mut_aa(...) from builtins.PyCapsule
set_mut_aa(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, mut_aa : rosetta.core.chemical.AA) -> NoneType

set_wt_aa(...) from builtins.PyCapsule
set_wt_aa(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, wt_aa : rosetta.core.chemical.AA) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.DDGMutationOptEData) -> int

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class NestedEnergyTermPNatAAOptEPositionData(PNatAAOptEPositionData)


Method resolution order:

NestedEnergyTermPNatAAOptEPositionData

PNatAAOptEPositionData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData,  : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) -> rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) -> int

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_unfolded_energy_emap_vector(...) from builtins.PyCapsule
set_unfolded_energy_emap_vector(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, emap_vector : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

unfolded_energy_emap_vector(...) from builtins.PyCapsule
unfolded_energy_emap_vector(rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) -> rosetta.utility.vector1_core_scoring_EMapVector

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from PNatAAOptEPositionData:

add_rotamer_line_data(...) from builtins.PyCapsule
add_rotamer_line_data(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in : rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> NoneType

data(...) from builtins.PyCapsule
data(*args, **kwargs) Overloaded function. 1. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t 2. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

native_aa(...) from builtins.PyCapsule
native_aa(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.core.chemical.AA

neighbor_count(...) from builtins.PyCapsule
neighbor_count(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

position(...) from builtins.PyCapsule
position(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

rotamer_data_begin(...) from builtins.PyCapsule
rotamer_data_begin(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(...) from builtins.PyCapsule
rotamer_data_end(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(...) from builtins.PyCapsule
set_native_aa(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in : rosetta.core.chemical.AA) -> NoneType

set_neighbor_count(...) from builtins.PyCapsule
set_neighbor_count(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in : int) -> NoneType

set_position(...) from builtins.PyCapsule
set_position(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in : int) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class OptEData(builtins.object)

    ////////////////////////////////////////////////////////////////////////////

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.optimize_weights.OptEData) -> NoneType 2. __init__(self : rosetta.protocols.optimize_weights.OptEData, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

add_position_data(...) from builtins.PyCapsule
add_position_data(self : rosetta.protocols.optimize_weights.OptEData, pos_data_in : rosetta.protocols.optimize_weights.OptEPositionData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.OptEData,  : rosetta.protocols.optimize_weights.OptEData) -> rosetta.protocols.optimize_weights.OptEData

energy_terms(...) from builtins.PyCapsule
energy_terms(rosetta.protocols.optimize_weights.OptEData) -> rosetta.utility.vector1_core_scoring_ScoreType

fixed_energy_terms(...) from builtins.PyCapsule
fixed_energy_terms(rosetta.protocols.optimize_weights.OptEData) -> rosetta.utility.vector1_core_scoring_ScoreType

num_positions(...) from builtins.PyCapsule
num_positions(rosetta.protocols.optimize_weights.OptEData) -> int

num_rotamers(...) from builtins.PyCapsule
num_rotamers(rosetta.protocols.optimize_weights.OptEData) -> int

position_data_begin(...) from builtins.PyCapsule
position_data_begin(rosetta.protocols.optimize_weights.OptEData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::OptEPositionData>, std::allocator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> > > >

position_data_end(...) from builtins.PyCapsule
position_data_end(rosetta.protocols.optimize_weights.OptEData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::OptEPositionData>, std::allocator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> > > >

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.OptEData, filename : str) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.OptEData, filename : str) -> NoneType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(*args, **kwargs) Overloaded function. 1. write_to_binary_file(rosetta.protocols.optimize_weights.OptEData) -> NoneType 2. write_to_binary_file(self : rosetta.protocols.optimize_weights.OptEData, filename : str) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(*args, **kwargs) Overloaded function. 1. write_to_file(rosetta.protocols.optimize_weights.OptEData) -> NoneType 2. write_to_file(self : rosetta.protocols.optimize_weights.OptEData, filename : str) -> NoneType

class OptEMultifunc(rosetta.core.optimization.Multifunc)

    OptE mode multifunction class

Method resolution order:

OptEMultifunc

rosetta.core.optimization.Multifunc

builtins.object

Methods defined here:

__call__(...) from builtins.PyCapsule
__call__(self : rosetta.protocols.optimize_weights.OptEMultifunc, vars : rosetta.utility.vector1_double) -> float

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, opte_data_in : rosetta.protocols.optimize_weights.OptEData, fixed_terms_in : rosetta.core.scoring.EMapVector, num_free_in : int, score_list_in : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list_in : rosetta.utility.vector1_core_scoring_ScoreType, component_weights : rosetta.utility.vector1_double) -> NoneType 2. __init__(self : handle, opte_data_in : rosetta.protocols.optimize_weights.OptEData, fixed_terms_in : rosetta.core.scoring.EMapVector, num_free_in : int, score_list_in : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list_in : rosetta.utility.vector1_core_scoring_ScoreType, reference_energies_in : rosetta.utility.vector1_double, component_weights : rosetta.utility.vector1_double) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

declare_minimization_over(...) from builtins.PyCapsule
declare_minimization_over(rosetta.protocols.optimize_weights.OptEMultifunc) -> NoneType For driver node: inform the non-driver nodes that minimization is over.  Must be called before object is destructed (Should not be called in the destructor, as dstors should not throw exceptions, and MPI communication can absolutely result in exceptions).

dfunc(...) from builtins.PyCapsule
dfunc(self : rosetta.protocols.optimize_weights.OptEMultifunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType OptE dfunc

fix_reference_energies(...) from builtins.PyCapsule
fix_reference_energies(*args, **kwargs) Overloaded function. 1. fix_reference_energies(self : rosetta.protocols.optimize_weights.OptEMultifunc, setting : bool) -> NoneType 2. fix_reference_energies(rosetta.protocols.optimize_weights.OptEMultifunc) -> bool Are the reference energies being optimized at all, or are they being held fixed?

get_dofs_from_energy_map(...) from builtins.PyCapsule
get_dofs_from_energy_map(self : rosetta.protocols.optimize_weights.OptEMultifunc, start_vals : rosetta.core.scoring.EMapVector) -> rosetta.utility.vector1_double Extract variable weights from an Energy Map

get_energy_map_from_dofs(...) from builtins.PyCapsule
get_energy_map_from_dofs(self : rosetta.protocols.optimize_weights.OptEMultifunc, dofs : rosetta.utility.vector1_double) -> rosetta.core.scoring.EMapVector Expand free variables and combine with fixed to make an Energy Map

get_reference_energies_from_dofs(...) from builtins.PyCapsule
get_reference_energies_from_dofs(self : rosetta.protocols.optimize_weights.OptEMultifunc, dofs : rosetta.utility.vector1_double) -> rosetta.utility.vector1_double

set_starting_reference_energies(...) from builtins.PyCapsule
set_starting_reference_energies(self : rosetta.protocols.optimize_weights.OptEMultifunc, values : rosetta.utility.vector1_double) -> NoneType

wait_for_remote_vars(...) from builtins.PyCapsule
wait_for_remote_vars(rosetta.protocols.optimize_weights.OptEMultifunc) -> NoneType Non-driver node wait for MPI vars to evaluate either the func or the dfunc.

Methods inherited from rosetta.core.optimization.Multifunc:

abort_min(...) from builtins.PyCapsule
abort_min(self : rosetta.core.optimization.Multifunc,  : rosetta.utility.vector1_double) -> bool Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

dump(...) from builtins.PyCapsule
dump(self : rosetta.core.optimization.Multifunc,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType Error state reached -- derivative does not match gradient Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect.

class OptEMultifuncMPIMessages(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages, rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages, int) -> NoneType 2. __init__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages, rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages) -> str

Data and other attributes defined here:

END_OF_MINIMIZATION = OptEMultifuncMPIMessages.END_OF_MINIMIZATION

EVAL_DFUNC = OptEMultifuncMPIMessages.EVAL_DFUNC

EVAL_FUNC = OptEMultifuncMPIMessages.EVAL_FUNC

class OptEPositionData(builtins.object)

    ////////////////////////////////////////////////////////////////////////////

Methods defined here:

__init__(self, /, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.OptEPositionData,  : rosetta.protocols.optimize_weights.OptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.OptEPositionData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.OptEPositionData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.OptEPositionData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType Return the upper and lower bound on the unweighted components at this position if they are larger (or smaller) than the unweighted values already in the two input EnergyMaps.

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.OptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.OptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.OptEPositionData) -> int

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.OptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.OptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.OptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

class OptEPositionDataFactory(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(rosetta.protocols.optimize_weights.OptEPositionDataFactory) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

create_position_data(...) from builtins.PyCapsule
create_position_data(type : rosetta.protocols.optimize_weights.OptEPositionDataType) -> rosetta.protocols.optimize_weights.OptEPositionData

is_optE_type_name(...) from builtins.PyCapsule
is_optE_type_name(name : str) -> bool

optE_type_from_name(...) from builtins.PyCapsule
optE_type_from_name(name : str) -> rosetta.protocols.optimize_weights.OptEPositionDataType

optE_type_name(...) from builtins.PyCapsule
optE_type_name(type : rosetta.protocols.optimize_weights.OptEPositionDataType) -> str

class OptEPositionDataType(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.optimize_weights.OptEPositionDataType, rosetta.protocols.optimize_weights.OptEPositionDataType) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.optimize_weights.OptEPositionDataType) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.optimize_weights.OptEPositionDataType, int) -> NoneType 2. __init__(rosetta.protocols.optimize_weights.OptEPositionDataType, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.optimize_weights.OptEPositionDataType) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.optimize_weights.OptEPositionDataType, rosetta.protocols.optimize_weights.OptEPositionDataType) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.optimize_weights.OptEPositionDataType) -> str

Data and other attributes defined here:

constrained_optimization_weight_func = OptEPositionDataType.constrained_optimization_weight_func

dG_binding_correlation = OptEPositionDataType.dG_binding_correlation

ddG_bind_correlation = OptEPositionDataType.n_optE_data_types

ddG_mutation_correlation = OptEPositionDataType.ddG_mutation_correlation

ddG_mutation_correlation_with_unfolded_energy = OptEPositionDataType.ddG_mutation_correlation_with_unfolded_energy

n_optE_data_types = OptEPositionDataType.n_optE_data_types

prob_native_amino_acid = OptEPositionDataType.prob_native_amino_acid

prob_native_amino_acid_with_unfolded_energy = OptEPositionDataType.prob_native_amino_acid_with_unfolded_energy

prob_native_ligand_pose = OptEPositionDataType.prob_native_ligand_pose

prob_native_rotamer = OptEPositionDataType.prob_native_rotamer

prob_native_structure = OptEPositionDataType.prob_native_structure

pssm_data = OptEPositionDataType.pssm_data

class OptEVariableExpression(rosetta.numeric.expression_parser.VariableExpression)


Method resolution order:

OptEVariableExpression

rosetta.numeric.expression_parser.VariableExpression

rosetta.numeric.expression_parser.Expression

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, name : str) -> NoneType 2. __init__(self : handle, name : str, value : float) -> NoneType 3. __init__(handle, rosetta.protocols.optimize_weights.OptEVariableExpression) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.OptEVariableExpression,  : rosetta.protocols.optimize_weights.OptEVariableExpression) -> rosetta.protocols.optimize_weights.OptEVariableExpression

id(...) from builtins.PyCapsule
id(rosetta.protocols.optimize_weights.OptEVariableExpression) -> int

set_id(...) from builtins.PyCapsule
set_id(self : rosetta.protocols.optimize_weights.OptEVariableExpression, id : int) -> NoneType

update_value_from_list(...) from builtins.PyCapsule
update_value_from_list(self : rosetta.protocols.optimize_weights.OptEVariableExpression, value_vector : rosetta.utility.vector1_double) -> NoneType

Methods inherited from rosetta.numeric.expression_parser.VariableExpression:

__call__(...) from builtins.PyCapsule
__call__(rosetta.numeric.expression_parser.VariableExpression) -> float

active_variables(...) from builtins.PyCapsule
active_variables(rosetta.numeric.expression_parser.VariableExpression) -> rosetta.std.list_std_string_std_allocator_std_string_t

differentiate(...) from builtins.PyCapsule
differentiate(self : rosetta.numeric.expression_parser.VariableExpression, varname : str) -> rosetta.numeric.expression_parser.Expression Returns the literal expression 1 if name_ == varname_ and null otherwise

name(...) from builtins.PyCapsule
name(rosetta.numeric.expression_parser.VariableExpression) -> str

set_value(...) from builtins.PyCapsule
set_value(self : rosetta.numeric.expression_parser.VariableExpression, value : float) -> NoneType

class PNatAAOptEPositionData(OptEPositionData)


Method resolution order:

PNatAAOptEPositionData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

add_rotamer_line_data(...) from builtins.PyCapsule
add_rotamer_line_data(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in : rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData,  : rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.protocols.optimize_weights.PNatAAOptEPositionData

data(...) from builtins.PyCapsule
data(*args, **kwargs) Overloaded function. 1. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t 2. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

native_aa(...) from builtins.PyCapsule
native_aa(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.core.chemical.AA

neighbor_count(...) from builtins.PyCapsule
neighbor_count(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

position(...) from builtins.PyCapsule
position(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

rotamer_data_begin(...) from builtins.PyCapsule
rotamer_data_begin(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(...) from builtins.PyCapsule
rotamer_data_end(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(...) from builtins.PyCapsule
set_native_aa(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in : rosetta.core.chemical.AA) -> NoneType

set_neighbor_count(...) from builtins.PyCapsule
set_neighbor_count(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in : int) -> NoneType

set_position(...) from builtins.PyCapsule
set_position(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in : int) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class PNatAAOptERotamerData(builtins.object)

    Methods defined here:

__getitem__(...) from builtins.PyCapsule
__getitem__(self : rosetta.protocols.optimize_weights.PNatAAOptERotamerData, i : int) -> float

__init__(...) from builtins.PyCapsule
__init__(self : rosetta.protocols.optimize_weights.PNatAAOptERotamerData, aa_in : rosetta.core.chemical.AA, rot_num_in : int, data_vec_in : rosetta.utility.vector1_double, fixed_data_vec_in : rosetta.utility.vector1_double) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatAAOptERotamerData,  : rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> rosetta.protocols.optimize_weights.PNatAAOptERotamerData

data(...) from builtins.PyCapsule
data(rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> rosetta.utility.vector1_double

fixed_data(...) from builtins.PyCapsule
fixed_data(rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> rosetta.utility.vector1_double

rot_number(...) from builtins.PyCapsule
rot_number(rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> int

this_aa(...) from builtins.PyCapsule
this_aa(rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> rosetta.core.chemical.AA

class PNatLigPoseOptEData(PNatStructureOptEData)


Method resolution order:

PNatLigPoseOptEData

PNatStructureOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.PNatLigPoseOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatLigPoseOptEData,  : rosetta.protocols.optimize_weights.PNatLigPoseOptEData) -> rosetta.protocols.optimize_weights.PNatLigPoseOptEData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.PNatLigPoseOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.PNatLigPoseOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

Methods inherited from PNatStructureOptEData:

add_decoy(...) from builtins.PyCapsule
add_decoy(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, decoy : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_native(...) from builtins.PyCapsule
add_native(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, native : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

n_top_natives_to_score(...) from builtins.PyCapsule
n_top_natives_to_score(*args, **kwargs) Overloaded function. 1. n_top_natives_to_score(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, n_top : int) -> NoneType 2. n_top_natives_to_score(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

nativeness(...) from builtins.PyCapsule
nativeness(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, rms : float) -> float

nativeness_high(...) from builtins.PyCapsule
nativeness_high() -> float

nativeness_low(...) from builtins.PyCapsule
nativeness_low() -> float

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_initial_decoy_stddev(...) from builtins.PyCapsule
set_initial_decoy_stddev(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, setting : float) -> NoneType

set_nativeness_high(...) from builtins.PyCapsule
set_nativeness_high(nativeness_rms_low : float) -> NoneType

set_nativeness_low(...) from builtins.PyCapsule
set_nativeness_low(nativeness_rms_low : float) -> NoneType

set_normalize_decoy_stddev(...) from builtins.PyCapsule
set_normalize_decoy_stddev(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, setting : bool) -> NoneType

set_total_residue(...) from builtins.PyCapsule
set_total_residue(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, total_residue : int) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class PNatRotOptEPositionData(OptEPositionData)


Method resolution order:

PNatRotOptEPositionData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

aa(...) from builtins.PyCapsule
aa(*args, **kwargs) Overloaded function. 1. aa(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.core.chemical.AA 2. aa(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.core.chemical.AA

add_rotamer_line_data(...) from builtins.PyCapsule
add_rotamer_line_data(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rot_in : rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData,  : rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.protocols.optimize_weights.PNatRotOptEPositionData

count_rotamer_as_native(...) from builtins.PyCapsule
count_rotamer_as_native(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rotamer : rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> bool

data(...) from builtins.PyCapsule
data(*args, **kwargs) Overloaded function. 1. data(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatRotOptERotamerData_t 2. data(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatRotOptERotamerData_t

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> int

phi(...) from builtins.PyCapsule
phi(*args, **kwargs) Overloaded function. 1. phi(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> float 2. phi(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> float

psi(...) from builtins.PyCapsule
psi(*args, **kwargs) Overloaded function. 1. psi(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> float 2. psi(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> float

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

rotamer_data_begin(...) from builtins.PyCapsule
rotamer_data_begin(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData> > > >

rotamer_data_end(...) from builtins.PyCapsule
rotamer_data_end(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatRotOptERotamerData> > > >

set_native_chi_periodicity(...) from builtins.PyCapsule
set_native_chi_periodicity(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_chi_periodicity : rosetta.utility.vector1_double) -> NoneType

set_native_rotamer_chi(...) from builtins.PyCapsule
set_native_rotamer_chi(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_chi : rosetta.utility.vector1_double) -> NoneType

set_native_rotamer_index(...) from builtins.PyCapsule
set_native_rotamer_index(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_rotamer_index : rosetta.utility.vector1_unsigned_long) -> NoneType

set_rotamer_well_counts(...) from builtins.PyCapsule
set_rotamer_well_counts(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rotamer_well_counts : rosetta.utility.vector1_unsigned_long) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.PNatRotOptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.PNatRotOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class PNatRotOptERotamerData(builtins.object)

    Methods defined here:

__getitem__(...) from builtins.PyCapsule
__getitem__(self : rosetta.protocols.optimize_weights.PNatRotOptERotamerData, i : int) -> float

__init__(...) from builtins.PyCapsule
__init__(self : rosetta.protocols.optimize_weights.PNatRotOptERotamerData, rotamer_index : rosetta.utility.vector1_unsigned_long, chi : rosetta.utility.vector1_double, free_data : rosetta.utility.vector1_double, fixed_data : rosetta.utility.vector1_double) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatRotOptERotamerData,  : rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> rosetta.protocols.optimize_weights.PNatRotOptERotamerData

chi(...) from builtins.PyCapsule
chi(rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> rosetta.utility.vector1_double

fixed_data(...) from builtins.PyCapsule
fixed_data(rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> rosetta.utility.vector1_double

free_data(...) from builtins.PyCapsule
free_data(rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> rosetta.utility.vector1_double

rotamer_index(...) from builtins.PyCapsule
rotamer_index(rosetta.protocols.optimize_weights.PNatRotOptERotamerData) -> rosetta.utility.vector1_unsigned_long

class PNatStructureOptEData(OptEPositionData)


Method resolution order:

PNatStructureOptEData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.PNatStructureOptEData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

add_decoy(...) from builtins.PyCapsule
add_decoy(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, decoy : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

add_native(...) from builtins.PyCapsule
add_native(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, native : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PNatStructureOptEData,  : rosetta.protocols.optimize_weights.PNatStructureOptEData) -> rosetta.protocols.optimize_weights.PNatStructureOptEData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

n_top_natives_to_score(...) from builtins.PyCapsule
n_top_natives_to_score(*args, **kwargs) Overloaded function. 1. n_top_natives_to_score(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, n_top : int) -> NoneType 2. n_top_natives_to_score(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

nativeness(...) from builtins.PyCapsule
nativeness(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, rms : float) -> float

nativeness_high(...) from builtins.PyCapsule
nativeness_high() -> float

nativeness_low(...) from builtins.PyCapsule
nativeness_low() -> float

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_initial_decoy_stddev(...) from builtins.PyCapsule
set_initial_decoy_stddev(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, setting : float) -> NoneType

set_nativeness_high(...) from builtins.PyCapsule
set_nativeness_high(nativeness_rms_low : float) -> NoneType

set_nativeness_low(...) from builtins.PyCapsule
set_nativeness_low(nativeness_rms_low : float) -> NoneType

set_normalize_decoy_stddev(...) from builtins.PyCapsule
set_normalize_decoy_stddev(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, setting : bool) -> NoneType

set_total_residue(...) from builtins.PyCapsule
set_total_residue(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, total_residue : int) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.PNatStructureOptEData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class PSSMOptEPositionData(PNatAAOptEPositionData)


Method resolution order:

PSSMOptEPositionData

PNatAAOptEPositionData

OptEPositionData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.PSSMOptEPositionData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData,  : rosetta.protocols.optimize_weights.PSSMOptEPositionData) -> rosetta.protocols.optimize_weights.PSSMOptEPositionData

get_score(...) from builtins.PyCapsule
get_score(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, component_weights : rosetta.utility.vector1_double, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double, num_energy_dofs : int, num_ref_dofs : int, num_total_dofs : int, fixed_terms : rosetta.core.scoring.EMapVector, score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType) -> float

memory_use(...) from builtins.PyCapsule
memory_use(rosetta.protocols.optimize_weights.PSSMOptEPositionData) -> int

read_from_binary_file(...) from builtins.PyCapsule
read_from_binary_file(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

read_from_file(...) from builtins.PyCapsule
read_from_file(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, infile : rosetta.std.basic_ifstream_char_std_char_traits_char_t) -> NoneType

set_pssm_probabilities(...) from builtins.PyCapsule
set_pssm_probabilities(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, pssm_probs : rosetta.utility.vector1_double) -> NoneType

type(...) from builtins.PyCapsule
type(rosetta.protocols.optimize_weights.PSSMOptEPositionData) -> rosetta.protocols.optimize_weights.OptEPositionDataType

write_to_binary_file(...) from builtins.PyCapsule
write_to_binary_file(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

write_to_file(...) from builtins.PyCapsule
write_to_file(self : rosetta.protocols.optimize_weights.PSSMOptEPositionData, outfile : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType

Methods inherited from PNatAAOptEPositionData:

add_rotamer_line_data(...) from builtins.PyCapsule
add_rotamer_line_data(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in : rosetta.protocols.optimize_weights.PNatAAOptERotamerData) -> NoneType

data(...) from builtins.PyCapsule
data(*args, **kwargs) Overloaded function. 1. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t 2. data(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

native_aa(...) from builtins.PyCapsule
native_aa(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> rosetta.core.chemical.AA

neighbor_count(...) from builtins.PyCapsule
neighbor_count(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

position(...) from builtins.PyCapsule
position(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

range(...) from builtins.PyCapsule
range(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, lower_bound : rosetta.core.scoring.EMapVector, upper_bound : rosetta.core.scoring.EMapVector) -> NoneType

rotamer_data_begin(...) from builtins.PyCapsule
rotamer_data_begin(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(...) from builtins.PyCapsule
rotamer_data_end(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData>, std::allocator<std::shared_ptr<protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(...) from builtins.PyCapsule
set_native_aa(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in : rosetta.core.chemical.AA) -> NoneType

set_neighbor_count(...) from builtins.PyCapsule
set_neighbor_count(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in : int) -> NoneType

set_position(...) from builtins.PyCapsule
set_position(self : rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in : int) -> NoneType

size(...) from builtins.PyCapsule
size(rosetta.protocols.optimize_weights.PNatAAOptEPositionData) -> int

Methods inherited from OptEPositionData:

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(self : rosetta.protocols.optimize_weights.OptEPositionData, tag_in : str) -> NoneType 2. tag(rosetta.protocols.optimize_weights.OptEPositionData) -> str

class SingleStructureData(builtins.object)

    Methods defined here:

__getitem__(...) from builtins.PyCapsule
__getitem__(self : rosetta.protocols.optimize_weights.SingleStructureData, i : int) -> float

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : rosetta.protocols.optimize_weights.SingleStructureData, free_data : rosetta.utility.vector1_double, fixed_data : rosetta.utility.vector1_double) -> NoneType 2. __init__(self : rosetta.protocols.optimize_weights.SingleStructureData,  : rosetta.protocols.optimize_weights.SingleStructureData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.SingleStructureData,  : rosetta.protocols.optimize_weights.SingleStructureData) -> rosetta.protocols.optimize_weights.SingleStructureData

fixed_data(...) from builtins.PyCapsule
fixed_data(rosetta.protocols.optimize_weights.SingleStructureData) -> rosetta.utility.vector1_double

free_data(...) from builtins.PyCapsule
free_data(rosetta.protocols.optimize_weights.SingleStructureData) -> rosetta.utility.vector1_double

rms(...) from builtins.PyCapsule
rms(*args, **kwargs) Overloaded function. 1. rms(rosetta.protocols.optimize_weights.SingleStructureData) -> float 2. rms(self : rosetta.protocols.optimize_weights.SingleStructureData, rms_in : float) -> NoneType

tag(...) from builtins.PyCapsule
tag(*args, **kwargs) Overloaded function. 1. tag(rosetta.protocols.optimize_weights.SingleStructureData) -> str 2. tag(self : rosetta.protocols.optimize_weights.SingleStructureData, setting : str) -> NoneType

class WeightRangeConstraint(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(rosetta.protocols.optimize_weights.WeightRangeConstraint) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

Data descriptors defined here:

active_

max_weight_

min_weight_

spring_constant_

class WrappedOptEExpressionCreator(rosetta.numeric.expression_parser.ExpressionCreator)


Method resolution order:

WrappedOptEExpressionCreator

rosetta.numeric.expression_parser.ExpressionCreator

rosetta.numeric.expression_parser.ASTVisitor

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(self : handle, multifunc : rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator,  : rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator) -> rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator

handle_function_expression(...) from builtins.PyCapsule
handle_function_expression(self : rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, function : rosetta.numeric.expression_parser.FunctionToken, args : rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) -> rosetta.numeric.expression_parser.Expression

handle_variable_expression(...) from builtins.PyCapsule
handle_variable_expression(self : rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTValue) -> rosetta.numeric.expression_parser.Expression

set_wrapping_optE_multifunc(...) from builtins.PyCapsule
set_wrapping_optE_multifunc(self : rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, multifunc : rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t) -> NoneType

Methods inherited from rosetta.numeric.expression_parser.ExpressionCreator:

create_expression_tree(...) from builtins.PyCapsule
create_expression_tree(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTExpression) -> numeric::expression_parser::Expression

visit(...) from builtins.PyCapsule
visit(*args, **kwargs) Overloaded function. 1. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTExpression) -> NoneType 2. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTFunction) -> NoneType 3. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTTerm) -> NoneType 4. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTFactor) -> NoneType 5. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTValue) -> NoneType 6. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTRestTerm) -> NoneType 7. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTRestExpression) -> NoneType 8. visit(self : rosetta.numeric.expression_parser.ExpressionCreator,  : rosetta.numeric.expression_parser.ArithmeticASTNode) -> NoneType

class WrapperOptEMultifunc(rosetta.core.optimization.Multifunc)

    DANGER DANGER DANGER This class must never be allocated on the stack.  Instead, it should be allocated (with "new") on the heap.  This class hands an owning-pointer to itself to another class to create a call-back mechanism; this owning pointer will be invalid and result in stack corruption if this class is allocated on the stack.

Method resolution order:

WrapperOptEMultifunc

rosetta.core.optimization.Multifunc

builtins.object

Methods defined here:

__call__(...) from builtins.PyCapsule
__call__(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars : rosetta.utility.vector1_double) -> float

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc,  : rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> rosetta.protocols.optimize_weights.WrapperOptEMultifunc

derived_dofs(...) from builtins.PyCapsule
derived_dofs(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars : rosetta.utility.vector1_double) -> rosetta.utility.vector1_double

dfunc(...) from builtins.PyCapsule
dfunc(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType OptE dfunc

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> rosetta.protocols.optimize_weights.WrapperOptEMultifunc self pointers 2. get_self_ptr(rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> rosetta.protocols.optimize_weights.WrapperOptEMultifunc

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> rosetta.std.weak_ptr_const_protocols_optimize_weights_WrapperOptEMultifunc_t 2. get_self_weak_ptr(rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t

init(...) from builtins.PyCapsule
init(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, free_score_list : rosetta.utility.vector1_core_scoring_ScoreType, free_count : int, fixed_score_list : rosetta.utility.vector1_core_scoring_ScoreType, fixed_scores : rosetta.core.scoring.EMapVector, optEfunc : rosetta.protocols.optimize_weights.OptEMultifunc) -> NoneType

n_real_dofs(...) from builtins.PyCapsule
n_real_dofs(rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> int

register_variable_expression(...) from builtins.PyCapsule
register_variable_expression(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, varname : str) -> rosetta.numeric.expression_parser.VariableExpression

set_multifunc(...) from builtins.PyCapsule
set_multifunc(self : rosetta.protocols.optimize_weights.WrapperOptEMultifunc, multifunc : rosetta.protocols.optimize_weights.OptEMultifunc) -> NoneType

Methods inherited from rosetta.core.optimization.Multifunc:

abort_min(...) from builtins.PyCapsule
abort_min(self : rosetta.core.optimization.Multifunc,  : rosetta.utility.vector1_double) -> bool Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

dump(...) from builtins.PyCapsule
dump(self : rosetta.core.optimization.Multifunc,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType Error state reached -- derivative does not match gradient Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect.

Functions

load_component_weights(...) method of builtins.PyCapsule instance
load_component_weights(component_weights : rosetta.utility.vector1_double) -> NoneType 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.

Data

ADDED_STRUCTURE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_AS_INTENDED
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
DID_NOT_ADD_STRUCTURE = AddStatus.DID_NOT_ADD_STRUCTURE
END_OF_MINIMIZATION = OptEMultifuncMPIMessages.END_OF_MINIMIZATION
EVAL_DFUNC = OptEMultifuncMPIMessages.EVAL_DFUNC
EVAL_FUNC = OptEMultifuncMPIMessages.EVAL_FUNC
constrained_optimization_weight_func = OptEPositionDataType.constrained_optimization_weight_func
dG_binding_correlation = OptEPositionDataType.dG_binding_correlation
ddG_bind_correlation = OptEPositionDataType.n_optE_data_types
ddG_mutation_correlation = OptEPositionDataType.ddG_mutation_correlation
ddG_mutation_correlation_with_unfolded_energy = OptEPositionDataType.ddG_mutation_correlation_with_unfolded_energy
n_optE_data_types = OptEPositionDataType.n_optE_data_types
prob_native_amino_acid = OptEPositionDataType.prob_native_amino_acid
prob_native_amino_acid_with_unfolded_energy = OptEPositionDataType.prob_native_amino_acid_with_unfolded_energy
prob_native_ligand_pose = OptEPositionDataType.prob_native_ligand_pose
prob_native_rotamer = OptEPositionDataType.prob_native_rotamer
prob_native_structure = OptEPositionDataType.prob_native_structure
pssm_data = OptEPositionDataType.pssm_data

Functions
		load_component_weights(...) method of builtins.PyCapsule instance `load_component_weights(component_weights : rosetta.utility.vector1_double) -> NoneType 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.`

Data
		ADDED_STRUCTURE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_AS_INTENDED ADDED_STRUCTURE_OPPOSITE_AS_INTENDED = AddStatus.ADDED_STRUCTURE_OPPOSITE_AS_INTENDED DID_NOT_ADD_STRUCTURE = AddStatus.DID_NOT_ADD_STRUCTURE END_OF_MINIMIZATION = OptEMultifuncMPIMessages.END_OF_MINIMIZATION EVAL_DFUNC = OptEMultifuncMPIMessages.EVAL_DFUNC EVAL_FUNC = OptEMultifuncMPIMessages.EVAL_FUNC constrained_optimization_weight_func = OptEPositionDataType.constrained_optimization_weight_func dG_binding_correlation = OptEPositionDataType.dG_binding_correlation ddG_bind_correlation = OptEPositionDataType.n_optE_data_types ddG_mutation_correlation = OptEPositionDataType.ddG_mutation_correlation ddG_mutation_correlation_with_unfolded_energy = OptEPositionDataType.ddG_mutation_correlation_with_unfolded_energy n_optE_data_types = OptEPositionDataType.n_optE_data_types prob_native_amino_acid = OptEPositionDataType.prob_native_amino_acid prob_native_amino_acid_with_unfolded_energy = OptEPositionDataType.prob_native_amino_acid_with_unfolded_energy prob_native_ligand_pose = OptEPositionDataType.prob_native_ligand_pose prob_native_rotamer = OptEPositionDataType.prob_native_rotamer prob_native_structure = OptEPositionDataType.prob_native_structure pssm_data = OptEPositionDataType.pssm_data