rotamer_recovery¶

Bindings for protocols::rotamer_recovery namespace

class pyrosetta.rosetta.protocols.rotamer_recovery.OutputLevel¶

Bases: pybind11_builtins.pybind11_object

Members:

OL_full

OL_features

OL_none

class pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer¶

Bases: pybind11_builtins.pybind11_object

The comparison functionality for the rotamer recovery test

Besides implementing the interface given in the base class RRComparer each RRComparer should have an entry in the conevience RotamerRecovery constructor so its use can be indicated by name.

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

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

get_parameters(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer) → str¶: C++: protocols::rotamer_recovery::RRComparer::get_parameters() const –> std::string

measure_rotamer_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, score: float, recovered: bool) → bool¶: C++: protocols::rotamer_recovery::RRComparer::measure_rotamer_recovery(const class core::pose::Pose &, const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, double &, bool &) –> bool

parse_attributes_from_tag(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::rotamer_recovery::RRComparer::parse_attributes_from_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

set_absolute_threshold(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer, absolute_threshold: float) → None¶: C++: protocols::rotamer_recovery::RRComparer::set_absolute_threshold(const double) –> void

set_recovery_threshold(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer, recovery_threshold: float) → None¶: C++: protocols::rotamer_recovery::RRComparer::set_recovery_threshold(const double) –> void

class pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator¶

Bases: pybind11_builtins.pybind11_object

The Creator class is responsible for creating a particular mover class.

append_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RRComparerCreator::append_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

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

create_comparer(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator) → pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer¶: C++: protocols::rotamer_recovery::RRComparerCreator::create_comparer() const –> class std::shared_ptr<class protocols::rotamer_recovery::RRComparer>

type_name(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator) → str¶: C++: protocols::rotamer_recovery::RRComparerCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol¶

Bases: pybind11_builtins.pybind11_object

The protocol to run to compute the rotamer recovery the rotamer recovery test

Besides implementing the interface given in the base class RRProtocol each RRProtocol should have an entry in the convenience RotamerRecovery constructor so its use can be indicated by name.

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

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

get_parameters(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol) → str¶: C++: protocols::rotamer_recovery::RRProtocol::get_parameters() const –> std::string

parse_attributes_from_tag(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol, dm: pyrosetta.rosetta.basic.datacache.DataMap, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶

As the RRProtocol is being read in

C++: protocols::rotamer_recovery::RRProtocol::parse_attributes_from_tag(const class basic::datacache::DataMap &, class std::shared_ptr<const class utility::tag::Tag>) –> void

run(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol, comparer: pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer, reporter: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter, pose: pyrosetta.rosetta.core.pose.Pose, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::rotamer_recovery::RRProtocol::run(class std::shared_ptr<class protocols::rotamer_recovery::RRComparer>, class std::shared_ptr<class protocols::rotamer_recovery::RRReporter>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &) –> void

class pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator¶

Bases: pybind11_builtins.pybind11_object

The Creator class is responsible for creating a particular mover class.

append_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RRProtocolCreator::append_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

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

create_protocol(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator) → pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol¶: C++: protocols::rotamer_recovery::RRProtocolCreator::create_protocol() const –> class std::shared_ptr<class protocols::rotamer_recovery::RRProtocol>

type_name(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator) → str¶: C++: protocols::rotamer_recovery::RRProtocolCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter¶

Bases: pybind11_builtins.pybind11_object

The reporting functionality for the rotamer recovery test

Besides implementing the interface given in the base class RRReporter each RRReporter should have an entry in the conevience RotamerRecovery constructor so its use can be indicated by name.

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

recovery_rate(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter) → float¶: C++: protocols::rotamer_recovery::RRReporter::recovery_rate() const –> double

report_rotamer_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, score: float, recovered: bool) → None¶: C++: protocols::rotamer_recovery::RRReporter::report_rotamer_recovery(const class core::pose::Pose &, const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, double, bool) –> void

reset_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter) → None¶: C++: protocols::rotamer_recovery::RRReporter::reset_recovery() –> void

set_comparer_info(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter, comparer_name: str, comparer_params: str) → None¶: C++: protocols::rotamer_recovery::RRReporter::set_comparer_info(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_protocol_info(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter, protocol_name: str, protocol_params: str) → None¶: C++: protocols::rotamer_recovery::RRReporter::set_protocol_info(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rotamer_recovery::RRReporter::show(class std::basic_ostream<char> &) const –> void

show(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter) -> None

C++: protocols::rotamer_recovery::RRReporter::show() const –> void

class pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator¶

Bases: pybind11_builtins.pybind11_object

The Creator class is responsible for creating a particular mover class.

append_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RRReporterCreator::append_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

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

create_reporter(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator) → pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter¶: C++: protocols::rotamer_recovery::RRReporterCreator::create_reporter() const –> class std::shared_ptr<class protocols::rotamer_recovery::RRReporter>

type_name(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator) → str¶: C++: protocols::rotamer_recovery::RRReporterCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman¶

Bases: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter

The reporting functionality for the rotamer recovery test in a human readable format.

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

recovery_rate(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman) → float¶: C++: protocols::rotamer_recovery::RRReporterHuman::recovery_rate() const –> double

report_rotamer_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, score: float, recovered: bool) → None¶: C++: protocols::rotamer_recovery::RRReporterHuman::report_rotamer_recovery(const class core::pose::Pose &, const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, double, bool) –> void

reset_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman) → None¶: C++: protocols::rotamer_recovery::RRReporterHuman::reset_recovery() –> void

set_comparer_info(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman, comparer_name: str, comparer_params: str) → None¶: C++: protocols::rotamer_recovery::RRReporterHuman::set_comparer_info(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_protocol_info(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman, protocol_name: str, protocol_params: str) → None¶: C++: protocols::rotamer_recovery::RRReporterHuman::set_protocol_info(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rotamer_recovery::RRReporterHuman::show(class std::basic_ostream<char> &) const –> void

show(self: pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman) -> None

C++: protocols::rotamer_recovery::RRReporterHuman::show() const –> void

class pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory¶

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t

Create Rotamer_Recovery Reporters

append_comparer_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::append_comparer_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

append_protocol_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::append_protocol_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

append_reporter_attributes(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::append_reporter_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) const –> void

get_instance() → protocols::rotamer_recovery::RotamerRecoveryFactory¶: C++: utility::SingletonBase<protocols::rotamer_recovery::RotamerRecoveryFactory>::get_instance() –> class protocols::rotamer_recovery::RotamerRecoveryFactory *

get_rotamer_recovery(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, protocol: str, comparer: str, reporter: str) → pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> class std::shared_ptr<class protocols::rotamer_recovery::RotamerRecovery>

get_rotamer_recovery_comparer(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name: str) → pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_comparer(const class std::basic_string<char> &) –> class std::shared_ptr<class protocols::rotamer_recovery::RRComparer>

get_rotamer_recovery_protocol(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name: str) → pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_protocol(const class std::basic_string<char> &) –> class std::shared_ptr<class protocols::rotamer_recovery::RRProtocol>

get_rotamer_recovery_reporter(self: pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name: str) → pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter¶: C++: protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_reporter(const class std::basic_string<char> &) –> class std::shared_ptr<class protocols::rotamer_recovery::RRReporter>