optimize_weights¶

Bindings for protocols::optimize_weights namespace

class pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData¶

Bases: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData

Score a “bound” and an “unbound” structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) -> None
__init__(self: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData, arg0: pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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 class std::basic_string<char> &) –> 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.OptEData¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) -> None
__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, fixed_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, free_score_list: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_position_data(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, pos_data_in: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) → None¶: C++: protocols::optimize_weights::OptEData::add_position_data(class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>) –> void

assign(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, : pyrosetta.rosetta.protocols.optimize_weights.OptEData) → pyrosetta.rosetta.protocols.optimize_weights.OptEData¶: C++: protocols::optimize_weights::OptEData::operator=(const class protocols::optimize_weights::OptEData &) –> class protocols::optimize_weights::OptEData &

energy_terms(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶: C++: protocols::optimize_weights::OptEData::energy_terms() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

fixed_energy_terms(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶: C++: protocols::optimize_weights::OptEData::fixed_energy_terms() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

num_positions(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → int¶: C++: protocols::optimize_weights::OptEData::num_positions() const –> unsigned long

num_rotamers(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → int¶: C++: protocols::optimize_weights::OptEData::num_rotamers() const –> unsigned long

position_data_begin(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::OptEPositionData>, std::allocator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> > > >¶: C++: protocols::optimize_weights::OptEData::position_data_begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> > > >

position_data_end(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData) → __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> const*, std::vector<std::shared_ptr<protocols::optimize_weights::OptEPositionData>, std::allocator<std::shared_ptr<protocols::optimize_weights::OptEPositionData> > > >¶: C++: protocols::optimize_weights::OptEData::position_data_end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> *, class std::vector<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData>, class std::allocator<class std::shared_ptr<class protocols::optimize_weights::OptEPositionData> > > >

read_from_binary_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) → None¶: C++: protocols::optimize_weights::OptEData::read_from_binary_file(class std::basic_string<char>) –> void

read_from_file(self: pyrosetta.rosetta.protocols.optimize_weights.OptEData, filename: str) → None¶: C++: protocols::optimize_weights::OptEData::read_from_file(class std::basic_string<char>) –> 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(class std::basic_string<char>) 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(class std::basic_string<char>) const –> void

class pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc¶

Bases: pyrosetta.rosetta.core.optimization.Multifunc

OptE mode multifunction class

__call__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) → float¶: C++: protocols::optimize_weights::OptEMultifunc::operator()(const class utility::vector1<double, class std::allocator<double> > &) const –> double

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, opte_data_in: pyrosetta.rosetta.protocols.optimize_weights.OptEData, fixed_terms_in: pyrosetta.rosetta.core.scoring.EMapVector, num_free_in: int, score_list_in: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list_in: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, component_weights: pyrosetta.rosetta.utility.vector1_double) -> None
__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc, opte_data_in: pyrosetta.rosetta.protocols.optimize_weights.OptEData, fixed_terms_in: pyrosetta.rosetta.core.scoring.EMapVector, num_free_in: int, score_list_in: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, fixed_score_list_in: pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType, reference_energies_in: pyrosetta.rosetta.utility.vector1_double, component_weights: pyrosetta.rosetta.utility.vector1_double) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.OptEPositionData¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> None
__init__(self: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData, arg0: pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_ostream<char> &, 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 class std::basic_string<char> &) –> 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.WrapperOptEMultifunc¶

Bases: pyrosetta.rosetta.core.optimization.Multifunc

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

__call__(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) → float¶: C++: protocols::optimize_weights::WrapperOptEMultifunc::operator()(const class utility::vector1<double, class std::allocator<double> > &) const –> double

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> None
__init__(self: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc, arg0: pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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> > &, class std::basic_ostream<char> &) 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(class std::basic_string<char>) –> 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