optimize_weights

Bindings for protocols::optimize_weights namespace

class pyrosetta.rosetta.protocols.optimize_weights.AddStatus

Bases: pybind11_builtins.pybind11_object

Members:

ADDED_STRUCTURE_AS_INTENDED

ADDED_STRUCTURE_OPPOSITE_AS_INTENDED

DID_NOT_ADD_STRUCTURE

ADDED_STRUCTURE_AS_INTENDED = <AddStatus.ADDED_STRUCTURE_AS_INTENDED: 0>
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED = <AddStatus.ADDED_STRUCTURE_OPPOSITE_AS_INTENDED: 1>
DID_NOT_ADD_STRUCTURE = <AddStatus.DID_NOT_ADD_STRUCTURE: 2>
property name
class pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

assign(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, : pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::operator=(const class protocols::optimize_weights::ConstraintedOptimizationWeightFunc &) –> class protocols::optimize_weights::ConstraintedOptimizationWeightFunc &

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

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

initialize_constraints_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::initialize_constraints_from_file(class std::basic_ifstream<char> &) –> void

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) int

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

range(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::read_from_file(class std::basic_ifstream<char> &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) int

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::ConstraintedOptimizationWeightFunc::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

class DDG_Bind_File_Index

Bases: pybind11_builtins.pybind11_object

Members:

WT_COMPLEXES_LIST_FILE

MUT_COMPLEXES_LIST_FILE

WT_UNBOUNDS_LIST_FILE

MUT_UNBOUNDS_LIST_FILE

MUT_COMPLEXES_LIST_FILE = <DDG_Bind_File_Index.MUT_COMPLEXES_LIST_FILE: 2>
MUT_UNBOUNDS_LIST_FILE = <DDG_Bind_File_Index.MUT_UNBOUNDS_LIST_FILE: 4>
WT_COMPLEXES_LIST_FILE = <DDG_Bind_File_Index.WT_COMPLEXES_LIST_FILE: 1>
WT_UNBOUNDS_LIST_FILE = <DDG_Bind_File_Index.WT_UNBOUNDS_LIST_FILE: 3>
property name
MUT_COMPLEXES_LIST_FILE = <DDG_Bind_File_Index.MUT_COMPLEXES_LIST_FILE: 2>
MUT_UNBOUNDS_LIST_FILE = <DDG_Bind_File_Index.MUT_UNBOUNDS_LIST_FILE: 4>
WT_COMPLEXES_LIST_FILE = <DDG_Bind_File_Index.WT_COMPLEXES_LIST_FILE: 1>
WT_UNBOUNDS_LIST_FILE = <DDG_Bind_File_Index.WT_UNBOUNDS_LIST_FILE: 3>
add_mutant_complex(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, mut: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGBindOptEData::add_mutant_complex(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_mutant_unbounds(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, mut: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGBindOptEData::add_mutant_unbounds(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_mutation(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, mutation: Tuple[int, Tuple[pyrosetta.rosetta.core.chemical.AA, pyrosetta.rosetta.core.chemical.AA]]) None

C++: protocols::optimize_weights::DDGBindOptEData::add_mutation(struct std::pair<unsigned long, struct std::pair<enum core::chemical::AA, enum core::chemical::AA> >) –> void

add_wt_complex(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, wt: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGBindOptEData::add_wt_complex(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_wt_unbounds(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, wt: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGBindOptEData::add_wt_unbounds(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, : pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData) pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData

C++: protocols::optimize_weights::DDGBindOptEData::operator=(const class protocols::optimize_weights::DDGBindOptEData &) –> class protocols::optimize_weights::DDGBindOptEData &

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

C++: protocols::optimize_weights::DDGBindOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData) int

C++: protocols::optimize_weights::DDGBindOptEData::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::DDGBindOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::DDGBindOptEData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::DDGBindOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, : pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGBindOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, : pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGBindOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

set_experimental_ddg_bind(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, exp_ddg_bind: float) None

C++: protocols::optimize_weights::DDGBindOptEData::set_experimental_ddg_bind(double) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData) int

C++: protocols::optimize_weights::DDGBindOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::DDGBindOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, : pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGBindOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData, : pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGBindOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

add_mutant(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, mut: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGMutationOptEData::add_mutant(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_wt(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, wt: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGMutationOptEData::add_wt(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, : pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData) pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData

C++: protocols::optimize_weights::DDGMutationOptEData::operator=(const class protocols::optimize_weights::DDGMutationOptEData &) –> class protocols::optimize_weights::DDGMutationOptEData &

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

C++: protocols::optimize_weights::DDGMutationOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData) int

C++: protocols::optimize_weights::DDGMutationOptEData::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::DDGMutationOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::DDGMutationOptEData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::DDGMutationOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

set_experimental_ddg(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, ddg: float) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_experimental_ddg(double) –> void

set_mut_aa(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, mut_aa: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_mut_aa(enum core::chemical::AA) –> void

set_wt_aa(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, wt_aa: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_wt_aa(enum core::chemical::AA) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData) int

C++: protocols::optimize_weights::DDGMutationOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::DDGMutationOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.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.

assign(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, : pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData

C++: protocols::optimize_weights::DGBindOptEData::operator=(const class protocols::optimize_weights::DGBindOptEData &) –> class protocols::optimize_weights::DGBindOptEData &

bound_struct(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, x: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DGBindOptEData::bound_struct(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

deltaG_bind(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, x: float) None

C++: protocols::optimize_weights::DGBindOptEData::deltaG_bind(double) –> void

do_score(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, print: bool) float

C++: protocols::optimize_weights::DGBindOptEData::do_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const bool) const –> double

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

C++: protocols::optimize_weights::DGBindOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) int

C++: protocols::optimize_weights::DGBindOptEData::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::DGBindOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

range(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::DGBindOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, : pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DGBindOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, : pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DGBindOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) int

C++: protocols::optimize_weights::DGBindOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::DGBindOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

unbound_struct(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, x: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DGBindOptEData::unbound_struct(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, : pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DGBindOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, : pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DGBindOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver

Bases: pybind11_builtins.pybind11_object

go(self: pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver) None

C++: protocols::optimize_weights::IterativeOptEDriver::go() –> void

task_factory(self: pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver, : pyrosetta.rosetta.core.pack.task.TaskFactory) None
take care when using a custom TaskFactory:

TaskOperations must not ‘accumulate state’ as they will be reused repeatedly

C++: protocols::optimize_weights::IterativeOptEDriver::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

class pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData

add_mutant(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, mut: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGMutationOptEData::add_mutant(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_wt(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, wt: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::DDGMutationOptEData::add_wt(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, : pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::operator=(const class protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData &) –> class protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData &

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

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) int

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::DDGMutationOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

set_experimental_ddg(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, ddg: float) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_experimental_ddg(double) –> void

set_mut_aa(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, mut_aa: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_mut_aa(enum core::chemical::AA) –> void

set_mut_unfolded_energies_emap(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, e: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_mut_unfolded_energies_emap(const class core::scoring::EMapVector &) –> void

set_wt_aa(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, wt_aa: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::DDGMutationOptEData::set_wt_aa(enum core::chemical::AA) –> void

set_wt_unfolded_energies_emap(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData, e: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_wt_unfolded_energies_emap(const class core::scoring::EMapVector &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData) int

C++: protocols::optimize_weights::DDGMutationOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::DDGMutationOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData

Bases: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData

add_rotamer_line_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::add_rotamer_line_data(class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, : pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::operator=(const class protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData &) –> class protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData &

data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

C++: protocols::optimize_weights::PNatAAOptEPositionData::data() –> class utility::vector1<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > &

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

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) int

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::memory_use() const –> unsigned long

native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.core.chemical.AA

C++: protocols::optimize_weights::PNatAAOptEPositionData::native_aa() const –> enum core::chemical::AA

neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::neighbor_count() const –> unsigned long

position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::position() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(class std::basic_ifstream<char> &) –> void

rotamer_data_begin(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_native_aa(enum core::chemical::AA) –> void

set_neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_neighbor_count(unsigned long) –> void

set_position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_position(unsigned long) –> void

set_unfolded_energy_emap_vector(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, emap_vector: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::set_unfolded_energy_emap_vector(class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> >) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

unfolded_energy_emap_vector(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData) pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::unfolded_energy_emap_vector() –> class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.OptEData

Bases: pybind11_builtins.pybind11_object

add_position_data(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, pos_data_in: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) None

C++: protocols::optimize_weights::OptEData::add_position_data(class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, : pyrosetta.rosetta.protocols.optimize_weights.OptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEData

C++: protocols::optimize_weights::OptEData::operator=(const class protocols::optimize_weights::OptEData &) –> class protocols::optimize_weights::OptEData &

energy_terms(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: protocols::optimize_weights::OptEData::energy_terms() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

fixed_energy_terms(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: protocols::optimize_weights::OptEData::fixed_energy_terms() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

num_positions(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) int

C++: protocols::optimize_weights::OptEData::num_positions() const –> unsigned long

num_rotamers(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) int

C++: protocols::optimize_weights::OptEData::num_rotamers() const –> unsigned long

position_data_begin(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::OptEData::position_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> > > >

position_data_end(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::OptEData::position_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> > > >

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) None

C++: protocols::optimize_weights::OptEData::read_from_binary_file(std::string) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) None

C++: protocols::optimize_weights::OptEData::read_from_file(std::string) –> void

write_to_binary_file(*args, **kwargs)

Overloaded function.

  1. write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) -> None

  2. write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) -> None

C++: protocols::optimize_weights::OptEData::write_to_binary_file(std::string) const –> void

write_to_file(*args, **kwargs)

Overloaded function.

  1. write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) -> None

  2. write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) -> None

C++: protocols::optimize_weights::OptEData::write_to_file(std::string) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc

Bases: pyrosetta.rosetta.core.optimization.Multifunc

OptE mode multifunction class

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.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!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

declare_minimization_over(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc) None
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).

C++: protocols::optimize_weights::OptEMultifunc::declare_minimization_over() const –> void

dfunc(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) None

OptE dfunc

C++: protocols::optimize_weights::OptEMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) None
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.

C++: core::optimization::Multifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

fix_reference_energies(*args, **kwargs)

Overloaded function.

  1. fix_reference_energies(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, setting: bool) -> None

C++: protocols::optimize_weights::OptEMultifunc::fix_reference_energies(bool) –> void

  1. fix_reference_energies(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc) -> bool

Are the reference energies being optimized at all, or are they being held fixed?

C++: protocols::optimize_weights::OptEMultifunc::fix_reference_energies() const –> bool

get_dofs_from_energy_map(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, start_vals: pyrosetta.rosetta.core.scoring.EMapVector) pyrosetta.rosetta.utility.vector1_double

Extract variable weights from an Energy Map

C++: protocols::optimize_weights::OptEMultifunc::get_dofs_from_energy_map(const class core::scoring::EMapVector &) const –> class utility::vector1<double, class std::allocator<double> >

get_energy_map_from_dofs(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, dofs: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.core.scoring.EMapVector

Expand free variables and combine with fixed to make an Energy Map

C++: protocols::optimize_weights::OptEMultifunc::get_energy_map_from_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class core::scoring::EMapVector

get_reference_energies_from_dofs(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, dofs: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::OptEMultifunc::get_reference_energies_from_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

set_starting_reference_energies(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, values: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::optimize_weights::OptEMultifunc::set_starting_reference_energies(const class utility::vector1<double, class std::allocator<double> > &) –> void

wait_for_remote_vars(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc) None

Non-driver node wait for MPI vars to evaluate either the func or the dfunc.

C++: protocols::optimize_weights::OptEMultifunc::wait_for_remote_vars() const –> void

class pyrosetta.rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages

Bases: pybind11_builtins.pybind11_object

Members:

EVAL_FUNC

EVAL_DFUNC

END_OF_MINIMIZATION

END_OF_MINIMIZATION = <OptEMultifuncMPIMessages.END_OF_MINIMIZATION: 2>
EVAL_DFUNC = <OptEMultifuncMPIMessages.EVAL_DFUNC: 1>
EVAL_FUNC = <OptEMultifuncMPIMessages.EVAL_FUNC: 0>
property name
class pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, : pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

C++: protocols::optimize_weights::OptEPositionData::operator=(const class protocols::optimize_weights::OptEPositionData &) –> class protocols::optimize_weights::OptEPositionData &

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

C++: protocols::optimize_weights::OptEPositionData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) int

C++: protocols::optimize_weights::OptEPositionData::memory_use() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::OptEPositionData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

range(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None
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.

C++: protocols::optimize_weights::OptEPositionData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::OptEPositionData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::OptEPositionData::read_from_file(class std::basic_ifstream<char> &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) int

C++: protocols::optimize_weights::OptEPositionData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::OptEPositionData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::OptEPositionData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::OptEPositionData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory

Bases: pybind11_builtins.pybind11_object

static create_position_data(type: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

C++: protocols::optimize_weights::OptEPositionDataFactory::create_position_data(const enum protocols::optimize_weights::OptEPositionDataType) –> class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>

static is_optE_type_name(name: str) bool

C++: protocols::optimize_weights::OptEPositionDataFactory::is_optE_type_name(const std::string &) –> bool

static optE_type_from_name(name: str) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::OptEPositionDataFactory::optE_type_from_name(const std::string &) –> enum protocols::optimize_weights::OptEPositionDataType

static optE_type_name(type: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType) str

C++: protocols::optimize_weights::OptEPositionDataFactory::optE_type_name(const enum protocols::optimize_weights::OptEPositionDataType) –> const std::string &

class pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

Bases: pybind11_builtins.pybind11_object

Members:

prob_native_amino_acid

pssm_data

prob_native_rotamer

prob_native_structure

prob_native_ligand_pose

dG_binding_correlation

ddG_mutation_correlation

constrained_optimization_weight_func

prob_native_amino_acid_with_unfolded_energy

ddG_mutation_correlation_with_unfolded_energy

ddG_bind_correlation

n_optE_data_types

constrained_optimization_weight_func = <OptEPositionDataType.constrained_optimization_weight_func: 8>
dG_binding_correlation = <OptEPositionDataType.dG_binding_correlation: 6>
ddG_bind_correlation = <OptEPositionDataType.ddG_bind_correlation: 11>
ddG_mutation_correlation = <OptEPositionDataType.ddG_mutation_correlation: 7>
ddG_mutation_correlation_with_unfolded_energy = <OptEPositionDataType.ddG_mutation_correlation_with_unfolded_energy: 10>
n_optE_data_types = <OptEPositionDataType.ddG_bind_correlation: 11>
property name
prob_native_amino_acid = <OptEPositionDataType.prob_native_amino_acid: 1>
prob_native_amino_acid_with_unfolded_energy = <OptEPositionDataType.prob_native_amino_acid_with_unfolded_energy: 9>
prob_native_ligand_pose = <OptEPositionDataType.prob_native_ligand_pose: 5>
prob_native_rotamer = <OptEPositionDataType.prob_native_rotamer: 3>
prob_native_structure = <OptEPositionDataType.prob_native_structure: 4>
pssm_data = <OptEPositionDataType.pssm_data: 2>
class pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression

Bases: pyrosetta.rosetta.numeric.expression_parser.VariableExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: numeric::expression_parser::VariableExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression, : pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression) pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression

C++: protocols::optimize_weights::OptEVariableExpression::operator=(const class protocols::optimize_weights::OptEVariableExpression &) –> class protocols::optimize_weights::OptEVariableExpression &

differentiate(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression, varname: str) pyrosetta.rosetta.numeric.expression_parser.Expression

Returns the literal expression 1 if name_ == varname_ and null otherwise

C++: numeric::expression_parser::VariableExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

id(self: pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression) int

C++: protocols::optimize_weights::OptEVariableExpression::id() const –> unsigned long

name(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression) str

C++: numeric::expression_parser::VariableExpression::name() const –> std::string

set_id(self: pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression, id: int) None

C++: protocols::optimize_weights::OptEVariableExpression::set_id(unsigned long) –> void

set_value(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression, value: float) None

C++: numeric::expression_parser::VariableExpression::set_value(double) –> void

update_value_from_list(self: pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression, value_vector: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::optimize_weights::OptEVariableExpression::update_value_from_list(const class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

add_rotamer_line_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::add_rotamer_line_data(class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, : pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData

C++: protocols::optimize_weights::PNatAAOptEPositionData::operator=(const class protocols::optimize_weights::PNatAAOptEPositionData &) –> class protocols::optimize_weights::PNatAAOptEPositionData &

data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

C++: protocols::optimize_weights::PNatAAOptEPositionData::data() –> class utility::vector1<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > &

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

C++: protocols::optimize_weights::PNatAAOptEPositionData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::memory_use() const –> unsigned long

native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.core.chemical.AA

C++: protocols::optimize_weights::PNatAAOptEPositionData::native_aa() const –> enum core::chemical::AA

neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::neighbor_count() const –> unsigned long

position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::position() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(class std::basic_ifstream<char> &) –> void

rotamer_data_begin(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_native_aa(enum core::chemical::AA) –> void

set_neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_neighbor_count(unsigned long) –> void

set_position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_position(unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::PNatAAOptEPositionData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData, : pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData

C++: protocols::optimize_weights::PNatAAOptERotamerData::operator=(const class protocols::optimize_weights::PNatAAOptERotamerData &) –> class protocols::optimize_weights::PNatAAOptERotamerData &

data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::PNatAAOptERotamerData::data() –> const class utility::vector1<double, class std::allocator<double> > &

fixed_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::PNatAAOptERotamerData::fixed_data() –> const class utility::vector1<double, class std::allocator<double> > &

rot_number(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) int

C++: protocols::optimize_weights::PNatAAOptERotamerData::rot_number() –> unsigned long

this_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) pyrosetta.rosetta.core.chemical.AA

C++: protocols::optimize_weights::PNatAAOptERotamerData::this_aa() –> enum core::chemical::AA

class pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData

add_decoy(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, decoy: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::PNatStructureOptEData::add_decoy(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_native(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, native: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::PNatStructureOptEData::add_native(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData, : pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData) pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData

C++: protocols::optimize_weights::PNatLigPoseOptEData::operator=(const class protocols::optimize_weights::PNatLigPoseOptEData &) –> class protocols::optimize_weights::PNatLigPoseOptEData &

do_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, print: bool) float

C++: protocols::optimize_weights::PNatLigPoseOptEData::do_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const bool) const –> double

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

C++: protocols::optimize_weights::PNatLigPoseOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) int

C++: protocols::optimize_weights::PNatStructureOptEData::memory_use() const –> unsigned long

n_top_natives_to_score(*args, **kwargs)

Overloaded function.

  1. n_top_natives_to_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, n_top: int) -> None

C++: protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score(unsigned long) –> void

  1. n_top_natives_to_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

C++: protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score() const –> unsigned long

nativeness(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, rms: float) float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness(double) const –> double

static nativeness_high() float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness_high() –> double

static nativeness_low() float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness_low() –> double

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::PNatLigPoseOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::PNatStructureOptEData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatStructureOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

set_initial_decoy_stddev(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, setting: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_initial_decoy_stddev(double) –> void

static set_nativeness_high(nativeness_rms_low: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_nativeness_high(double) –> void

static set_nativeness_low(nativeness_rms_low: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_nativeness_low(double) –> void

set_normalize_decoy_stddev(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, setting: bool) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_normalize_decoy_stddev(bool) –> void

set_total_residue(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, total_residue: int) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_total_residue(unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) int

C++: protocols::optimize_weights::PNatStructureOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::PNatLigPoseOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) pyrosetta.rosetta.core.chemical.AA

C++: protocols::optimize_weights::PNatRotOptEPositionData::aa() –> enum core::chemical::AA &

add_rotamer_line_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rot_in: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::add_rotamer_line_data(class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, : pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData

C++: protocols::optimize_weights::PNatRotOptEPositionData::operator=(const class protocols::optimize_weights::PNatRotOptEPositionData &) –> class protocols::optimize_weights::PNatRotOptEPositionData &

count_rotamer_as_native(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rotamer: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) bool

C++: protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native(class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData>) const –> bool

data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatRotOptERotamerData_t

C++: protocols::optimize_weights::PNatRotOptEPositionData::data() –> class utility::vector1<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData> > > &

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

C++: protocols::optimize_weights::PNatRotOptEPositionData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) int

C++: protocols::optimize_weights::PNatRotOptEPositionData::memory_use() const –> unsigned long

phi(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) float

C++: protocols::optimize_weights::PNatRotOptEPositionData::phi() –> double &

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, : int, : int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::PNatRotOptEPositionData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

psi(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) float

C++: protocols::optimize_weights::PNatRotOptEPositionData::psi() –> double &

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::read_from_file(class std::basic_ifstream<char> &) –> void

rotamer_data_begin(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData> > > >

rotamer_data_end(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatRotOptERotamerData> > > >

set_native_chi_periodicity(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_chi_periodicity: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::set_native_chi_periodicity(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_native_rotamer_chi(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_chi: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_chi(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_native_rotamer_index(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, native_rotamer_index: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rotamer_well_counts(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, rotamer_well_counts: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::set_rotamer_well_counts(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) int

C++: protocols::optimize_weights::PNatRotOptEPositionData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::PNatRotOptEPositionData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatRotOptEPositionData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData, : pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData

C++: protocols::optimize_weights::PNatRotOptERotamerData::operator=(const class protocols::optimize_weights::PNatRotOptERotamerData &) –> class protocols::optimize_weights::PNatRotOptERotamerData &

chi(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::PNatRotOptERotamerData::chi() const –> const class utility::vector1<double, class std::allocator<double> > &

fixed_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::PNatRotOptERotamerData::fixed_data() const –> const class utility::vector1<double, class std::allocator<double> > &

free_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::PNatRotOptERotamerData::free_data() const –> const class utility::vector1<double, class std::allocator<double> > &

rotamer_index(self: pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::optimize_weights::PNatRotOptERotamerData::rotamer_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

class pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

add_decoy(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, decoy: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::PNatStructureOptEData::add_decoy(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

add_native(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, native: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) None

C++: protocols::optimize_weights::PNatStructureOptEData::add_native(class std::shared_ptr<class protocols::optimize_weights::SingleStructureData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, : pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData

C++: protocols::optimize_weights::PNatStructureOptEData::operator=(const class protocols::optimize_weights::PNatStructureOptEData &) –> class protocols::optimize_weights::PNatStructureOptEData &

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

C++: protocols::optimize_weights::PNatStructureOptEData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) int

C++: protocols::optimize_weights::PNatStructureOptEData::memory_use() const –> unsigned long

n_top_natives_to_score(*args, **kwargs)

Overloaded function.

  1. n_top_natives_to_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, n_top: int) -> None

C++: protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score(unsigned long) –> void

  1. n_top_natives_to_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) -> int

C++: protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score() const –> unsigned long

nativeness(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, rms: float) float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness(double) const –> double

static nativeness_high() float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness_high() –> double

static nativeness_low() float

C++: protocols::optimize_weights::PNatStructureOptEData::nativeness_low() –> double

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::PNatStructureOptEData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

process_score(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, ostr: pyrosetta.rosetta.std.ostream, print: bool, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) float

C++: protocols::optimize_weights::PNatStructureOptEData::process_score(std::ostream &, bool, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatStructureOptEData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::read_from_file(class std::basic_ifstream<char> &) –> void

set_initial_decoy_stddev(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, setting: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_initial_decoy_stddev(double) –> void

static set_nativeness_high(nativeness_rms_low: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_nativeness_high(double) –> void

static set_nativeness_low(nativeness_rms_low: float) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_nativeness_low(double) –> void

set_normalize_decoy_stddev(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, setting: bool) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_normalize_decoy_stddev(bool) –> void

set_total_residue(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, total_residue: int) None

C++: protocols::optimize_weights::PNatStructureOptEData::set_total_residue(unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) int

C++: protocols::optimize_weights::PNatStructureOptEData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::PNatStructureOptEData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PNatStructureOptEData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData

Bases: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData

add_rotamer_line_data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, rot_in: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::add_rotamer_line_data(class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, : pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData

C++: protocols::optimize_weights::PSSMOptEPositionData::operator=(const class protocols::optimize_weights::PSSMOptEPositionData &) –> class protocols::optimize_weights::PSSMOptEPositionData &

data(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_optimize_weights_PNatAAOptERotamerData_t

C++: protocols::optimize_weights::PNatAAOptEPositionData::data() –> class utility::vector1<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > &

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

C++: protocols::optimize_weights::PSSMOptEPositionData::get_score(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> double

memory_use(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData) int

C++: protocols::optimize_weights::PSSMOptEPositionData::memory_use() const –> unsigned long

native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) pyrosetta.rosetta.core.chemical.AA

C++: protocols::optimize_weights::PNatAAOptEPositionData::native_aa() const –> enum core::chemical::AA

neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::neighbor_count() const –> unsigned long

position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::position() const –> unsigned long

print_score(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, ostr: pyrosetta.rosetta.std.ostream, component_weights: pyrosetta.rosetta.utility.vector1_double, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double, num_energy_dofs: int, num_ref_dofs: int, num_total_dofs: int, fixed_terms: pyrosetta.rosetta.core.scoring.EMapVector, score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) None

C++: protocols::optimize_weights::PSSMOptEPositionData::print_score(std::ostream &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const int, const int, const class core::scoring::EMapVector &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &) const –> void

range(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, lower_bound: pyrosetta.rosetta.core.scoring.EMapVector, upper_bound: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::range(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PSSMOptEPositionData::read_from_binary_file(class std::basic_ifstream<char> &) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, infile: pyrosetta.rosetta.std.ifstream) None

C++: protocols::optimize_weights::PSSMOptEPositionData::read_from_file(class std::basic_ifstream<char> &) –> void

rotamer_data_begin(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

rotamer_data_end(self: pyrosetta.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> > > >

C++: protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::PNatAAOptERotamerData> > > >

set_native_aa(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nat_in: pyrosetta.rosetta.core.chemical.AA) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_native_aa(enum core::chemical::AA) –> void

set_neighbor_count(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, nb_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_neighbor_count(unsigned long) –> void

set_position(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData, pos_in: int) None

C++: protocols::optimize_weights::PNatAAOptEPositionData::set_position(unsigned long) –> void

set_pssm_probabilities(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, pssm_probs: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::optimize_weights::PSSMOptEPositionData::set_pssm_probabilities(const class utility::vector1<double, class std::allocator<double> > &) –> void

size(self: pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData) int

C++: protocols::optimize_weights::PNatAAOptEPositionData::size() const –> unsigned long

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, tag_in: str) -> None

C++: protocols::optimize_weights::OptEPositionData::tag(const std::string &) –> void

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> str

C++: protocols::optimize_weights::OptEPositionData::tag() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData) pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType

C++: protocols::optimize_weights::PSSMOptEPositionData::type() const –> enum protocols::optimize_weights::OptEPositionDataType

write_to_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PSSMOptEPositionData::write_to_binary_file(class std::basic_ofstream<char> &) const –> void

write_to_file(self: pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData, outfile: pyrosetta.rosetta.std.ofstream) None

C++: protocols::optimize_weights::PSSMOptEPositionData::write_to_file(class std::basic_ofstream<char> &) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData, : pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData

C++: protocols::optimize_weights::SingleStructureData::operator=(const class protocols::optimize_weights::SingleStructureData &) –> class protocols::optimize_weights::SingleStructureData &

fixed_data(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::SingleStructureData::fixed_data() const –> const class utility::vector1<double, class std::allocator<double> > &

free_data(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::SingleStructureData::free_data() const –> const class utility::vector1<double, class std::allocator<double> > &

rms(*args, **kwargs)

Overloaded function.

  1. rms(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) -> float

C++: protocols::optimize_weights::SingleStructureData::rms() const –> double

  1. rms(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData, rms_in: float) -> None

C++: protocols::optimize_weights::SingleStructureData::rms(double) –> void

tag(*args, **kwargs)

Overloaded function.

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData) -> str

C++: protocols::optimize_weights::SingleStructureData::tag() const –> std::string

  1. tag(self: pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData, setting: str) -> None

C++: protocols::optimize_weights::SingleStructureData::tag(const std::string &) –> void

class pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint

Bases: pybind11_builtins.pybind11_object

property active_
property max_weight_
property min_weight_
property spring_constant_
class pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator

Bases: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator

assign(self: pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, : pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator) pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator

C++: protocols::optimize_weights::WrappedOptEExpressionCreator::operator=(const class protocols::optimize_weights::WrappedOptEExpressionCreator &) –> class protocols::optimize_weights::WrappedOptEExpressionCreator &

create_expression_tree(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) numeric::expression_parser::Expression

C++: numeric::expression_parser::ExpressionCreator::create_expression_tree(const class numeric::expression_parser::ArithmeticASTExpression &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_function_expression(self: pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::optimize_weights::WrappedOptEExpressionCreator::handle_function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_variable_expression(self: pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::optimize_weights::WrappedOptEExpressionCreator::handle_variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_wrapping_optE_multifunc(self: pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator, multifunc: pyrosetta.rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t) None

C++: protocols::optimize_weights::WrappedOptEExpressionCreator::set_wrapping_optE_multifunc(class std::weak_ptr<class protocols::optimize_weights::WrapperOptEMultifunc>) –> void

visit(*args, **kwargs)

Overloaded function.

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTExpression &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTAndClause &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTOrClause &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFunction &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTTerm &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFactor &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTValue &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestTerm &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestAndClause &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestOrClause &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestExpression &) –> void

  1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTNode &) –> void

class pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc

Bases: pyrosetta.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.

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.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!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, : pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc

C++: protocols::optimize_weights::WrapperOptEMultifunc::operator=(const class protocols::optimize_weights::WrapperOptEMultifunc &) –> class protocols::optimize_weights::WrapperOptEMultifunc &

derived_dofs(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) pyrosetta.rosetta.utility.vector1_double

C++: protocols::optimize_weights::WrapperOptEMultifunc::derived_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

dfunc(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) None

OptE dfunc

C++: protocols::optimize_weights::WrapperOptEMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) None
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.

C++: core::optimization::Multifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc

C++: protocols::optimize_weights::WrapperOptEMultifunc::get_self_ptr() –> class std::shared_ptr<class protocols::optimize_weights::WrapperOptEMultifunc>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) pyrosetta.rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t

C++: protocols::optimize_weights::WrapperOptEMultifunc::get_self_weak_ptr() –> class std::weak_ptr<class protocols::optimize_weights::WrapperOptEMultifunc>

init(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, free_count: int, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_scores: pyrosetta.rosetta.core.scoring.EMapVector, optEfunc: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc) None

C++: protocols::optimize_weights::WrapperOptEMultifunc::init(const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, unsigned long, const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &, const class core::scoring::EMapVector &, class std::shared_ptr<class protocols::optimize_weights::OptEMultifunc>) –> void

n_real_dofs(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) int

C++: protocols::optimize_weights::WrapperOptEMultifunc::n_real_dofs() const –> unsigned long

print_dofs(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, ostr: pyrosetta.rosetta.std.ostream) None

C++: protocols::optimize_weights::WrapperOptEMultifunc::print_dofs(const class utility::vector1<double, class std::allocator<double> > &, std::ostream &) const –> void

register_variable_expression(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, varname: str) pyrosetta.rosetta.numeric.expression_parser.VariableExpression

C++: protocols::optimize_weights::WrapperOptEMultifunc::register_variable_expression(std::string) –> class std::shared_ptr<class numeric::expression_parser::VariableExpression>

set_multifunc(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, multifunc: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc) None

C++: protocols::optimize_weights::WrapperOptEMultifunc::set_multifunc(class std::shared_ptr<class protocols::optimize_weights::OptEMultifunc>) –> void

pyrosetta.rosetta.protocols.optimize_weights.load_component_weights(component_weights: pyrosetta.rosetta.utility.vector1_double) 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++: protocols::optimize_weights::load_component_weights(class utility::vector1<double, class std::allocator<double> > &) –> void