optimize_weights¶

Bindings for protocols::optimize_weights namespace

class pyrosetta.rosetta.protocols.optimize_weights.AddStatus¶

Bases: 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¶

property value¶

class pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc¶

Bases: 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.

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

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

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: OptEPositionData

class DDG_Bind_File_Index¶

Bases: 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¶

property value¶

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.

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

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

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: 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.

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

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

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: 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.

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

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

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_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: 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.

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

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

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: 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

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.

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

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

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_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

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.

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

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

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

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

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_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¶

property value¶

class pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData¶

Bases: 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.

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

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

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_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_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>¶

property value¶

class pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression¶

Bases: VariableExpression

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

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.

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

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

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_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: 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.

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

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.

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

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

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: 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

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.

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

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

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_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: 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.

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

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.

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

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

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: 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

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.

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

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

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_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.

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

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

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.

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

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

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_object

property active_¶

property max_weight_¶

property min_weight_¶

property spring_constant_¶

class pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator¶

Bases: 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.

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

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

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

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

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

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

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

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

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

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

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

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: 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