parametric

Bindings for core::conformation::parametric namespace

class pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

Bases: Parameter

BooleanValuedParameter class, used to store a single Boolean-valued parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, : pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

C++: core::conformation::parametric::BooleanValuedParameter::operator=(const class core::conformation::parametric::BooleanValuedParameter &) –> class core::conformation::parametric::BooleanValuedParameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::BooleanValuedParameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: core::conformation::parametric::Parameters, this_parameter_collection: core::conformation::parametric::Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

C++: core::conformation::parametric::BooleanValuedParameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

default_value(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → bool

Get the default value of this parameter.

C++: core::conformation::parametric::BooleanValuedParameter::default_value() const –> bool

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

Must be implemented by derived classes.

C++: core::conformation::parametric::BooleanValuedParameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, provide_copying: bool, provide_grid_sampling: bool, provide_perturbation: bool) → None

Return the XSD information for this parameter.

Currently, boolean values can’t be sampled or perturbed, so this only provides setting information.

C++: core::conformation::parametric::BooleanValuedParameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::BooleanValuedParameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → None

Reset the value settings for this Parameter object.

C++: core::conformation::parametric::BooleanValuedParameter::reset_value_settings() –> void

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_default_value(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, value_in: bool) → None

Set the default value of this parameter.

C++: core::conformation::parametric::BooleanValuedParameter::set_default_value(const bool) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Sets the parameter type.

Override is limited to Boolean types.

C++: core::conformation::parametric::BooleanValuedParameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

set_value(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter, value_in: bool) → None

Set the value of this parameter.

C++: core::conformation::parametric::BooleanValuedParameter::set_value(const bool) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value(self: pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter) → bool

Get the value of this parameter.

C++: core::conformation::parametric::BooleanValuedParameter::value() const –> bool

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool

class pyrosetta.rosetta.core.conformation.parametric.Parameter

Bases: pybind11_object

Parameter class, used to store a single parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, : pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

C++: core::conformation::parametric::Parameter::operator=(const class core::conformation::parametric::Parameter &) –> class core::conformation::parametric::Parameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::Parameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: core::conformation::parametric::Parameters, this_parameter_collection: core::conformation::parametric::Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Must be implemented by derived classes. Type checking can be performed by derived classes.

Returns TRUE for failure and FALSE for success.

C++: core::conformation::parametric::Parameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. If parse_copying is true, this parses options for copying. Note that, if multiple options are true an error should be thrown if more than one of these is provided.

Must be implemented by derived classes.

C++: core::conformation::parametric::Parameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, provide_copying: bool, provide_grid_sampling: bool, provide_perturbation: bool) → None

Return the XSD information for this parameter.

Must be implemented by derived classes.

C++: core::conformation::parametric::Parameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::Parameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the value settings for this Parameter object.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::Parameter::reset_value_settings() –> void

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Set the parameter type.

C++: core::conformation::parametric::Parameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool

class pyrosetta.rosetta.core.conformation.parametric.ParameterType

Bases: pybind11_object

The types of parameters possible.

Members:

PT_generic_real

PT_generic_nonnegative_valued_real

PT_generic_positive_valued_real

PT_angle

PT_boolean

PT_generic_integer

PT_generic_whole_number

PT_generic_natural_number

PT_generic_integer_vector

PT_generic_whole_number_vector

PT_generic_natural_number_vector

PT_generic_real_vector

PT_generic_nonnegative_valued_real_vector

PT_generic_positive_valued_real_vector

PT_angle_vector

PT_invalid_type

PT_end_of_list

PT_angle = <ParameterType.PT_angle: 4>

PT_angle_vector = <ParameterType.PT_angle_vector: 15>

PT_boolean = <ParameterType.PT_boolean: 5>

PT_end_of_list = <ParameterType.PT_invalid_type: 16>

PT_generic_integer = <ParameterType.PT_generic_integer: 6>

PT_generic_integer_vector = <ParameterType.PT_generic_integer_vector: 9>

PT_generic_natural_number = <ParameterType.PT_generic_natural_number: 8>

PT_generic_natural_number_vector = <ParameterType.PT_generic_natural_number_vector: 11>

PT_generic_nonnegative_valued_real = <ParameterType.PT_generic_nonnegative_valued_real: 2>

PT_generic_nonnegative_valued_real_vector = <ParameterType.PT_generic_nonnegative_valued_real_vector: 13>

PT_generic_positive_valued_real = <ParameterType.PT_generic_positive_valued_real: 3>

PT_generic_positive_valued_real_vector = <ParameterType.PT_generic_positive_valued_real_vector: 14>

PT_generic_real = <ParameterType.PT_generic_real: 1>

PT_generic_real_vector = <ParameterType.PT_generic_real_vector: 12>

PT_generic_whole_number = <ParameterType.PT_generic_whole_number: 7>

PT_generic_whole_number_vector = <ParameterType.PT_generic_whole_number_vector: 10>

PT_invalid_type = <ParameterType.PT_invalid_type: 16>

property name

property value

class pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties

Bases: pybind11_object

property can_be_copied

property can_be_perturbed

property can_be_sampled

property can_be_set

property global_for_parameters_set

class pyrosetta.rosetta.core.conformation.parametric.Parameters

Bases: pybind11_object

Parameters class, used to store sets of parameters for parametric backbone generation.

add_parameter(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Add a parameter.

Does NOT clone the parameter, but stores the OP directly.

C++: core::conformation::parametric::Parameters::add_parameter(class std::shared_ptr<class core::conformation::parametric::Parameter>) –> void

add_residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, residue: pyrosetta.rosetta.core.conformation.Residue) → None

Add a residue to the list of residues that these parameters describe.

C++: core::conformation::parametric::Parameters::add_residue(class std::shared_ptr<const class core::conformation::Residue>) –> void

assign(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, : pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.core.conformation.parametric.Parameters

C++: core::conformation::parametric::Parameters::operator=(const class core::conformation::parametric::Parameters &) –> class core::conformation::parametric::Parameters &

clone(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.core.conformation.parametric.Parameters

Copy this residue( allocate actual memory for it )

C++: core::conformation::parametric::Parameters::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameters>

first_residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.core.conformation.Residue

Get a const owning pointer to the first residue in the list of residues that these parameters describe.

Note that this might not be the first residue in linear sequence, if the residues were put in in non-

sequential order or the residue numbering has changed.

C++: core::conformation::parametric::Parameters::first_residue() const –> class std::shared_ptr<const class core::conformation::Residue>

first_residue_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → int

Get the index of the first residue.

MUST BE REWRITTEN when the OP issue is resolved.

C++: core::conformation::parametric::Parameters::first_residue_index() const –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.core.conformation.parametric.Parameters

C++: core::conformation::parametric::Parameters::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameters>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameters_t

C++: core::conformation::parametric::Parameters::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameters>

last_residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → pyrosetta.rosetta.core.conformation.Residue

Get a const owning pointer to the last residue in the list of residues that these parameters describe.

Note that this might not be the last residue in linear sequence, if the residues were put in in non-

sequential order or the residue numbering has changed.

C++: core::conformation::parametric::Parameters::last_residue() const –> class std::shared_ptr<const class core::conformation::Residue>

last_residue_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → int

Get the index of the last residue.

MUST BE REWRITTEN when the OP issue is resolved.

C++: core::conformation::parametric::Parameters::last_residue_index() const –> unsigned long

n_residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → int

Returns the number (count) of residues that these parameters describe.

C++: core::conformation::parametric::Parameters::n_residue() const –> unsigned long

num_parameters(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → int

Get the number of parameters stored in this Parameters object.

C++: core::conformation::parametric::Parameters::num_parameters() const –> unsigned long

parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, index: int) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter, by index.

Const access.

C++: core::conformation::parametric::Parameters::parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::Parameter>

parameter_op(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, index: int) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter, by index.

Non-const access.

C++: core::conformation::parametric::Parameters::parameter_op(const unsigned long) const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

replace_parameter_via_clone(*args, **kwargs)

Overloaded function.

1. replace_parameter_via_clone(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, param_index: int, new_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter) -> None

2. replace_parameter_via_clone(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, param_index: int, new_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, reset_sampling_copying_perturbing: bool) -> None

Replace one of the contained parameter objects with

a copy of an input parameter object.

If reset_sampling_copying_perturbing is true, then the sampling, copying, and perturbing information of the copied parameter object are all reset. True by default.

C++: core::conformation::parametric::Parameters::replace_parameter_via_clone(const unsigned long, class std::shared_ptr<const class core::conformation::parametric::Parameter>, const bool) –> void

reset_residue_list(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → None

Clears the list of residues that these parameters describe.

C++: core::conformation::parametric::Parameters::reset_residue_list() –> void

reset_sampling_and_perturbing_info(self: pyrosetta.rosetta.core.conformation.parametric.Parameters) → None

Clears the sampling and perturbing information in the individual parameters.

C++: core::conformation::parametric::Parameters::reset_sampling_and_perturbing_info() const –> void

residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, index: int) → pyrosetta.rosetta.core.conformation.Residue

Get an owning pointer to a residue in the list of residues that these parameters describe.

C++: core::conformation::parametric::Parameters::residue(const unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

set_residue(self: pyrosetta.rosetta.core.conformation.parametric.Parameters, index: int, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Assign an element in the residue list to be an owning pointer to an existing residue.

C++: core::conformation::parametric::Parameters::set_residue(const unsigned long, class std::shared_ptr<const class core::conformation::Residue>) –> void

class pyrosetta.rosetta.core.conformation.parametric.ParametersSet

Bases: pybind11_object

ParametersSet class, used to store sets of parameters for parametric backbone generation.

add_parameters(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet, new_parameters: pyrosetta.rosetta.core.conformation.parametric.Parameters) → None

Add a Parameters object to the set included in this ParametersSet object.

C++: core::conformation::parametric::ParametersSet::add_parameters(class std::shared_ptr<class core::conformation::parametric::Parameters>) –> void

assign(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet, : pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → pyrosetta.rosetta.core.conformation.parametric.ParametersSet

C++: core::conformation::parametric::ParametersSet::operator=(const class core::conformation::parametric::ParametersSet &) –> class core::conformation::parametric::ParametersSet &

clear_parameters_list(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → None

Delete all owning pointers in the parameters_ list and reset the list.

C++: core::conformation::parametric::ParametersSet::clear_parameters_list() –> void

clone(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → pyrosetta.rosetta.core.conformation.parametric.ParametersSet

Copy this residue( allocate actual memory for it )

C++: core::conformation::parametric::ParametersSet::clone() const –> class std::shared_ptr<class core::conformation::parametric::ParametersSet>

get_pdb_remark(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet, remark: pyrosetta.rosetta.std.stringstream) → None

Get a summary of this ParametersSet object, for output to remark lines of a PDB file.

Default function can be overridden by derived classes. The default message just says that the parameterization does not support output to PDB remark lines. Note that messages must have lines less than about fifty characters, or they get truncated in REMARK output.

C++: core::conformation::parametric::ParametersSet::get_pdb_remark(class std::basic_stringstream<char> &) const –> void

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → pyrosetta.rosetta.core.conformation.parametric.ParametersSet

C++: core::conformation::parametric::ParametersSet::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::ParametersSet>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_ParametersSet_t

C++: core::conformation::parametric::ParametersSet::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::ParametersSet>

n_parameters(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → int

Get the number of Parameters objects associated with this ParametersSet.

C++: core::conformation::parametric::ParametersSet::n_parameters() const –> unsigned long

parameters(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet, index: int) → pyrosetta.rosetta.core.conformation.parametric.Parameters

Get a Parameters object by index.

C++: core::conformation::parametric::ParametersSet::parameters(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::Parameters>

update_residue_links(self: pyrosetta.rosetta.core.conformation.parametric.ParametersSet, new_conf: pyrosetta.rosetta.core.conformation.Conformation) → None

Only for copying Conformation objects, this ensures that the new ParametersSet object’s

Parameters objects have lists of ResidueOPs that point to residues in the new Conformation object, rather than to residues that only exist in the Parameters objects.

C++: core::conformation::parametric::ParametersSet::update_residue_links(class core::conformation::Conformation &) –> void

class pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

Bases: pybind11_object

ParametrizationCalculator class, used for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, : pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) → pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

C++: core::conformation::parametric::ParametrizationCalculator::operator=(const class core::conformation::parametric::ParametrizationCalculator &) –> class core::conformation::parametric::ParametrizationCalculator &

boolean_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

Accesses a boolean-valued parameter.

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::boolean_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::BooleanValuedParameter>

boolean_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

Accesses a boolean-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::boolean_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::BooleanValuedParameter>

clone(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) → pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

Copy this object ( allocate actual memory for it )

Must be implemented by derived classes.

C++: core::conformation::parametric::ParametrizationCalculator::clone() const –> class std::shared_ptr<class core::conformation::parametric::ParametrizationCalculator>

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) → pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

C++: core::conformation::parametric::ParametrizationCalculator::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::ParametrizationCalculator>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_ParametrizationCalculator_t

C++: core::conformation::parametric::ParametrizationCalculator::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::ParametrizationCalculator>

parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter.

C++: core::conformation::parametric::ParametrizationCalculator::parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::Parameter>

parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter.

Const-access

C++: core::conformation::parametric::ParametrizationCalculator::parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::Parameter>

parameters_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) → pyrosetta.rosetta.core.conformation.parametric.Parameters

Get a const-owning pointer to the Parameters object.

C++: core::conformation::parametric::ParametrizationCalculator::parameters_cop() const –> class std::shared_ptr<const class core::conformation::parametric::Parameters>

real_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::RealValuedParameter

Accesses a real-valued parameter.

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::real_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::RealValuedParameter>

real_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::RealValuedParameter

Accesses a real-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::real_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::RealValuedParameter>

realvector_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::RealVectorValuedParameter

Accesses a realvector-valued parameter.

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::realvector_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::RealVectorValuedParameter>

realvector_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::RealVectorValuedParameter

Accesses a realvector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::realvector_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::RealVectorValuedParameter>

size_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::SizeValuedParameter

Accesses a size-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::size_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::SizeValuedParameter>

size_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::SizeValuedParameter

Accesses a size-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::size_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::SizeValuedParameter>

sizevector_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::SizeVectorValuedParameter

Accesses a sizevector-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::sizevector_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::SizeVectorValuedParameter>

sizevector_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) → core::conformation::parametric::SizeVectorValuedParameter

Accesses a sizevector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::sizevector_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::SizeVectorValuedParameter>

class pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType

Bases: pybind11_object

The types of perturbations.

If you add to this list, be sure to update the perturbation_type_string_from_enum() function.

Members:

RPT_gaussian

RPT_uniform

RPT_unknown_type

RPT_end_of_list

RPT_end_of_list = <RealPerturbationType.RPT_unknown_type: 3>

RPT_gaussian = <RealPerturbationType.RPT_gaussian: 1>

RPT_uniform = <RealPerturbationType.RPT_uniform: 2>

RPT_unknown_type = <RealPerturbationType.RPT_unknown_type: 3>

property name

property value

class pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter

Bases: Parameter

RealValuedParameter class, used to store a single real-valued parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, : pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter

C++: core::conformation::parametric::RealValuedParameter::operator=(const class core::conformation::parametric::RealValuedParameter &) –> class core::conformation::parametric::RealValuedParameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::RealValuedParameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters, this_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

Returns TRUE for failure, FALSE for success.

C++: core::conformation::parametric::RealValuedParameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

default_value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → float

Get the default value of this parameter.

C++: core::conformation::parametric::RealValuedParameter::default_value() const –> const double &

generate_perturbed_value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, current_value: float) → float

Given the current value of this parameter and the current perturbation

settings, return a perturbed value.

Does not alter the value of this parameter.

C++: core::conformation::parametric::RealValuedParameter::generate_perturbed_value(const double &) const –> double

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

Must be implemented by derived classes.

C++: core::conformation::parametric::RealValuedParameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

perturbation_magnitude(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → float

Get the perturbation magnitude of this parameter.

C++: core::conformation::parametric::RealValuedParameter::perturbation_magnitude() const –> const double &

perturbation_set(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → bool

Has the perturbation information for this parameter been set?

C++: core::conformation::parametric::RealValuedParameter::perturbation_set() const –> bool

perturbation_type(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType

Get the perturbation type.

C++: core::conformation::parametric::RealValuedParameter::perturbation_type() const –> enum core::conformation::parametric::RealPerturbationType

static perturbation_type_enum_from_string(type_string: str) → pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType

Given a perturbation type string, get the enum for that string.

Returns RPT_unknown_type if unknown string provided.

C++: core::conformation::parametric::RealValuedParameter::perturbation_type_enum_from_string(const std::string &) –> enum core::conformation::parametric::RealPerturbationType

static perturbation_type_string_from_enum(type_enum: pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType) → str

Given a perturbation type enum, get the string for that enum.

Throws an error for an invalid enum.

C++: core::conformation::parametric::RealValuedParameter::perturbation_type_string_from_enum(const enum core::conformation::parametric::RealPerturbationType) –> const std::string &

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, provide_copying: bool, provide_grid_sampling: bool, provide_perturbation: bool) → None

Return the XSD information for this parameter.

Must be implemented by derived classes.

C++: core::conformation::parametric::RealValuedParameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::RealValuedParameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → None

Reset the value settings for this Parameter object.

C++: core::conformation::parametric::RealValuedParameter::reset_value_settings() –> void

sampling_set(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → bool

Has the sampling information for this parameter been set?

C++: core::conformation::parametric::RealValuedParameter::sampling_set() const –> bool

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_default_value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, value_in: float) → None

Sets the initial value of this parameter, keeping the value_set_ boolean false.

Also sets default_value_.

C++: core::conformation::parametric::RealValuedParameter::set_default_value(const double &) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_input_is_angle_in_degrees(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, setting: bool) → None

Set whether this parameter expects that its input is an angle in degrees.

Must be set before any values are set.

C++: core::conformation::parametric::RealValuedParameter::set_input_is_angle_in_degrees(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Sets the parameter type.

Override is limited to real types.

C++: core::conformation::parametric::RealValuedParameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_perturbation_options(*args, **kwargs)

Overloaded function.

1. set_perturbation_options(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, pert_magnitude_in: float, pert_type_in: str) -> None

Set the options for perturbing this parameter (with perturbation type set by string).

C++: core::conformation::parametric::RealValuedParameter::set_perturbation_options(const double &, const std::string &) –> void

2. set_perturbation_options(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, pert_magnitude_in: float, pert_type_in: pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType) -> None

Set the options for perturbing this parameter (with perturbation type set by enum).

C++: core::conformation::parametric::RealValuedParameter::set_perturbation_options(const double &, const enum core::conformation::parametric::RealPerturbationType) –> void

set_perturbation_type(*args, **kwargs)

Overloaded function.

1. set_perturbation_type(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, pert_type_in: str) -> None

Set the perturbation type, by string.

Throws an error if not a valid type.

C++: core::conformation::parametric::RealValuedParameter::set_perturbation_type(const std::string &) –> void

2. set_perturbation_type(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, pert_type_in: pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType) -> None

Set the perturbation type, by enum.

Throws an error if invalid enum.

C++: core::conformation::parametric::RealValuedParameter::set_perturbation_type(const enum core::conformation::parametric::RealPerturbationType) –> void

set_sampling_options(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, value_min_in: float, value_max_in: float, samples_in: int) → None

Set the options for sampling this parameter.

C++: core::conformation::parametric::RealValuedParameter::set_sampling_options(const double &, const double &, const unsigned long) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

set_value(*args, **kwargs)

Overloaded function.

1. set_value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, value_in: float) -> None

2. set_value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, value_in: float, ignore_use_degrees: bool) -> None

Set the value of this parameter.

If ignore_use_degrees is true, this will just set the value to the input value. Otherwise, it convert from degrees to radians if input_is_angle_in_degrees_ is true.

This makes the value_set_ boolean true.

C++: core::conformation::parametric::RealValuedParameter::set_value(const double &, const bool) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → float

Get the value of this parameter.

C++: core::conformation::parametric::RealValuedParameter::value() const –> const double &

value_max(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → float

Get the maximum value of this parameter.

C++: core::conformation::parametric::RealValuedParameter::value_max() const –> const double &

value_min(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → float

Get the minimum value of this parameter.

C++: core::conformation::parametric::RealValuedParameter::value_min() const –> const double &

value_samples(self: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter) → int

Get the samples.

C++: core::conformation::parametric::RealValuedParameter::value_samples() const –> unsigned long

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool

class pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter

Bases: Parameter

RealVectorValuedParameter class, used to store a single vector-valued parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, : pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter

C++: core::conformation::parametric::RealVectorValuedParameter::operator=(const class core::conformation::parametric::RealVectorValuedParameter &) –> class core::conformation::parametric::RealVectorValuedParameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::RealVectorValuedParameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters, this_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

C++: core::conformation::parametric::RealVectorValuedParameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

default_value(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → pyrosetta.rosetta.utility.vector1_double

Get the defaults for this parameter.

C++: core::conformation::parametric::RealVectorValuedParameter::default_value() const –> const class utility::vector1<double, class std::allocator<double> > &

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

A vector of floats must be provided as a whitespace-separated string.

C++: core::conformation::parametric::RealVectorValuedParameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, : bool, : bool, : bool) → None

Return the XSD information for this parameter.

Currently, RealVector-valued parameters can’t be sampled or perturbed, so this only provides setting information.

C++: core::conformation::parametric::RealVectorValuedParameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::RealVectorValuedParameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → None

Reset the value settings for this Parameter object.

C++: core::conformation::parametric::RealVectorValuedParameter::reset_value_settings() –> void

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_default_value(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, value_in: pyrosetta.rosetta.utility.vector1_double) → None

Set the default value for this parameter.

C++: core::conformation::parametric::RealVectorValuedParameter::set_default_value(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Sets the parameter type.

Override is limited to real types.

C++: core::conformation::parametric::RealVectorValuedParameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

set_value(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter, value_in: pyrosetta.rosetta.utility.vector1_double) → None

Set the value of this parameter.

C++: core::conformation::parametric::RealVectorValuedParameter::set_value(const class utility::vector1<double, class std::allocator<double> > &) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value(self: pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter) → pyrosetta.rosetta.utility.vector1_double

Get the value of this parameter.

C++: core::conformation::parametric::RealVectorValuedParameter::value() const –> const class utility::vector1<double, class std::allocator<double> > &

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool

class pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter

Bases: Parameter

SizeValuedParameter class, used to store a single core::Size-valued parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, : pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter

C++: core::conformation::parametric::SizeValuedParameter::operator=(const class core::conformation::parametric::SizeValuedParameter &) –> class core::conformation::parametric::SizeValuedParameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::SizeValuedParameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters, this_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

C++: core::conformation::parametric::SizeValuedParameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

default_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → int

Get the default value of this parameter.

C++: core::conformation::parametric::SizeValuedParameter::default_value() const –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

Must be implemented by derived classes.

C++: core::conformation::parametric::SizeValuedParameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, : bool, : bool, : bool) → None

Return the XSD information for this parameter.

Currently, Size-valued parameters can’t be sampled or perturbed, so this only provides setting information.

C++: core::conformation::parametric::SizeValuedParameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::SizeValuedParameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → None

Reset the value settings for this Parameter object.

C++: core::conformation::parametric::SizeValuedParameter::reset_value_settings() –> void

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_default_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, value_in: int) → None

Set the default value for this parameter.

C++: core::conformation::parametric::SizeValuedParameter::set_default_value(const unsigned long) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Sets the parameter type.

Override is limited to nonnegative or positive integer types.

C++: core::conformation::parametric::SizeValuedParameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

set_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter, value_in: int) → None

Set the value of this parameter.

C++: core::conformation::parametric::SizeValuedParameter::set_value(const unsigned long) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value(self: pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter) → int

Get the value of this parameter.

C++: core::conformation::parametric::SizeValuedParameter::value() const –> unsigned long

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool

class pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter

Bases: Parameter

SizeVectorValuedParameter class, used to store a single utility::vector1<core::Size>-valued parameter for parametric backbone generation.

assign(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, : pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter

C++: core::conformation::parametric::SizeVectorValuedParameter::operator=(const class core::conformation::parametric::SizeVectorValuedParameter &) –> class core::conformation::parametric::SizeVectorValuedParameter &

can_be_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be copied from another parameter?

Default true.

C++: core::conformation::parametric::Parameter::can_be_copied() const –> bool

can_be_perturbed(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_perturbed() const –> bool

can_be_sampled(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_sampled() const –> bool

can_be_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::can_be_set() const –> bool

clone(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Make a copy of this object ( allocate actual memory for it )

C++: core::conformation::parametric::SizeVectorValuedParameter::clone() const –> class std::shared_ptr<class core::conformation::parametric::Parameter>

copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → int

Get the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::copy_from_parameters_index() const –> unsigned long

copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

Does not include the leading underscore.

C++: core::conformation::parametric::Parameter::copy_suffix() const –> const std::string &

copy_value_from_parameter(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, other_parameter: pyrosetta.rosetta.core.conformation.parametric.Parameter, other_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters, this_parameter_collection: pyrosetta.rosetta.core.conformation.parametric.Parameters) → bool

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

C++: core::conformation::parametric::SizeVectorValuedParameter::copy_value_from_parameter(class std::shared_ptr<const class core::conformation::parametric::Parameter>, class std::shared_ptr<const class core::conformation::parametric::Parameters>, class std::shared_ptr<const class core::conformation::parametric::Parameters>) –> bool

copying_information_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the copying information been set?

C++: core::conformation::parametric::Parameter::copying_information_was_set() const –> bool

default_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get the default value for this parameter.

C++: core::conformation::parametric::SizeVectorValuedParameter::default_value() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.Parameter

Self pointers (nonconst shared pointer).

C++: core::conformation::parametric::Parameter::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::Parameter>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t

Self pointers (nonconst weak pointer).

C++: core::conformation::parametric::Parameter::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::Parameter>

global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Get whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::global_for_parameters_set() const –> bool

parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::parameter_description() const –> const std::string &

parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get parameter name.

C++: core::conformation::parametric::Parameter::parameter_name() const –> const std::string &

parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type.

C++: core::conformation::parametric::Parameter::parameter_type() const –> enum core::conformation::parametric::ParameterType

parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get units.

C++: core::conformation::parametric::Parameter::parameter_units() const –> const std::string &

parse_setting(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, tag: utility::tag::Tag, parse_setting: bool, parse_grid_sampling: bool, parse_perturbation: bool, parse_copying: bool) → None

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

A vector of integers must be provided as a whitespace-separated string.

C++: core::conformation::parametric::SizeVectorValuedParameter::parse_setting(class std::shared_ptr<const class utility::tag::Tag>, const bool, const bool, const bool, const bool) –> void

provide_xsd_information(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, xsd: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, provide_setting: bool, : bool, : bool, : bool) → None

Return the XSD information for this parameter.

Currently, SizeVector-valued parameters can’t be sampled or perturbed, so this only provides setting information.

C++: core::conformation::parametric::SizeVectorValuedParameter::provide_xsd_information(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const bool, const bool, const bool, const bool) const –> void

reset_copying_settings(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → None

Reset the copying options.

C++: core::conformation::parametric::Parameter::reset_copying_settings() –> void

reset_sampling_and_perturbation_settings(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → None

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

C++: core::conformation::parametric::SizeVectorValuedParameter::reset_sampling_and_perturbation_settings() –> void

reset_value_settings(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → None

Reset the value settings for this Parameter object.

C++: core::conformation::parametric::SizeVectorValuedParameter::reset_value_settings() –> void

set_can_be_set_sampled_perturbed_copied(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, can_be_set: bool, can_be_copied: bool, can_be_sampled: bool, can_be_perturbed: bool) → None

Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

C++: core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(const bool, const bool, const bool, const bool) –> void

set_copy_from_parameters_index(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: int) → None

Set the index of the Parameters object from which we will copy this parameter’s value.

A setting of zero means no copying.

C++: core::conformation::parametric::Parameter::set_copy_from_parameters_index(const unsigned long) –> void

set_copy_suffix(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, suffix_in: str) → None

Set the suffix for the copy tag (e.g. “copies_helix” in the case of helical bundles).

The leading underscore should be omitted.

C++: core::conformation::parametric::Parameter::set_copy_suffix(const std::string &) –> void

set_default_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, values_in: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Sets the default value.

C++: core::conformation::parametric::SizeVectorValuedParameter::set_default_value(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_global_for_parameters_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, setting: bool) → None

Set whether this property is meant to be global for a parameters set.

C++: core::conformation::parametric::Parameter::set_global_for_parameters_set(const bool) –> void

set_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, description_in: str) → None

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

C++: core::conformation::parametric::Parameter::set_parameter_description(const std::string &) –> void

set_parameter_name(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, name_in: str) → None

Set parameter name.

C++: core::conformation::parametric::Parameter::set_parameter_name(const std::string &) –> void

set_parameter_type(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, type_in: pyrosetta.rosetta.core.conformation.parametric.ParameterType) → None

Sets the parameter type.

Override is limited to nonnegative or positive integer types.

C++: core::conformation::parametric::SizeVectorValuedParameter::set_parameter_type(const enum core::conformation::parametric::ParameterType) –> void

set_parameter_units(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, units_in: str) → None

Set parameter units.

C++: core::conformation::parametric::Parameter::set_parameter_units(const std::string &) –> void

set_short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter, short_description_in: str) → None

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::set_short_parameter_description(const std::string &) –> void

set_value(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter, values_in: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Set the value of this parameter.

C++: core::conformation::parametric::SizeVectorValuedParameter::set_value(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

short_parameter_description(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → str

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

C++: core::conformation::parametric::Parameter::short_parameter_description() const –> const std::string &

value(self: pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get the value of this parameter.

C++: core::conformation::parametric::SizeVectorValuedParameter::value() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

value_was_set(self: pyrosetta.rosetta.core.conformation.parametric.Parameter) → bool

Has the value been set?

C++: core::conformation::parametric::Parameter::value_was_set() const –> bool