cyclic_peptide

Bindings for protocols::cyclic_peptide namespace

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::CreateAngleConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint) pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint

C++: protocols::cyclic_peptide::CreateAngleConstraint::operator=(const class protocols::cyclic_peptide::CreateAngleConstraint &) –> class protocols::cyclic_peptide::CreateAngleConstraint &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateAngleConstraint::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateAngleConstraint::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint) str

C++: protocols::cyclic_peptide::CreateAngleConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::CreateAngleConstraint::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::CreateAngleConstraint::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateAngleConstraint::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint, : pyrosetta.rosetta.utility.vector1_unsigned_long, : pyrosetta.rosetta.utility.vector1_std_string, : pyrosetta.rosetta.utility.vector1_unsigned_long, : pyrosetta.rosetta.utility.vector1_std_string, : pyrosetta.rosetta.utility.vector1_unsigned_long, : pyrosetta.rosetta.utility.vector1_std_string, : pyrosetta.rosetta.utility.vector1_std_string) None

C++: protocols::cyclic_peptide::CreateAngleConstraint::set(class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<std::string, class std::allocator<std::string > >) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator) pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator

C++: protocols::cyclic_peptide::CreateAngleConstraintCreator::operator=(const class protocols::cyclic_peptide::CreateAngleConstraintCreator &) –> class protocols::cyclic_peptide::CreateAngleConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateAngleConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator) str

C++: protocols::cyclic_peptide::CreateAngleConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateAngleConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::CreateDistanceConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint) pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint

C++: protocols::cyclic_peptide::CreateDistanceConstraint::operator=(const class protocols::cyclic_peptide::CreateDistanceConstraint &) –> class protocols::cyclic_peptide::CreateDistanceConstraint &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateDistanceConstraint::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateDistanceConstraint::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint) str

C++: protocols::cyclic_peptide::CreateDistanceConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::CreateDistanceConstraint::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::CreateDistanceConstraint::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateDistanceConstraint::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint, res1: pyrosetta.rosetta.utility.vector1_unsigned_long, atom1: pyrosetta.rosetta.utility.vector1_std_string, res2: pyrosetta.rosetta.utility.vector1_unsigned_long, atom2: pyrosetta.rosetta.utility.vector1_std_string, cst_function: pyrosetta.rosetta.utility.vector1_std_string) None
Setter for options for this mover, so that it can be called from

outside of RosettaScripts.

C++: protocols::cyclic_peptide::CreateDistanceConstraint::set(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator) pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator

C++: protocols::cyclic_peptide::CreateDistanceConstraintCreator::operator=(const class protocols::cyclic_peptide::CreateDistanceConstraintCreator &) –> class protocols::cyclic_peptide::CreateDistanceConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateDistanceConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator) str

C++: protocols::cyclic_peptide::CreateDistanceConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateDistanceConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint

Bases: pyrosetta.rosetta.protocols.moves.Mover

ambiguous(*args, **kwargs)

Overloaded function.

  1. ambiguous(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint, setting: bool) -> None

C++: protocols::cyclic_peptide::CreateTorsionConstraint::ambiguous(bool) –> void

  1. ambiguous(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint) -> bool

C++: protocols::cyclic_peptide::CreateTorsionConstraint::ambiguous() const –> bool

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::CreateTorsionConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint) pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint

C++: protocols::cyclic_peptide::CreateTorsionConstraint::operator=(const class protocols::cyclic_peptide::CreateTorsionConstraint &) –> class protocols::cyclic_peptide::CreateTorsionConstraint &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateTorsionConstraint::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateTorsionConstraint::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint) str

C++: protocols::cyclic_peptide::CreateTorsionConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::CreateTorsionConstraint::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::CreateTorsionConstraint::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateTorsionConstraint::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint, res1: pyrosetta.rosetta.utility.vector1_unsigned_long, atom1: pyrosetta.rosetta.utility.vector1_std_string, res2: pyrosetta.rosetta.utility.vector1_unsigned_long, atom2: pyrosetta.rosetta.utility.vector1_std_string, res3: pyrosetta.rosetta.utility.vector1_unsigned_long, atom3: pyrosetta.rosetta.utility.vector1_std_string, res4: pyrosetta.rosetta.utility.vector1_unsigned_long, atom4: pyrosetta.rosetta.utility.vector1_std_string, cst_func: pyrosetta.rosetta.utility.vector1_std_string) None

Set function: allows the mover to be set up outside of a RosettaScripts context.

C++: protocols::cyclic_peptide::CreateTorsionConstraint::set(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator) pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator

C++: protocols::cyclic_peptide::CreateTorsionConstraintCreator::operator=(const class protocols::cyclic_peptide::CreateTorsionConstraintCreator &) –> class protocols::cyclic_peptide::CreateTorsionConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CreateTorsionConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator) str

C++: protocols::cyclic_peptide::CreateTorsionConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CreateTorsionConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker

Bases: pybind11_builtins.pybind11_object

Enumeration of allowed crosslinkers.

Members:

no_crosslinker

TBMB

One_Four_BBMB

TMA

tetrahedral_metal

octahedral_metal

trigonal_planar_metal

trigonal_pyramidal_metal

square_planar_metal

square_pyramidal_metal

unknown_crosslinker

end_of_crosslinker_list

One_Four_BBMB = <CrossLinker.One_Four_BBMB: 3>
TBMB = <CrossLinker.TBMB: 2>
TMA = <CrossLinker.TMA: 4>
end_of_crosslinker_list = <CrossLinker.unknown_crosslinker: 11>
property name
no_crosslinker = <CrossLinker.no_crosslinker: 1>
octahedral_metal = <CrossLinker.octahedral_metal: 6>
square_planar_metal = <CrossLinker.square_planar_metal: 9>
square_pyramidal_metal = <CrossLinker.square_pyramidal_metal: 10>
tetrahedral_metal = <CrossLinker.tetrahedral_metal: 5>
trigonal_planar_metal = <CrossLinker.trigonal_planar_metal: 7>
trigonal_pyramidal_metal = <CrossLinker.trigonal_pyramidal_metal: 8>
unknown_crosslinker = <CrossLinker.unknown_crosslinker: 11>
class pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure.

add_linker(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) bool

Get whether we’re adding the linker.

C++: protocols::cyclic_peptide::CrosslinkerMover::add_linker() const –> bool

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::cyclic_peptide::CrosslinkerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, : pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover

C++: protocols::cyclic_peptide::CrosslinkerMover::operator=(const class protocols::cyclic_peptide::CrosslinkerMover &) –> class protocols::cyclic_peptide::CrosslinkerMover &

static class_name() str

Show the contents of the Mover

C++: protocols::cyclic_peptide::CrosslinkerMover::class_name() –> std::string

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::cyclic_peptide::CrosslinkerMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

constrain_linker(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) bool

Get whether we’re adding the linker constraints.

C++: protocols::cyclic_peptide::CrosslinkerMover::constrain_linker() const –> bool

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

do_final_fastrelax(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) bool

Get whether we’re doing a final FastRelax on the whole structure.

C++: protocols::cyclic_peptide::CrosslinkerMover::do_final_fastrelax() const –> bool

final_frlx_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) int

Get the number of rounds of FastRelax to apply at the end.

C++: protocols::cyclic_peptide::CrosslinkerMover::final_frlx_rounds() const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::cyclic_peptide::CrosslinkerMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

static get_crosslinker_enum(name: str) pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker

Given a CrossLinker name, get its enum.

C++: protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_enum(const std::string &) –> enum protocols::cyclic_peptide::CrossLinker

static get_crosslinker_name(crosslinker: pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker) str

Given a CrossLinker enum, get its name.

C++: protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_name(const enum protocols::cyclic_peptide::CrossLinker) –> std::string

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) str

Get the name of the Mover

C++: protocols::cyclic_peptide::CrosslinkerMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

linker_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) str

Get the linker name.

C++: protocols::cyclic_peptide::CrosslinkerMover::linker_name() const –> std::string

metal_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) str

For metal-mediated crosslinkers, what metal mediates the crosslink?

C++: protocols::cyclic_peptide::CrosslinkerMover::metal_type() const –> const std::string &

static mover_name() str

Returns the name of this Mover.

C++: protocols::cyclic_peptide::CrosslinkerMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

pack_and_minimize_linker_and_sidechains(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) bool

Get whether we’re packing and minimizing the linker and the side-chains to which it is connected.

C++: protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse XML tag (to use this Mover in Rosetta Scripts).

C++: protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

Provide information on what options are available in XML tag.

C++: protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector that this mover uses.

C++: protocols::cyclic_peptide::CrosslinkerMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) pyrosetta.rosetta.core.scoring.ScoreFunction

Get the scorefunction to use for packing and minimization.

C++: protocols::cyclic_peptide::CrosslinkerMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_behaviour(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, add_linker: bool, constrain_linker: bool, pack_and_minimize_linker_and_sidechains: bool, do_final_fastrelax: bool) None

Set the behaviour of this mover.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_behaviour(const bool, const bool, const bool, const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_filter_behaviour(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, filter_by_sidechain_distance: bool, filter_by_constraints_energy: bool, filter_by_total_score: bool, filter_by_total_score_cutoff_energy: float, sidechain_distance_filter_multiplier: float, constraints_energy_filter_multiplier: float) None

Set the filtering behaviour of this mover.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_filter_behaviour(const bool, const bool, const bool, const double &, const double &, const double &) –> void

set_final_frlx_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, rounds_in: int) None

Set the number of rounds of FastRelax to apply at the end.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_final_frlx_rounds(const unsigned long) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_linker_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, name_in: str) None

Set the linker name.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_linker_name(const std::string &) –> void

set_metal_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, metal_in: str) None

For metal-mediated crosslinkers, set what metal mediates the crosslink.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_metal_type(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector to use.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set the scorefunction to use for packing and minimization.

Cloned at apply time. (That is, the scorefunction is shared until apply time).

C++: protocols::cyclic_peptide::CrosslinkerMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_sidechain_frlx_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, rounds_in: int) None
Set the number of rounds of FastRelax to apply when minimizing the linker and the

side-chains that connect to it.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_sidechain_frlx_rounds(const unsigned long) –> void

set_symm_count(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, count_in: int) None

Set the symmetry copy count.

For example, symm_type_=’C’ and symm_count_=3 would specify C3 symmetry. A value of 1 means asymmetry. 1 by default.

Deliberately a signed int.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_symm_count(const int) –> void

set_symm_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, type_in: str) None

Set the symmety type.

‘C’ for cylic, ‘S’ for mirror cyclic, ‘D’ for dihedral, ‘A’ for asymmetric.

‘A’ (asymmetric) by default.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_symm_type(const char) –> void

set_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, symmetry_in: str) None

Parse a string with a symmetry type (e.g. “C3”) and set the symmetry accordingly.

C++: protocols::cyclic_peptide::CrosslinkerMover::set_symmetry(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover, output: pyrosetta.rosetta.std.ostream) -> None

Show the contents of the Mover

C++: protocols::cyclic_peptide::CrosslinkerMover::show(std::ostream &) const –> void

sidechain_frlx_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) int
Get the number of rounds of FastRelax to apply when minimizing the linker and the

side-chains that connect to it.

C++: protocols::cyclic_peptide::CrosslinkerMover::sidechain_frlx_rounds() const –> unsigned long

symm_count(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) int

Get the symmetry copy count.

For example, symm_type_=’C’ and symm_count_=3 would specify C3 symmetry. A value of 1 means asymmetry. 1 by default.

C++: protocols::cyclic_peptide::CrosslinkerMover::symm_count() const –> unsigned long

symm_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover) str

Get the symmetry type.

‘C’ for cylic, ‘S’ for mirror cyclic, ‘D’ for dihedral, ‘A’ for asymmetric.

‘A’ (asymmetric) by default.

C++: protocols::cyclic_peptide::CrosslinkerMover::symm_type() const –> char

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator) pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator

C++: protocols::cyclic_peptide::CrosslinkerMoverCreator::operator=(const class protocols::cyclic_peptide::CrosslinkerMoverCreator &) –> class protocols::cyclic_peptide::CrosslinkerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::CrosslinkerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator) str

C++: protocols::cyclic_peptide::CrosslinkerMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CrosslinkerMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

A filter that examines a cyclic peptide’s structure and returns TRUE if and only if it has a desired backbone symmetry.

angle_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) float
The cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to

be considered to have the “same” value for that mainchain degree of freedom.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::angle_threshold() const –> const double &

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

returns true if the structure passes the filter, false otherwise

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

static class_name() str

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::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.cyclic_peptide.CycpepSymmetryFilter) pyrosetta.rosetta.protocols.filters.Filter

required in the context of the parser/scripting scheme

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

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) pyrosetta.rosetta.protocols.filters.Filter

required in the context of the parser/scripting scheme

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::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

mirror_symm(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) bool
Gets whether we’re considering mirror (e.g. s4, s6) or non-mirror

(e.g. c4, c6) symmetry.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::mirror_symm() const –> bool

name(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) str

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

allows printing data to a stream

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

required for reporting score values

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::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

selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Gets the residue selector.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_angle_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, setting: float) None
Set the cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to

be considered to have the “same” value for that mainchain degree of freedom.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::set_angle_threshold(const double &) –> void

set_mirror_symm(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, symm_in: bool) None
Sets whether we’re considering mirror (e.g. s4, s6) or non-mirror

(e.g. c4, c6) symmetry.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::set_mirror_symm(const bool) –> void

set_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Sets the residue selector.

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_symm_repeats(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter, repeats_in: int) None
Sets the repeats in the symmetry that we’re looking for

(e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.).

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::set_symm_repeats(const unsigned long) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

symm_repeats(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter) int
Gets the repeats in the symmetry that we’re looking for

(e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.).

C++: protocols::cyclic_peptide::CycpepSymmetryFilter::symm_repeats() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator) pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator

C++: protocols::cyclic_peptide::CycpepSymmetryFilterCreator::operator=(const class protocols::cyclic_peptide::CycpepSymmetryFilterCreator &) –> class protocols::cyclic_peptide::CycpepSymmetryFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::cyclic_peptide::CycpepSymmetryFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator) str

C++: protocols::cyclic_peptide::CycpepSymmetryFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::CycpepSymmetryFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::DeclareBond::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, : pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond) pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond

C++: protocols::cyclic_peptide::DeclareBond::operator=(const class protocols::cyclic_peptide::DeclareBond &) –> class protocols::cyclic_peptide::DeclareBond &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::DeclareBond::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::DeclareBond::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond) str

C++: protocols::cyclic_peptide::DeclareBond::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::DeclareBond::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::DeclareBond::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::DeclareBond::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set(*args, **kwargs)

Overloaded function.

  1. set(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool) -> None

  2. set(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool) -> None

  3. set(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int) -> None

  4. set(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int, kic_res2: int) -> None

  5. set(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, res1: int, atom1: str, res2: int, atom2: str, add_termini: bool, run_kic: bool, kic_res1: int, kic_res2: int, rebuild_fold_tree: bool) -> None

C++: protocols::cyclic_peptide::DeclareBond::set(const unsigned long, const std::string &, const unsigned long, const std::string &, const bool, const bool, const unsigned long, const unsigned long, const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_selector_for_res1(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::cyclic_peptide::DeclareBond::set_selector_for_res1(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_selector_for_res2(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBond, selector2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::cyclic_peptide::DeclareBond::set_selector_for_res2(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator) pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator

C++: protocols::cyclic_peptide::DeclareBondCreator::operator=(const class protocols::cyclic_peptide::DeclareBondCreator &) –> class protocols::cyclic_peptide::DeclareBondCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::DeclareBondCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator) str

C++: protocols::cyclic_peptide::DeclareBondCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.DeclareBondCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::DeclareBondCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::FlipChiralityMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover) pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover

C++: protocols::cyclic_peptide::FlipChiralityMover::operator=(const class protocols::cyclic_peptide::FlipChiralityMover &) –> class protocols::cyclic_peptide::FlipChiralityMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::FlipChiralityMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::FlipChiralityMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_center(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::cyclic_peptide::FlipChiralityMover::get_center(class utility::vector1<bool, class std::allocator<bool> >, const class core::pose::Pose &) –> const class numeric::xyzVector<double> &

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover) str

C++: protocols::cyclic_peptide::FlipChiralityMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_normal(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::cyclic_peptide::FlipChiralityMover::get_normal() –> const class numeric::xyzVector<double> &

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::FlipChiralityMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::FlipChiralityMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::FlipChiralityMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_center(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : float, : float, : float) None

C++: protocols::cyclic_peptide::FlipChiralityMover::set_center(const double &, const double &, const double &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_normal(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, : float, : float, : float) None

C++: protocols::cyclic_peptide::FlipChiralityMover::set_normal(const double &, const double &, const double &) –> void

set_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::cyclic_peptide::FlipChiralityMover::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator) pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator

C++: protocols::cyclic_peptide::FlipChiralityMoverCreator::operator=(const class protocols::cyclic_peptide::FlipChiralityMoverCreator &) –> class protocols::cyclic_peptide::FlipChiralityMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::FlipChiralityMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator) str

C++: protocols::cyclic_peptide::FlipChiralityMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::FlipChiralityMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta’s pairwise-decomposible scorefunction, which can’t penalize excessive hydrogen bonds.

acceptor_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector for acceptor residues.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

Returns true if the structure passes the filter, false otherwise.

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

static class_name() str

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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.cyclic_peptide.OversaturatedHbondAcceptorFilter) pyrosetta.rosetta.protocols.filters.Filter

Required in the context of the parser/scripting scheme.

Make a copy of this object and return an owning pointer to the copy.

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

consider_mainchain_only(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) bool
Get whether we only consider mainchain hydrogen bond

donors and acceptors.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::consider_mainchain_only() const –> bool

donor_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector for donor residues.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) pyrosetta.rosetta.protocols.filters.Filter

Required in the context of the parser/scripting scheme.

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

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) str

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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

hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) float
Get the threshold for considering something to be a

hydrogen bond.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::hbond_energy_cutoff() const –> const double &

max_allowed_oversaturated(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) int
Get the maximum allowed number of instances of an oversaturated

hydrogen bond acceptor.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated() const –> unsigned long

name(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) str

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse XML tag (to use this Mover in RosettaScripts).

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

Allows printing a summary of this filter to a stream.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

Required for reporting score values.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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

scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter) pyrosetta.rosetta.core.scoring.ScoreFunction

Get the scorefunction.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_acceptor_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, acceptor_selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector for acceptor residues.

Clones the input.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_acceptor_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_consider_mainchain_only(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, input_setting: bool) None
Set whether we only consider mainchain hydrogen bond

donors and acceptors.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_consider_mainchain_only(const bool) –> void

set_donor_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, donor_selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector for donor residues.

Clones the input.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_donor_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, input_value: float) None
Set the threshold for considering something to be a

hydrogen bond.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_hbond_energy_cutoff(const double &) –> void

set_max_allowed_oversaturated(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, max_allowed: int) None
Set the maximum allowed number of instances of an oversaturated

hydrogen bond acceptor.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_max_allowed_oversaturated(const unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set the scorefunction.

Clones the input.

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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 std::string &) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator) pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::operator=(const class protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator &) –> class protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator) str

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode

Bases: pybind11_builtins.pybind11_object

Members:

PSM_append

PSM_prepend

PSM_insert

PSM_append = <PSM_StubMode.PSM_append: 0>
PSM_insert = <PSM_StubMode.PSM_insert: 2>
PSM_prepend = <PSM_StubMode.PSM_prepend: 1>
property name
class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover

C++: protocols::cyclic_peptide::PeptideCyclizeMover::operator=(const class protocols::cyclic_peptide::PeptideCyclizeMover &) –> class protocols::cyclic_peptide::PeptideCyclizeMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideCyclizeMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideCyclizeMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover) str

C++: protocols::cyclic_peptide::PeptideCyclizeMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::PeptideCyclizeMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_angle(*args, **kwargs)

Overloaded function.

  1. set_angle(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : int, : str, : int, : str, : int, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_angle(unsigned long, std::string, unsigned long, std::string, unsigned long, std::string, std::string) –> void

  1. set_angle(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_angle(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, std::string) –> void

set_bond(*args, **kwargs)

Overloaded function.

  1. set_bond(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : int, : str, : int, : str, : bool, : bool) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_bond(unsigned long, std::string, unsigned long, std::string, bool, bool) –> void

  1. set_bond(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : bool, : bool) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_bond(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, bool, bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_default(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover) None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_default() –> void

set_distance(*args, **kwargs)

Overloaded function.

  1. set_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : int, : str, : int, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_distance(unsigned long, std::string, unsigned long, std::string, std::string) –> void

  1. set_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_distance(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, std::string) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_torsion(*args, **kwargs)

Overloaded function.

  1. set_torsion(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : int, : str, : int, : str, : int, : str, : int, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_torsion(unsigned long, std::string, unsigned long, std::string, unsigned long, std::string, unsigned long, std::string, std::string) –> void

  1. set_torsion(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : str, : str) -> None

C++: protocols::cyclic_peptide::PeptideCyclizeMover::set_torsion(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, std::string, std::string) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator

C++: protocols::cyclic_peptide::PeptideCyclizeMoverCreator::operator=(const class protocols::cyclic_peptide::PeptideCyclizeMoverCreator &) –> class protocols::cyclic_peptide::PeptideCyclizeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideCyclizeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator) str

C++: protocols::cyclic_peptide::PeptideCyclizeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideCyclizeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

A filter that thinly wraps the PeptideInternalHbondsMetric.

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool
returns true if the structure has internal hbonds equal to or greater than

the cutoff, false otherwise.

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

backbone_backbone(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) bool

Get whether we’re counting backbone-backbone hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::backbone_backbone() const –> bool

backbone_sidechain(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) bool

Get whether we’re counting backbone-sidechain hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::backbone_sidechain() const –> bool

static class_name() str

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::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.cyclic_peptide.PeptideInternalHbondsFilter) pyrosetta.rosetta.protocols.filters.Filter

Make a copy of this filter and return an owning pointer to the copy.

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

exclusion_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) int
Get the number of residues apart in terms of covalent connectivity that two residues have to be in order for their

hydrogen bonds to be counted.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::exclusion_distance() const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) pyrosetta.rosetta.protocols.filters.Filter

Required in the context of the parser/scripting scheme.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::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

hbond_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) int

Get the threshold number of internal hydrogen bonds, below which the filter fails.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_cutoff() const –> unsigned long

hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) float

Get the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_energy_cutoff() const –> double

hbond_metric(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) protocols::cyclic_peptide::PeptideInternalHbondsMetric

Access the internal PeptideInternalHbondsMetric used by this filter (non-const access).

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_metric() –> class protocols::cyclic_peptide::PeptideInternalHbondsMetric &

name(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) str

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse XML tag (to use this Filter in Rosetta Scripts).

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

Describe the XML interface in a machine-readable way.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

allows printing data to a stream.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

Required for reporting score values.

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

residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the scorefunction for selecting the peptide. If this nullptr, whole pose is counted.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) pyrosetta.rosetta.core.scoring.ScoreFunction
Get the scorefunction for identifying hydrogen bonds. Note that if this is nullptr, the

default scorefunction is used.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_exclusion_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, setting: int) None
Set the number of residues apart in terms of covalent connectivity that two residues have to be in order for their

hydrogen bonds to be counted.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_exclusion_distance(const unsigned long) –> void

set_hbond_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, setting: int) None

Set the threshold number of internal hydrogen bonds, below which the filter fails.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_hbond_cutoff(const unsigned long) –> void

set_hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, setting: float) None

Set the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_hbond_energy_cutoff(const double) –> void

set_hbond_types(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, backbone_backbone_setting: bool, backbone_sidechain_setting: bool, sidechain_sidechain_setting: bool) None

Set whether we’re counting backbone-backbone, backbone-sidechain, and sidechain-sidechain hydrogen bonds.

Throws if all are set to false. Defaults to only backbone-backbone being true.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_hbond_types(const bool, const bool, const bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, res_selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the scorefunction for selecting the peptide. If this is not called, whole pose is counted.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set the scorefunction for identifying hydrogen bonds. If this is not called, the default scorefunction is used.

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_scorefxn(const 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 std::string &) –> void

sidechain_sidechain(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter) bool

Get whether we’re counting sidechain-sidechain hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilter::sidechain_sidechain() const –> bool

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator::operator=(const class protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator &) –> class protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator) str

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A simple metric for measuring the backbone hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds.

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None

  3. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None

  4. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None

  5. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose as a score.

labeled as out_label.

Score is added to the SimpleMetricData cache

Data is output into the final score file, but can be accessed if needed through the cache.

C++: core::simple_metrics::RealMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::operator=(const class protocols::cyclic_peptide::PeptideInternalHbondsMetric &) –> class protocols::cyclic_peptide::PeptideInternalHbondsMetric &

backbone_backbone(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) bool

Get whether we’re counting backbone-backbone hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_backbone() const –> bool

backbone_sidechain(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) bool

Get whether we’re counting backbone-sidechain hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_sidechain() const –> bool

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> float

  2. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> float

  3. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> float

  4. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> float

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

C++: core::simple_metrics::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the metric.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Duplicate this object, and return a smart pointer to the copy.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

configure_from_filter_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None
Configure this metric from the tag passed to the companion filter (the

PeptideInternalHbondsFilter).

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::configure_from_filter_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

exclusion_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) int
Get the number of residues apart in terms of covalent connectivity that two residues have to be in order for their

hydrogen bonds to be counted.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::exclusion_distance() const –> unsigned long

get_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Output data name will be prefix+custom_type+type+suffix

C++: core::simple_metrics::SimpleMetric::get_custom_type() const –> std::string

get_final_sm_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

C++: core::simple_metrics::SimpleMetric::get_final_sm_type() const –> std::string

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

C++: core::simple_metrics::RealMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) float

Get the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::hbond_energy_cutoff() const –> double

metric(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) str

Return text indicating what we’re measuring.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) str

Name of the class

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_shared_xml_schema_elements(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

Provide descriptions of XML interface elements shared between this metric and the companion filter.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

Provide a description of the XML interface.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, outstream: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

allows printing data to a stream.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::report(std::ostream &, const class core::pose::Pose &) const –> void

residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the scorefunction for selecting the peptide. If this nullptr, whole pose is counted.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) pyrosetta.rosetta.core.scoring.ScoreFunction
Get the scorefunction for identifying hydrogen bonds. Note that if this is nullptr, the

default scorefunction is used.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_exclusion_distance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, setting: int) None
Set the number of residues apart in terms of covalent connectivity that two residues have to be in order for their

hydrogen bonds to be counted.

Defaults to 1.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_exclusion_distance(const unsigned long) –> void

set_hbond_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, setting: float) None

Set the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_hbond_energy_cutoff(const double) –> void

set_hbond_types(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, backbone_backbone_setting: bool, backbone_sidechain_setting: bool, sidechain_sidechain_setting: bool) None

Set whether we’re counting backbone-backbone, backbone-sidechain, and sidechain-sidechain hydrogen bonds.

Throws if all are set to false. Defaults to only backbone-backbone being true.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_hbond_types(const bool, const bool, const bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, res_selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the scorefunction for selecting the peptide. If this is not called, whole pose is counted.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set the scorefunction for identifying hydrogen bonds. If this is not called, the default scorefunction is used.

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_scorefxn(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void

sidechain_sidechain(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric) bool

Get whether we’re counting sidechain-sidechain hbonds:

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetric::sidechain_sidechain() const –> bool

simple_metric_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

C++: core::simple_metrics::SimpleMetric::simple_metric_type() const –> std::string

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::operator=(const class protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator &) –> class protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator) str

Return a string that will be used to instantiate the particular SimpleMetric

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_residue(*args, **kwargs)

Overloaded function.

  1. add_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, stubmode: str, resname: str, position: int, jumpmode: bool, connecting_atom: str, repeat: int, anchor_rsd: int, anchor_rsd_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, anchor_atom: str) -> None

Adds a residue to the list of residues to be appended, prepended, or inserted.

Calls add_residue() override that uses PSM_StubMode.

C++: protocols::cyclic_peptide::PeptideStubMover::add_residue(const std::string &, const std::string &, const unsigned long, const bool, const std::string &, const unsigned long, const unsigned long, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, const std::string &) –> void

  1. add_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, stubmode: pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode, resname: str, position: int, jumpmode: bool, connecting_atom: str, repeat: int, anchor_rsd: int, anchor_rsd_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, anchor_atom: str) -> None

Adds a residue to the list of residues to be appended, prepended, or inserted.

This version uses enums.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::cyclic_peptide::PeptideStubMover::add_residue(const enum protocols::cyclic_peptide::PSM_StubMode, const std::string &, const unsigned long, const bool, const std::string &, const unsigned long, const unsigned long, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::PeptideStubMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover

C++: protocols::cyclic_peptide::PeptideStubMover::operator=(const class protocols::cyclic_peptide::PeptideStubMover &) –> class protocols::cyclic_peptide::PeptideStubMover &

static assign_chain_ids(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::cyclic_peptide::PeptideStubMover::assign_chain_ids(class core::pose::Pose &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideStubMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

static default_label() str

C++: protocols::cyclic_peptide::PeptideStubMover::default_label() –> std::string

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideStubMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) str

C++: protocols::cyclic_peptide::PeptideStubMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) None

C++: protocols::cyclic_peptide::PeptideStubMover::init() –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::cyclic_peptide::PeptideStubMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::PeptideStubMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideStubMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_mover_data(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover) None

Reset mover data

C++: protocols::cyclic_peptide::PeptideStubMover::reset_mover_data() –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_reset_mode(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, reset_mode: bool) None

Sets whether the pose gets reset (i.e. all residues deleted) or not.

C++: protocols::cyclic_peptide::PeptideStubMover::set_reset_mode(bool) –> void

set_residue_label(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, label: str) None

add label to residues that are created with this mover

Jack Maguire, jackmaguire1444.com

C++: protocols::cyclic_peptide::PeptideStubMover::set_residue_label(const std::string &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_update_pdb_numbering_mode(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover, mode: bool) None

Sets whether pdb numbering gets updated or not.

C++: protocols::cyclic_peptide::PeptideStubMover::set_update_pdb_numbering_mode(bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator) pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator

C++: protocols::cyclic_peptide::PeptideStubMoverCreator::operator=(const class protocols::cyclic_peptide::PeptideStubMoverCreator &) –> class protocols::cyclic_peptide::PeptideStubMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::PeptideStubMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator) str

C++: protocols::cyclic_peptide::PeptideStubMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::PeptideStubMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type.

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: protocols::cyclic_peptide::RamaMutationSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, : pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector

C++: protocols::cyclic_peptide::RamaMutationSelector::operator=(const class protocols::cyclic_peptide::RamaMutationSelector &) –> class protocols::cyclic_peptide::RamaMutationSelector &

static class_name() str

Get the mover class name.

C++: protocols::cyclic_peptide::RamaMutationSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: protocols::cyclic_peptide::RamaMutationSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) str

Get the mover class name.

C++: protocols::cyclic_peptide::RamaMutationSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: protocols::cyclic_peptide::RamaMutationSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

Provide XSD information, enabling mechanical validation of input XML.

C++: protocols::cyclic_peptide::RamaMutationSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rama_prepro_multiplier(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) float

Get the weight multiplier of the rama_prepro term.

Defaults to 0.45 to match beta_nov15.

C++: protocols::cyclic_peptide::RamaMutationSelector::rama_prepro_multiplier() const –> const double &

score_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) float

Get the score threshold.

Positions which, when mutated to the target type, have a rama_prepro score above this threshold are not selected.

C++: protocols::cyclic_peptide::RamaMutationSelector::score_threshold() const –> const double &

set_rama_prepro_multiplier(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, multiplier_in: float) None

Set the weight multiplier of the rama_prepro term.

Defaults to 0.45 to match beta_nov15.

C++: protocols::cyclic_peptide::RamaMutationSelector::set_rama_prepro_multiplier(const double &) –> void

set_score_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, threshold_in: float) None

Set the score threshold.

Positions which, when mutated to the target type, have a rama_prepro score above this threshold are not selected.

C++: protocols::cyclic_peptide::RamaMutationSelector::set_score_threshold(const double &) –> void

set_target_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector, type_in: str) None
Set the residue type (full name) to which we are considering

mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position.

C++: protocols::cyclic_peptide::RamaMutationSelector::set_target_type(const std::string &) –> void

target_type(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector) str
Get the residue type (full name) to which we are considering

mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position.

C++: protocols::cyclic_peptide::RamaMutationSelector::target_type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator) pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator

C++: protocols::cyclic_peptide::RamaMutationSelectorCreator::operator=(const class protocols::cyclic_peptide::RamaMutationSelectorCreator &) –> class protocols::cyclic_peptide::RamaMutationSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::cyclic_peptide::RamaMutationSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator) str

C++: protocols::cyclic_peptide::RamaMutationSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::RamaMutationSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign

Bases: pyrosetta.rosetta.protocols.moves.Mover

Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover.

angle_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) float

Get the angle threshold for counting poses as symmetric.

Two dihedral values from different residues must fall within this cutoff, in degrees, for them to be considered the “same”. Default 10 degrees.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::angle_threshold() const –> const double &

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, : pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::operator=(const class protocols::cyclic_peptide::SymmetricCycpepAlign &) –> class protocols::cyclic_peptide::SymmetricCycpepAlign &

auto_detect_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) bool

Get whether we’re auto-detecting symmetry.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::auto_detect_symmetry() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) str

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

invert(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) bool

Are we aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true)?

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::invert() const –> bool

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

last_symmetry_mirror(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) bool

Report whether the symmetry of the last auto-detected peptide was mirror symmetry.

Returns false always if auto-detection is not enabled.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_mirror() const –> bool

last_symmetry_repeats(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) int

Report the symmetry of the last auto-detected peptide.

Returns 0 if auto-detection is not enabled.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_repeats() const –> unsigned long

mirror_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) bool

Get whether we’re using mirror symmetry (e.g. s2 symmetry vs. c2 symmetry).

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::mirror_symmetry() const –> bool

static mover_name() str

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

repeat_to_preserve(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) int

If trim_to_single_repeat_ is true, this is the symmetry repeat to preserve.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::repeat_to_preserve() const –> unsigned long

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_angle_threshold(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, setting: float) None

Set the angle threshold for counting poses as symmetric.

Two dihedral values from different residues must fall within this cutoff, in degrees, for them to be considered the “same”. Default 10 degrees.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::set_angle_threshold(const double &) –> void

set_auto_detect_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, setting: bool) None

Set whether we’re auto-detecting symmetry.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::set_auto_detect_symmetry(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_invert(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, setting: bool) None

Set whether we’re aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true).

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::set_invert(const bool) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, repeats_in: int, mirror_in: bool) None
Set the number of symmetry repeats and whether we’re using mirror symmetry. For example, for c4

symmetry, inputs are “4”, “false”. For s4, they’d be “4”, “true”.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::set_symmetry(const unsigned long, const bool) –> void

set_trim_info(*args, **kwargs)

Overloaded function.

  1. set_trim_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, do_trim: bool) -> None

  2. set_trim_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, do_trim: bool, repeat_to_preserve: int) -> None

Set whether we’re going to delete all geometry that isn’t the protein backbone of a single

symmetry repeat, and which repeat to preserve.

If set to true, the peptide will be trimmed down to a single repeat. False by default (no trimming).

If do_trim is set to true, this is the repeat that should be preserved. 1 by default.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::set_trim_info(const bool, const unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) -> None

  2. show(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::show(std::ostream &) const –> void

symmetry_repeats(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) int
Get the number of symmetry repeats. For example, for c4 or s4 symmetry,

this would be “4”. Defaults to “2”.

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::symmetry_repeats() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

trim_to_single_repeat(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign) bool
Get whether all geometry that is not the protein backbone of a single symmetry repeat will be

deleted. (This includes any crosslinkers.)

C++: protocols::cyclic_peptide::SymmetricCycpepAlign::trim_to_single_repeat() const –> bool

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator) pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator

C++: protocols::cyclic_peptide::SymmetricCycpepAlignCreator::operator=(const class protocols::cyclic_peptide::SymmetricCycpepAlignCreator &) –> class protocols::cyclic_peptide::SymmetricCycpepAlignCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::SymmetricCycpepAlignCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator) str

C++: protocols::cyclic_peptide::SymmetricCycpepAlignCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::SymmetricCycpepAlignCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::cyclic_peptide::TryDisulfPermutations::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, : pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations

C++: protocols::cyclic_peptide::TryDisulfPermutations::operator=(const class protocols::cyclic_peptide::TryDisulfPermutations &) –> class protocols::cyclic_peptide::TryDisulfPermutations &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::TryDisulfPermutations::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

consider_already_bonded(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) bool

Will this mover consider alternative disulfides involving residues currently in a disulfide bond?

C++: protocols::cyclic_peptide::TryDisulfPermutations::consider_already_bonded() const –> bool

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::TryDisulfPermutations::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) str

C++: protocols::cyclic_peptide::TryDisulfPermutations::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mintolerance(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) float

Get the minimizer tolerance.

C++: protocols::cyclic_peptide::TryDisulfPermutations::mintolerance() const –> const double &

mintype(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations) str

Get the minmization flavour.

C++: protocols::cyclic_peptide::TryDisulfPermutations::mintype() const –> const std::string &

static mover_name() str

C++: protocols::cyclic_peptide::TryDisulfPermutations::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::cyclic_peptide::TryDisulfPermutations::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::TryDisulfPermutations::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_consider_already_bonded(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, setting: bool) None

Set whether this mover will consider alternative disulfides involving residues currently in a disulfide bond.

C++: protocols::cyclic_peptide::TryDisulfPermutations::set_consider_already_bonded(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mintolerance(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, val: float) None

Set the minimizer tolerance.

C++: protocols::cyclic_peptide::TryDisulfPermutations::set_mintolerance(const double &) –> void

set_mintype(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, type: str) None

Set the minimization flavour.

C++: protocols::cyclic_peptide::TryDisulfPermutations::set_mintype(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_selector(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set the residue selector.

CLONES the input.

C++: protocols::cyclic_peptide::TryDisulfPermutations::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator, : pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator) pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator

C++: protocols::cyclic_peptide::TryDisulfPermutationsCreator::operator=(const class protocols::cyclic_peptide::TryDisulfPermutationsCreator &) –> class protocols::cyclic_peptide::TryDisulfPermutationsCreator &

create_mover(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::cyclic_peptide::TryDisulfPermutationsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator) str

C++: protocols::cyclic_peptide::TryDisulfPermutationsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::cyclic_peptide::TryDisulfPermutationsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void