calc_taskop_filters¶

Bindings for protocols::calc_taskop_filters namespace

class pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product)

apply(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::compute(const class core::pose::Pose &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) → str¶

allows within-trajectory resetting of the baseline. Notice this is nonconst, so can’t be called from apply. attempt_read_from_checkpoint should be true for MC trials > 1, but false otherwise

C++: protocols::calc_taskop_filters::MultipleSigmoids::name() const –> std::string

operator_filter(*args, **kwargs)¶

Overloaded function.

operator_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) -> protocols::calc_taskop_filters::Operator

C++: protocols::calc_taskop_filters::MultipleSigmoids::operator_filter() const –> class std::shared_ptr<class protocols::calc_taskop_filters::Operator>

operator_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, opt: protocols::calc_taskop_filters::Operator) -> None

C++: protocols::calc_taskop_filters::MultipleSigmoids::operator_filter(class std::shared_ptr<class protocols::calc_taskop_filters::Operator>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

relative_pose_filter(*args, **kwargs)¶

Overloaded function.

relative_pose_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) -> protocols::calc_taskop_filters::RelativePoseFilter

C++: protocols::calc_taskop_filters::MultipleSigmoids::relative_pose_filter() const –> class std::shared_ptr<class protocols::calc_taskop_filters::RelativePoseFilter>

relative_pose_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, rpose: protocols::calc_taskop_filters::RelativePoseFilter) -> None

C++: protocols::calc_taskop_filters::MultipleSigmoids::relative_pose_filter(class std::shared_ptr<class protocols::calc_taskop_filters::RelativePoseFilter>) –> void

report(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::report_sm(const class core::pose::Pose &) const –> double

reset_baseline(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, pose: pyrosetta.rosetta.core.pose.Pose, attempt_read_from_checkpoint: bool) → None¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::reset_baseline(const class core::pose::Pose &, const bool) –> void

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

sigmoid_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) → protocols::calc_taskop_filters::Sigmoid¶: C++: protocols::calc_taskop_filters::MultipleSigmoids::sigmoid_filter() const –> class std::shared_ptr<class protocols::calc_taskop_filters::Sigmoid>

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids) -> float

C++: protocols::calc_taskop_filters::MultipleSigmoids::threshold() const –> double

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids, t: float) -> None

C++: protocols::calc_taskop_filters::MultipleSigmoids::threshold(const double) –> void

class pyrosetta.rosetta.protocols.calc_taskop_filters.Operation¶

Bases: pybind11_builtins.pybind11_object

Members:

SUM

PRODUCT

NORMALIZED_SUM

MAX

MIN

SUBTRACT

ABS

BOOLEAN_OR

XOR

class pyrosetta.rosetta.protocols.calc_taskop_filters.Operator¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

simply take a list of filters and combine them using the operation above

add_filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, f: pyrosetta.rosetta.protocols.filters.Filter) → None¶: C++: protocols::calc_taskop_filters::Operator::add_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

apply(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::calc_taskop_filters::Operator::apply(const class core::pose::Pose &) const –> bool

attributes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::calc_taskop_filters::Operator::attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

class_name() → str¶: C++: protocols::calc_taskop_filters::Operator::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::Operator::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::Operator::compute(const class core::pose::Pose &) const –> double

filters(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t¶: C++: protocols::calc_taskop_filters::Operator::filters() const –> class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >

fresh_instance(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::Operator::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

logarithm(*args, **kwargs)¶

Overloaded function.

logarithm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> bool

C++: protocols::calc_taskop_filters::Operator::logarithm() const –> bool

logarithm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, b: bool) -> None

C++: protocols::calc_taskop_filters::Operator::logarithm(const bool) –> void

modify_relative_filters_pdb_names(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) → None¶: C++: protocols::calc_taskop_filters::Operator::modify_relative_filters_pdb_names() –> void

multi_relative(*args, **kwargs)¶

Overloaded function.

multi_relative(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> bool

C++: protocols::calc_taskop_filters::Operator::multi_relative() const –> bool

multi_relative(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, m: bool) -> None

C++: protocols::calc_taskop_filters::Operator::multi_relative(const bool) –> void

name(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) → str¶: C++: protocols::calc_taskop_filters::Operator::name() const –> std::string

negate(*args, **kwargs)¶

Overloaded function.

negate(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, b: bool) -> None

C++: protocols::calc_taskop_filters::Operator::negate(const bool) –> void

negate(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> bool

C++: protocols::calc_taskop_filters::Operator::negate() const –> bool

operation(*args, **kwargs)¶

Overloaded function.

operation(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> pyrosetta.rosetta.protocols.calc_taskop_filters.Operation

C++: protocols::calc_taskop_filters::Operator::operation() const –> enum protocols::calc_taskop_filters::Operation

operation(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, o: pyrosetta.rosetta.protocols.calc_taskop_filters.Operation) -> None

C++: protocols::calc_taskop_filters::Operator::operation(const enum protocols::calc_taskop_filters::Operation) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::Operator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::calc_taskop_filters::Operator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

relative_pose_names(*args, **kwargs)¶

Overloaded function.

relative_pose_names(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::calc_taskop_filters::Operator::relative_pose_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

relative_pose_names(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, s: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::calc_taskop_filters::Operator::relative_pose_names(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

report(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::Operator::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::Operator::report_sm(const class core::pose::Pose &) const –> double

report_subvalues(*args, **kwargs)¶

Overloaded function.

report_subvalues(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, report: bool) -> None

C++: protocols::calc_taskop_filters::Operator::report_subvalues(const bool) –> void

report_subvalues(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> bool

C++: protocols::calc_taskop_filters::Operator::report_subvalues() const –> bool

reset_baseline(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, pose: pyrosetta.rosetta.core.pose.Pose, attempt_read_from_checkpoint: bool) → None¶: C++: protocols::calc_taskop_filters::Operator::reset_baseline(const class core::pose::Pose &, const bool) –> void

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator) -> float

goes over Sigmoid filters and resets them. Note that this is nonconst, and cannot be called from apply

C++: protocols::calc_taskop_filters::Operator::threshold() const –> double

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Operator, t: float) -> None

C++: protocols::calc_taskop_filters::Operator::threshold(const double) –> void

class pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

Next-generation RotamerBoltzmannWeight filter

class ScoreType¶

Bases: pybind11_builtins.pybind11_object

Members:

MEAN_PROBABILITY

MAX_PROBABILITY

MODIFIED_DDG

PROBABILITY

MIN_PROBABILITY

apply(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

returns true if the structure passes the filter, false otherwise

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::apply(const class core::pose::Pose &) const –> bool

calculator_id(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2) → str¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::calculator_id() const –> const std::string &

class_name() → str¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_name(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2) → str¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::get_name() const –> std::string

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2) → str¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

allows printing data to a stream

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

required for reporting score values

C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_energy_landscape_evaluator(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, evaluator: protocols::toolbox::EnergyLandscapeEvaluator) → None¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_energy_landscape_evaluator(class std::shared_ptr<const class protocols::toolbox::EnergyLandscapeEvaluator>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_score_type(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, scoretype: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType) → None¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_score_type(const enum protocols::calc_taskop_filters::RotamerBoltzmannWeight2::ScoreType) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It’s 0.5 at the offset and steepness determines its slope at the offset

apply(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::calc_taskop_filters::Sigmoid::apply(const class core::pose::Pose &) const –> bool

attributes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::calc_taskop_filters::Sigmoid::attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

baseline_checkpointing_filename(*args, **kwargs)¶

Overloaded function.

baseline_checkpointing_filename(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, s: str) -> None

C++: protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename(const class std::basic_string<char> &) –> void

baseline_checkpointing_filename(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> str

C++: protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename() const –> std::string

class_name() → str¶: C++: protocols::calc_taskop_filters::Sigmoid::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::Sigmoid::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::Sigmoid::compute(const class core::pose::Pose &) const –> double

filter(*args, **kwargs)¶

Overloaded function.

filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::calc_taskop_filters::Sigmoid::filter() const –> class std::shared_ptr<class protocols::filters::Filter>

filter(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::calc_taskop_filters::Sigmoid::filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::calc_taskop_filters::Sigmoid::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) → str¶: C++: protocols::calc_taskop_filters::Sigmoid::name() const –> std::string

negate(*args, **kwargs)¶

Overloaded function.

negate(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> bool

C++: protocols::calc_taskop_filters::Sigmoid::negate() const –> bool

negate(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, b: bool) -> None

C++: protocols::calc_taskop_filters::Sigmoid::negate(const bool) –> void

offset(*args, **kwargs)¶

Overloaded function.

offset(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> float

C++: protocols::calc_taskop_filters::Sigmoid::offset() –> double

offset(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, o: float) -> None

C++: protocols::calc_taskop_filters::Sigmoid::offset(const double) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::Sigmoid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::calc_taskop_filters::Sigmoid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::calc_taskop_filters::Sigmoid::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::calc_taskop_filters::Sigmoid::report_sm(const class core::pose::Pose &) const –> double

reset_baseline(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, pose: pyrosetta.rosetta.core.pose.Pose, attempt_read_from_checkpoint: bool) → None¶: C++: protocols::calc_taskop_filters::Sigmoid::reset_baseline(const class core::pose::Pose &, const bool) –> void

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

steepness(*args, **kwargs)¶

Overloaded function.

steepness(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> float

C++: protocols::calc_taskop_filters::Sigmoid::steepness() const –> double

steepness(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, s: float) -> None

C++: protocols::calc_taskop_filters::Sigmoid::steepness(const double) –> void

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid) -> float

allows within-trajectory resetting of the baseline. Notice this is nonconst, so can’t be called from apply. attempt_read_from_checkpoint should be true for MC trials > 1, but false otherwise

C++: protocols::calc_taskop_filters::Sigmoid::threshold() const –> double

threshold(self: pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid, t: float) -> None

C++: protocols::calc_taskop_filters::Sigmoid::threshold(const double) –> void