environment

• claims

Bindings for protocols::environment namespace

class pyrosetta.rosetta.protocols.environment.AutoCutData

Bases: WriteableCacheableData

assign(self: pyrosetta.rosetta.protocols.environment.AutoCutData, : pyrosetta.rosetta.protocols.environment.AutoCutData) → pyrosetta.rosetta.protocols.environment.AutoCutData

C++: protocols::environment::AutoCutData::operator=(const class protocols::environment::AutoCutData &) –> class protocols::environment::AutoCutData &

clone(self: pyrosetta.rosetta.protocols.environment.AutoCutData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::environment::AutoCutData::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

cuts(self: pyrosetta.rosetta.protocols.environment.AutoCutData) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::environment::AutoCutData::cuts() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

datatype(self: pyrosetta.rosetta.protocols.environment.AutoCutData) → str

C++: protocols::environment::AutoCutData::datatype() const –> std::string

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

hash(self: pyrosetta.rosetta.protocols.environment.AutoCutData) → int

C++: protocols::environment::AutoCutData::hash() const –> const unsigned long &

shared_from_this(self: pyrosetta.rosetta.basic.datacache.WriteableCacheableData) → pyrosetta.rosetta.basic.datacache.WriteableCacheableData

C++: basic::datacache::WriteableCacheableData::shared_from_this() –> class std::shared_ptr<class basic::datacache::WriteableCacheableData>

write(self: pyrosetta.rosetta.protocols.environment.AutoCutData, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::environment::AutoCutData::write(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.environment.AutoCutDataCreator

Bases: WriteableCacheableDataCreator

assign(self: pyrosetta.rosetta.protocols.environment.AutoCutDataCreator, : pyrosetta.rosetta.protocols.environment.AutoCutDataCreator) → pyrosetta.rosetta.protocols.environment.AutoCutDataCreator

C++: protocols::environment::AutoCutDataCreator::operator=(const class protocols::environment::AutoCutDataCreator &) –> class protocols::environment::AutoCutDataCreator &

create_data(self: pyrosetta.rosetta.protocols.environment.AutoCutDataCreator, in: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.basic.datacache.WriteableCacheableData

C++: protocols::environment::AutoCutDataCreator::create_data(std::istream &) const –> class std::shared_ptr<class basic::datacache::WriteableCacheableData>

keyname(self: pyrosetta.rosetta.protocols.environment.AutoCutDataCreator) → str

C++: protocols::environment::AutoCutDataCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.environment.ClientMover

Bases: Mover

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

Main Method

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

assign(self: pyrosetta.rosetta.protocols.environment.ClientMover, : pyrosetta.rosetta.protocols.environment.ClientMover) → pyrosetta.rosetta.protocols.environment.ClientMover

C++: protocols::environment::ClientMover::operator=(const class protocols::environment::ClientMover &) –> class protocols::environment::ClientMover &

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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.moves.Mover) → str

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::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_t

non-const accessor

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

initialize(self: pyrosetta.rosetta.protocols.environment.ClientMover, conf: pyrosetta.rosetta.core.pose.Pose) → None

this method is called by the broking system in response to a

successful initialization claim by this mover. The passport will prevent any unauthorized changes.

C++: protocols::environment::ClientMover::initialize(class core::pose::Pose &) –> void

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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 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_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

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

Get the set ‘type’ string

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

yield_claims(self: pyrosetta.rosetta.protocols.environment.ClientMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.basic.datacache.WriteableCacheableMap) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t

Returns a list of claims for this mover.

The pose passed as an argument is used for reference informational

purposes only (for example, you want to know the sequence) or access the pose cache. Any changes to the conformation will get overwritten!

C++: protocols::environment::ClientMover::yield_claims(const class core::pose::Pose &, class std::shared_ptr<class basic::datacache::WriteableCacheableMap>) –> class std::list<class std::shared_ptr<class protocols::environment::claims::EnvClaim>, class std::allocator<class std::shared_ptr<class protocols::environment::claims::EnvClaim> > >

yield_submovers(self: pyrosetta.rosetta.protocols.environment.ClientMover, : pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t) → None

this method is used to make sure any movers contained in this

mover (that want to make claims) also get registered with the environment.

C++: protocols::environment::ClientMover::yield_submovers(class std::set<class std::shared_ptr<class protocols::environment::ClientMover>, struct std::less<class std::shared_ptr<class protocols::environment::ClientMover> >, class std::allocator<class std::shared_ptr<class protocols::environment::ClientMover> > > &) const –> void

class pyrosetta.rosetta.protocols.environment.CoMTrackerCM

Bases: ClientMover

apply(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::environment::CoMTrackerCM::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, : pyrosetta.rosetta.protocols.environment.CoMTrackerCM) → pyrosetta.rosetta.protocols.environment.CoMTrackerCM

C++: protocols::environment::CoMTrackerCM::operator=(const class protocols::environment::CoMTrackerCM &) –> class protocols::environment::CoMTrackerCM &

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.environment.CoMTrackerCM) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::environment::CoMTrackerCM::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.environment.CoMTrackerCM) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::environment::CoMTrackerCM::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.environment.CoMTrackerCM) → str

C++: protocols::environment::CoMTrackerCM::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_t

non-const accessor

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

initialize(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::environment::CoMTrackerCM::initialize(class core::pose::Pose &) –> 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::environment::CoMTrackerCM::mover_name() –> std::string

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM) -> str

C++: protocols::environment::CoMTrackerCM::name() const –> const std::string &

2. name(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, name: str) -> None

C++: protocols::environment::CoMTrackerCM::name(const std::string &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::environment::CoMTrackerCM::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::environment::CoMTrackerCM::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_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

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

Get the set ‘type’ string

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

yield_claims(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCM, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.basic.datacache.WriteableCacheableMap) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t

C++: protocols::environment::CoMTrackerCM::yield_claims(const class core::pose::Pose &, class std::shared_ptr<class basic::datacache::WriteableCacheableMap>) –> class std::list<class std::shared_ptr<class protocols::environment::claims::EnvClaim>, class std::allocator<class std::shared_ptr<class protocols::environment::claims::EnvClaim> > >

yield_submovers(self: pyrosetta.rosetta.protocols.environment.ClientMover, : pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t) → None

this method is used to make sure any movers contained in this

mover (that want to make claims) also get registered with the environment.

C++: protocols::environment::ClientMover::yield_submovers(class std::set<class std::shared_ptr<class protocols::environment::ClientMover>, struct std::less<class std::shared_ptr<class protocols::environment::ClientMover> >, class std::allocator<class std::shared_ptr<class protocols::environment::ClientMover> > > &) const –> void

class pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator, : pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator) → pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator

C++: protocols::environment::CoMTrackerCMCreator::operator=(const class protocols::environment::CoMTrackerCMCreator &) –> class protocols::environment::CoMTrackerCMCreator &

create_mover(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator) → str

C++: protocols::environment::CoMTrackerCMCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.environment.DofUnlock

Bases: pybind11_object

class pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport

Bases: EXCN_Env_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport, : pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport) → pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport

C++: protocols::environment::EXCN_Env_Passport::operator=(const class protocols::environment::EXCN_Env_Passport &) –> class protocols::environment::EXCN_Env_Passport &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

2. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception

Bases: EXCN_Env_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.environment.EXCN_Env_Exception, : pyrosetta.rosetta.core.environment.EXCN_Env_Exception) → pyrosetta.rosetta.core.environment.EXCN_Env_Exception

C++: core::environment::EXCN_Env_Exception::operator=(const class core::environment::EXCN_Env_Exception &) –> class core::environment::EXCN_Env_Exception &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::file() –> const std::string &

id(self: pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception) → pyrosetta.rosetta.core.id.DOF_ID

C++: protocols::environment::EXCN_Env_Security_Exception::id() const –> const class core::id::DOF_ID &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

2. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

passport(self: pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception) → pyrosetta.rosetta.core.environment.DofPassport

C++: protocols::environment::EXCN_Env_Security_Exception::passport() const –> class std::shared_ptr<const class core::environment::DofPassport>

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.environment.EnvClaimBroker

Bases: pybind11_object

class BrokerResult

Bases: pybind11_object

property ann

assign(self: pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult, : pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult) → pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult

C++: protocols::environment::EnvClaimBroker::BrokerResult::operator=(const struct protocols::environment::EnvClaimBroker::BrokerResult &) –> struct protocols::environment::EnvClaimBroker::BrokerResult &

property auto_cuts

property cached_data

property closer_ft

property new_vrts

property pose

result(self: pyrosetta.rosetta.protocols.environment.EnvClaimBroker) → protocols::environment::EnvClaimBroker::BrokerResult

C++: protocols::environment::EnvClaimBroker::result() const –> const struct protocols::environment::EnvClaimBroker::BrokerResult &

class pyrosetta.rosetta.protocols.environment.EnvMover

Bases: Mover

add_apply_mover(self: pyrosetta.rosetta.protocols.environment.EnvMover, : pyrosetta.rosetta.protocols.moves.Mover) → None

C++: protocols::environment::EnvMover::add_apply_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

add_registered_mover(self: pyrosetta.rosetta.protocols.environment.EnvMover, : pyrosetta.rosetta.protocols.moves.Mover) → None

C++: protocols::environment::EnvMover::add_registered_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

apply(self: pyrosetta.rosetta.protocols.environment.EnvMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::environment::EnvMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.environment.EnvMover, : pyrosetta.rosetta.protocols.environment.EnvMover) → pyrosetta.rosetta.protocols.environment.EnvMover

C++: protocols::environment::EnvMover::operator=(const class protocols::environment::EnvMover &) –> class protocols::environment::EnvMover &

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.environment.EnvMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::environment::EnvMover::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>

env(self: pyrosetta.rosetta.protocols.environment.EnvMover) → pyrosetta.rosetta.protocols.environment.Environment

C++: protocols::environment::EnvMover::env() –> class protocols::environment::Environment &

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.environment.EnvMover) → str

C++: protocols::environment::EnvMover::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_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::environment::EnvMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.environment.EnvMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::environment::EnvMover::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::environment::EnvMover::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_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

2. 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.environment.EnvMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.environment.EnvMoverCreator, : pyrosetta.rosetta.protocols.environment.EnvMoverCreator) → pyrosetta.rosetta.protocols.environment.EnvMoverCreator

C++: protocols::environment::EnvMoverCreator::operator=(const class protocols::environment::EnvMoverCreator &) –> class protocols::environment::EnvMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.environment.EnvMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.environment.EnvMoverCreator) → str

C++: protocols::environment::EnvMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.environment.EnvMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.environment.Environment

Bases: EnvCore

allow_pure_movers(*args, **kwargs)

Overloaded function.

1. allow_pure_movers(self: pyrosetta.rosetta.protocols.environment.Environment) -> bool

C++: protocols::environment::Environment::allow_pure_movers() const –> bool

2. allow_pure_movers(self: pyrosetta.rosetta.protocols.environment.Environment, : bool) -> None

C++: protocols::environment::Environment::allow_pure_movers(bool) –> void

annotations(self: pyrosetta.rosetta.protocols.environment.Environment) → pyrosetta.rosetta.core.environment.SequenceAnnotation

C++: protocols::environment::Environment::annotations() const –> class std::shared_ptr<const class core::environment::SequenceAnnotation>

auto_cut(*args, **kwargs)

Overloaded function.

1. auto_cut(self: pyrosetta.rosetta.protocols.environment.Environment) -> bool

C++: protocols::environment::Environment::auto_cut() const –> bool

2. auto_cut(self: pyrosetta.rosetta.protocols.environment.Environment, : bool) -> None

C++: protocols::environment::Environment::auto_cut(bool) –> void

broker(self: pyrosetta.rosetta.protocols.environment.Environment) → protocols::environment::EnvClaimBroker

C++: protocols::environment::Environment::broker() const –> class std::shared_ptr<const class protocols::environment::EnvClaimBroker>

end(self: pyrosetta.rosetta.protocols.environment.Environment, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::environment::Environment::end(const class core::pose::Pose &) –> class core::pose::Pose

get_self_ptr(self: pyrosetta.rosetta.protocols.environment.Environment) → pyrosetta.rosetta.protocols.environment.Environment

C++: protocols::environment::Environment::get_self_ptr() –> class std::shared_ptr<class protocols::environment::Environment>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.environment.Environment) → pyrosetta.rosetta.std.weak_ptr_protocols_environment_Environment_t

C++: protocols::environment::Environment::get_self_weak_ptr() –> class std::weak_ptr<class protocols::environment::Environment>

id(self: pyrosetta.rosetta.core.environment.EnvCore) → int

C++: core::environment::EnvCore::id() const –> const unsigned long &

inherit_cuts(*args, **kwargs)

Overloaded function.

1. inherit_cuts(self: pyrosetta.rosetta.protocols.environment.Environment) -> bool

C++: protocols::environment::Environment::inherit_cuts() const –> bool

2. inherit_cuts(self: pyrosetta.rosetta.protocols.environment.Environment, : bool) -> None

C++: protocols::environment::Environment::inherit_cuts(bool) –> void

is_registered(self: pyrosetta.rosetta.protocols.environment.Environment, : protocols::environment::ClientMover) → bool

C++: protocols::environment::Environment::is_registered(class std::shared_ptr<class protocols::environment::ClientMover>) const –> bool

name(self: pyrosetta.rosetta.core.environment.EnvCore) → str

C++: core::environment::EnvCore::name() const –> const std::string &

pconf_creation(self: pyrosetta.rosetta.protocols.environment.Environment, ptr: pyrosetta.rosetta.core.conformation.Conformation) → None

C++: protocols::environment::Environment::pconf_creation(class core::conformation::Conformation *) const –> void

pconf_destruction(self: pyrosetta.rosetta.protocols.environment.Environment, ptr: pyrosetta.rosetta.core.conformation.Conformation) → None

C++: protocols::environment::Environment::pconf_destruction(class core::conformation::Conformation *) const –> void

register_mover(self: pyrosetta.rosetta.protocols.environment.Environment, : pyrosetta.rosetta.protocols.moves.Mover) → None

C++: protocols::environment::Environment::register_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

start(self: pyrosetta.rosetta.protocols.environment.Environment, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::environment::Environment::start(const class core::pose::Pose &) –> class core::pose::Pose

superenv(self: pyrosetta.rosetta.protocols.environment.Environment) → pyrosetta.rosetta.std.weak_ptr_const_protocols_environment_Environment_t

C++: protocols::environment::Environment::superenv() const –> class std::weak_ptr<const class protocols::environment::Environment>

class pyrosetta.rosetta.protocols.environment.ProtectedConformation

Bases: Conformation

aa(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.AA

Returns the AA enum for position <seqpos>

C++: core::conformation::Conformation::aa(unsigned long) const –> const enum core::chemical::AA &

add_disulfide_bond(self: pyrosetta.rosetta.core.conformation.Conformation, res1: int, res2: int) → bool

Attempt to add a disulfide bond between the two residues.

Returns true on success and false on failure

C++: core::conformation::Conformation::add_disulfide_bond(unsigned long, unsigned long) –> bool

add_parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation, newset: core::conformation::parametric::ParametersSet) → None

Add a (predefined) ParametersSet object (via its owning pointer)

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

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

align_virtual_atoms_in_carbohydrate_residue(self: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → None

Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this

conformation.

C++: core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(const unsigned long) –> void

annotated_sequence(self: pyrosetta.rosetta.core.conformation.Conformation, show_all_variants: bool) → str

Returns the variant-tagged string representing the

residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]

C++: core::conformation::Conformation::annotated_sequence(bool) const –> std::string

annotations(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → pyrosetta.rosetta.core.environment.SequenceAnnotation

C++: protocols::environment::ProtectedConformation::annotations() const –> class std::shared_ptr<const class core::environment::SequenceAnnotation>

append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : bool) → None

C++: protocols::environment::ProtectedConformation::append_polymer_residue_after_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void

append_residue_by_bond(*args, **kwargs)

Overloaded function.

1. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

2. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool) -> None

3. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int) -> None

4. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int) -> None

5. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int) -> None

6. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int, start_new_chain: bool) -> None

7. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int, start_new_chain: bool, lookup_bond_length: bool) -> None

Append a new residue by a bond.

C++: core::conformation::Conformation::append_residue_by_bond(const class core::conformation::Residue &, const bool, int, unsigned long, int, const bool, const bool) –> void

append_residue_by_jump(*args, **kwargs)

Overloaded function.

1. append_residue_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int) -> None

2. append_residue_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : str) -> None

3. append_residue_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : str, : str) -> None

4. append_residue_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : str, : str, _: bool) -> None

C++: protocols::environment::ProtectedConformation::append_residue_by_jump(const class core::conformation::Residue &, const unsigned long, const std::string &, const std::string &, const bool) –> void

append_residues(self: pyrosetta.rosetta.core.conformation.Conformation, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, jump_connection: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Function for building poses

Append all the residues to the Conformation. If the corresponding jump connection is zero, attach by polymeric connection to the previous residue

C++: core::conformation::Conformation::append_residues(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.conformation.Conformation, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::conformation::Conformation::apply_transform_Rx_plus_v(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, src: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.conformation.Conformation

C++: protocols::environment::ProtectedConformation::operator=(const class core::conformation::Conformation &) –> class core::conformation::Conformation &

2. assign(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.protocols.environment.ProtectedConformation) -> pyrosetta.rosetta.protocols.environment.ProtectedConformation

C++: protocols::environment::ProtectedConformation::operator=(const class protocols::environment::ProtectedConformation &) –> class protocols::environment::ProtectedConformation &

atom_is_backbone_norefold(self: pyrosetta.rosetta.core.conformation.Conformation, pos: int, atomno: int) → bool

returns true if atom is part of backbone.

C++: core::conformation::Conformation::atom_is_backbone_norefold(unsigned long, unsigned long) const –> bool

atom_tree(self: pyrosetta.rosetta.core.conformation.Conformation) → core::kinematics::AtomTree

Returns the conformation’s AtomTree

C++: core::conformation::Conformation::atom_tree() const –> const class core::kinematics::AtomTree &

atoms_are_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID) → bool

Helper method to determine whether two atoms have a chemical bond linking them.

Intended for internal use, but there’s really no reason not to make this a public method. This works for atoms within the same residue or in different residues. AMW went and made this a public method.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::atoms_are_bonded(const class core::id::AtomID &, const class core::id::AtomID &) const –> bool

backbone_torsion_angle_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID, id4: pyrosetta.rosetta.core.id.AtomID) → bool

get four backbone atoms which define this backbone torsion

Returns TRUE to signal FAILURE

C++: core::conformation::Conformation::backbone_torsion_angle_atoms(const class core::id::TorsionID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &) const –> bool

batch_get_xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.utility.vector1_core_id_AtomID, position: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: core::conformation::Conformation::batch_get_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> void

batch_set_xyz(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, id: pyrosetta.rosetta.utility.vector1_core_id_AtomID, position: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: protocols::environment::ProtectedConformation::batch_set_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

block_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None

block signals from being sent

C++: core::conformation::Conformation::block_signals() –> void

blocking_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

are signals being blocked?

C++: core::conformation::Conformation::blocking_signals() const –> bool

bond_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID) → float

Returns the bond angle defined by <atom[1-3]> through the AtomTree

C++: core::conformation::Conformation::bond_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> double

bond_length(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID) → float

Returns the bond length between <atom1> and <atom2> through the AtomTree

C++: core::conformation::Conformation::bond_length(const class core::id::AtomID &, const class core::id::AtomID &) const –> double

bond_orientation(*args, **kwargs)

Overloaded function.

1. bond_orientation(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Return the normalized vector of the bond between these two atoms.

C++: core::conformation::Conformation::bond_orientation(const class core::id::AtomID &, const class core::id::AtomID &) const –> class numeric::xyzVector<double>

2. bond_orientation(self: pyrosetta.rosetta.core.conformation.Conformation, torsion: core::id::TorsionID) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Return the normalized vector of the bond about which this torsion angle twists.

C++: core::conformation::Conformation::bond_orientation(const class core::id::TorsionID) const –> class numeric::xyzVector<double>

bonded_neighbor_all_res(*args, **kwargs)

Overloaded function.

1. bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

2. bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

3. bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

4. bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool, intra_res: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

5. bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool, intra_res: bool, inter_res: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

Get all atoms bonded to another

If intra_res is false, we only find inter - residue neighbors

C++: core::conformation::Conformation::bonded_neighbor_all_res(const class core::id::AtomID &, bool, bool, bool, bool) const –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

buffer_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None

block signals from being sent and buffer them to be sent after unblocking

C++: core::conformation::Conformation::buffer_signals() –> void

buffering_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

are signals being blocked and buffered?

C++: core::conformation::Conformation::buffering_signals() const –> bool

chain_begin(self: pyrosetta.rosetta.core.conformation.Conformation, chain: int) → int

Returns the position number of the first residue in chain number <chain>

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_begin(unsigned long) const –> unsigned long

chain_end(self: pyrosetta.rosetta.core.conformation.Conformation, chain: int) → int

Returns the position number of the last residue in chain number <chain>

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_end(unsigned long) const –> unsigned long

chain_endings(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::environment::ProtectedConformation::chain_endings(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

chains_from_termini(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → None

C++: protocols::environment::ProtectedConformation::chains_from_termini() –> void

check_valid_membrane(self: pyrosetta.rosetta.core.conformation.Conformation) → None

Check that a new membrane position is valid

Given a new membrane normal/center pair, check that the newly constructed stub represents an orthogonal coordinate frame

C++: core::conformation::Conformation::check_valid_membrane() const –> void

clear(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → None

C++: protocols::environment::ProtectedConformation::clear() –> void

clear_glycan_trees(self: pyrosetta.rosetta.core.conformation.Conformation) → None

Safely detaches any tree observers and clears it to null.

C++: core::conformation::Conformation::clear_glycan_trees() –> void

clear_observers(self: pyrosetta.rosetta.core.conformation.Conformation) → None

clear all observers

C++: core::conformation::Conformation::clear_observers() –> void

clear_parameters_set_list(self: pyrosetta.rosetta.core.conformation.Conformation) → None

Delete the list of ParametersSetOP objects.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::clear_parameters_set_list() –> void

clone(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → pyrosetta.rosetta.core.conformation.Conformation

C++: protocols::environment::ProtectedConformation::clone() const –> class std::shared_ptr<class core::conformation::Conformation>

const_residues(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

Inefficient – constructs copy of residues_

C++: core::conformation::Conformation::const_residues() const –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

contains_carbohydrate_residues(*args, **kwargs)

Overloaded function.

1. contains_carbohydrate_residues(self: pyrosetta.rosetta.core.conformation.Conformation) -> bool

Return true if this conformation contains any carbohydrate residues.

C++: core::conformation::Conformation::contains_carbohydrate_residues() const –> bool

2. contains_carbohydrate_residues(self: pyrosetta.rosetta.core.conformation.Conformation, setting: bool) -> None

Set whether this conformation contains any carbohydrate residues.

C++: core::conformation::Conformation::contains_carbohydrate_residues(bool) –> void

copy_segment(self: pyrosetta.rosetta.core.conformation.Conformation, size: int, src: pyrosetta.rosetta.core.conformation.Conformation, begin: int, src_begin: int) → None

copy a stretch of coordinates/torsions from another Conformation

C++: core::conformation::Conformation::copy_segment(unsigned long, const class core::conformation::Conformation &, unsigned long, unsigned long) –> void

create_new_parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation) → None

Create a new (empty) ParametersSet object and add its owning pointer

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::create_new_parameters_set() –> void

debug_pause(*args, **kwargs)

Overloaded function.

1. debug_pause(self: pyrosetta.rosetta.core.conformation.Conformation, flag: bool) -> None

wait for stdin after sending a GeneralEvent signal

C++: core::conformation::Conformation::debug_pause(bool) const –> void

2. debug_pause(self: pyrosetta.rosetta.core.conformation.Conformation) -> bool

waiting for stdin after sending a GeneralEvent signal?

C++: core::conformation::Conformation::debug_pause() const –> bool

debug_residue_torsions(*args, **kwargs)

Overloaded function.

1. debug_residue_torsions(self: pyrosetta.rosetta.core.conformation.Conformation) -> None

2. debug_residue_torsions(self: pyrosetta.rosetta.core.conformation.Conformation, verbose: bool) -> None

debugging

C++: core::conformation::Conformation::debug_residue_torsions(bool) const –> void

declare_chemical_bond(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int, : str, : int, : str) → None

C++: protocols::environment::ProtectedConformation::declare_chemical_bond(const unsigned long, const std::string &, const unsigned long, const std::string &) –> void

delete_chain_ending(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int) → None

C++: protocols::environment::ProtectedConformation::delete_chain_ending(const unsigned long) –> void

delete_polymer_residue(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int) → None

C++: protocols::environment::ProtectedConformation::delete_polymer_residue(const unsigned long) –> void

delete_residue_range_slow(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, range_begin: int, range_end: int) → None

C++: protocols::environment::ProtectedConformation::delete_residue_range_slow(const unsigned long, const unsigned long) –> void

delete_residue_slow(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int) → None

C++: protocols::environment::ProtectedConformation::delete_residue_slow(const unsigned long) –> void

detached_copy(self: pyrosetta.rosetta.core.conformation.Conformation, src: pyrosetta.rosetta.core.conformation.Conformation) → None

copy the other conformation into this, but make sure that the two

share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system).

C++: core::conformation::Conformation::detached_copy(const class core::conformation::Conformation &) –> void

detect_bonds(self: pyrosetta.rosetta.core.conformation.Conformation) → None

C++: core::conformation::Conformation::detect_bonds() –> void

detect_disulfides(*args, **kwargs)

Overloaded function.

1. detect_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation, disulfs: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None

Detect existing disulfides from the protein structure,

using the provided pairs as a starting point

C++: core::conformation::Conformation::detect_disulfides(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

2. detect_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation) -> None

Detect existing disulfides from the protein structure.

Non-virtual, simply defers to the virtual function with an empty parameter.

C++: core::conformation::Conformation::detect_disulfides() –> void

detect_pseudobonds(self: pyrosetta.rosetta.core.conformation.Conformation) → None

C++: core::conformation::Conformation::detect_pseudobonds() –> void

dof(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.DOF_ID) → float

Returns the AtomTree degree of freedom (DOF) <id>

C++: core::conformation::Conformation::dof(const class core::id::DOF_ID &) const –> double

dof_id_from_atom_ids(*args, **kwargs)

Overloaded function.

1. dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID, id4: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the torsion angle defined by these four atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

2. dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the bond angle defined by these three atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

3. dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the bond distance defined by these two atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

4. dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID defined by these atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) const –> class core::id::DOF_ID

dof_id_from_torsion_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID) → pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to this TorsionID.

C++: core::conformation::Conformation::dof_id_from_torsion_id(const class core::id::TorsionID &) const –> class core::id::DOF_ID

downstream_jump_stub(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → core::kinematics::Stub

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming

C++: core::conformation::Conformation::downstream_jump_stub(int) const –> class core::kinematics::Stub

empty(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

Returns true if this conformation does not have any residues

C++: core::conformation::Conformation::empty() const –> bool

env_destruction(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → None

C++: protocols::environment::ProtectedConformation::env_destruction() –> void

environment(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → pyrosetta.rosetta.std.weak_ptr_const_protocols_environment_Environment_t

C++: protocols::environment::ProtectedConformation::environment() const –> class std::weak_ptr<const class protocols::environment::Environment>

fill_missing_atoms(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) → None

C++: protocols::environment::ProtectedConformation::fill_missing_atoms(class core::id::AtomID_Map<bool>) –> void

fix_disulfides(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

C++: protocols::environment::ProtectedConformation::fix_disulfides(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

fold_tree(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::environment::ProtectedConformation::fold_tree(const class core::kinematics::FoldTree &) –> void

get_jump_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int, upstream_id: pyrosetta.rosetta.core.id.AtomID, downstream_id: pyrosetta.rosetta.core.id.AtomID) → bool

get two atoms connect by jump

C++: core::conformation::Conformation::get_jump_atom_ids(unsigned long, class core::id::AtomID &, class core::id::AtomID &) const –> bool

get_residue_mask(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.utility.vector1_bool

returns a mask of residues to be used in scoring

C++: core::conformation::Conformation::get_residue_mask() const –> class utility::vector1<bool, class std::allocator<bool> >

get_residue_weight(self: pyrosetta.rosetta.core.conformation.Conformation, : int, : int) → float

returns a residue-pair weight

C++: core::conformation::Conformation::get_residue_weight(unsigned long, unsigned long) const –> double

get_self_ptr(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.conformation.Conformation

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

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.std.weak_ptr_core_conformation_Conformation_t

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

get_stub_transform(self: pyrosetta.rosetta.core.conformation.Conformation, stub_id1: pyrosetta.rosetta.core.id.StubID, stub_id2: pyrosetta.rosetta.core.id.StubID) → core::kinematics::RT

get the transform between two stubs

C++: core::conformation::Conformation::get_stub_transform(const class core::id::StubID &, const class core::id::StubID &) const –> class core::kinematics::RT

get_torsion_angle_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, tor_id: core::id::TorsionID, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID, id4: pyrosetta.rosetta.core.id.AtomID) → bool

get four atoms which defined this torsion

C++: core::conformation::Conformation::get_torsion_angle_atom_ids(const class core::id::TorsionID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &) const –> bool

glycan_tree_set(self: pyrosetta.rosetta.core.conformation.Conformation) → core::conformation::carbohydrates::GlycanTreeSet

Get the glycan tree set. Nullptr if not present.

C++: core::conformation::Conformation::glycan_tree_set() const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTreeSet>

has_passport(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

C++: core::conformation::Conformation::has_passport() const –> bool

insert_chain_ending(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int) → None

C++: protocols::environment::ProtectedConformation::insert_chain_ending(const unsigned long) –> void

insert_conformation_by_jump(*args, **kwargs)

Overloaded function.

1. insert_conformation_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Conformation, : int, : int, : int, : int) -> None

2. insert_conformation_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Conformation, : int, : int, : int, : int, : str) -> None

3. insert_conformation_by_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Conformation, : int, : int, : int, : int, : str, : str) -> None

C++: protocols::environment::ProtectedConformation::insert_conformation_by_jump(const class core::conformation::Conformation &, const unsigned long, const unsigned long, const unsigned long, const unsigned long, const std::string &, const std::string &) –> void

insert_ideal_geometry_at_polymer_bond(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, seqpos: int) → None

C++: protocols::environment::ProtectedConformation::insert_ideal_geometry_at_polymer_bond(const unsigned long) –> void

insert_ideal_geometry_at_residue_connection(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, pos1: int, connid1: int) → None

C++: protocols::environment::ProtectedConformation::insert_ideal_geometry_at_residue_connection(const unsigned long, const unsigned long) –> void

insert_residue_by_bond(*args, **kwargs)

Overloaded function.

1. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None

2. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool) -> None

3. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str) -> None

4. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str) -> None

5. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool) -> None

6. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool, lookup_bond_length: bool) -> None

Insert a new residue by jump. If new_chain is “true”, then seqpos must be the last

residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

C++: core::conformation::Conformation::insert_residue_by_bond(const class core::conformation::Residue &, const unsigned long, unsigned long, const bool, const std::string &, const std::string &, bool, const bool) –> void

insert_residue_by_jump(*args, **kwargs)

Overloaded function.

1. insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None

2. insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str) -> None

3. insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str, root_atom: str) -> None

4. insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str, root_atom: str, new_chain: bool) -> None

Insert a new residue by jump. If new_chain is “true”, then seqpos must be the last

residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

C++: core::conformation::Conformation::insert_residue_by_jump(const class core::conformation::Residue &, unsigned long, unsigned long, const std::string &, const std::string &, bool) –> void

inter_residue_connection_partner(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, connection_index: int) → pyrosetta.rosetta.core.id.AtomID

This returns the AtomID of the atom in the other residue to which the “connection_index”-th

connection of residue seqpos is connected to.

C++: core::conformation::Conformation::inter_residue_connection_partner(unsigned long, int) const –> class core::id::AtomID

is_bonded(*args, **kwargs)

Overloaded function.

1. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID) -> bool

2. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID, virt: bool) -> bool

3. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool) -> bool

Returns a boolean for two atomIDs to be bonded.

Uses bonded_neighbor_all_res, which iterates through residue connections. To speed up, we would need to turn the connects into a proper bonded graph

C++: core::conformation::Conformation::is_bonded(const class core::id::AtomID &, const class core::id::AtomID &, bool, bool) const –> bool

is_centroid(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_centroid() const –> bool

is_fullatom(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_fullatom() const –> bool

is_membrane(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

convenience test for if the conformation contains information for a membrane protein

C++: core::conformation::Conformation::is_membrane() const –> bool

is_mixed_mode(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_mixed_mode() const –> bool

is_protected(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → bool

C++: protocols::environment::ProtectedConformation::is_protected() const –> bool

jump(*args, **kwargs)

Overloaded function.

1. jump(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) -> core::kinematics::Jump

Returns the Jump with jump number <jump_number>

C++: core::conformation::Conformation::jump(int) const –> const class core::kinematics::Jump &

2. jump(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID) -> core::kinematics::Jump

access a jump

C++: core::conformation::Conformation::jump(const class core::id::AtomID &) const –> const class core::kinematics::Jump &

jump_atom_id(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → pyrosetta.rosetta.core.id.AtomID

C++: core::conformation::Conformation::jump_atom_id(int) const –> class core::id::AtomID

match_variants(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, seqpos: int, in_rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::environment::ProtectedConformation::match_variants(unsigned long, const class core::conformation::Residue &) const –> class std::shared_ptr<class core::conformation::Residue>

membrane_info(self: pyrosetta.rosetta.core.conformation.Conformation) → core::conformation::membrane::MembraneInfo

Returns the const MembraneInfo object in conformation

Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data

C++: core::conformation::Conformation::membrane_info() –> class std::shared_ptr<class core::conformation::membrane::MembraneInfo>

modifiable_residue_type_set_for_conf(*args, **kwargs)

Overloaded function.

1. modifiable_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

2. modifiable_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const)

Modifications to this RTS won’t be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn’t have it already.

C++: core::conformation::Conformation::modifiable_residue_type_set_for_conf(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>

n_parameters_sets(self: pyrosetta.rosetta.core.conformation.Conformation) → int

Get the number of parameters sets defined for this Conformation.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::n_parameters_sets() const –> unsigned long

num_chains(self: pyrosetta.rosetta.core.conformation.Conformation) → int

Returns the number of chains

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::num_chains() const –> unsigned long

parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation, index: int) → core::conformation::parametric::ParametersSet

Access one of the ParametersSets objects linked to this Conformation.

Vikram K. Mulligan (vmullig.edu)

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

pop_passport(self: pyrosetta.rosetta.core.conformation.Conformation) → core::environment::DofPassport

C++: core::conformation::Conformation::pop_passport() –> class std::shared_ptr<const class core::environment::DofPassport>

prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : bool) → None

C++: protocols::environment::ProtectedConformation::prepend_polymer_residue_before_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void

push_passport(self: pyrosetta.rosetta.core.conformation.Conformation, : core::environment::DofPassport) → None

C++: core::conformation::Conformation::push_passport(class std::shared_ptr<const class core::environment::DofPassport>) –> void

rebuild_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int) → None

C++: protocols::environment::ProtectedConformation::rebuild_polymer_bond_dependent_atoms(const unsigned long) –> void

rebuild_polymer_bond_dependent_atoms_this_residue_only(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None

Rebuilds the atoms that are dependent on polymer bonds for the specified residue only.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only(const unsigned long) –> void

rebuild_residue_connection_dependent_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, connid: int) → None

C++: core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(unsigned long, unsigned long) –> void

receive_observers_from(self: pyrosetta.rosetta.core.conformation.Conformation, src: pyrosetta.rosetta.core.conformation.Conformation) → None

fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation

C++: core::conformation::Conformation::receive_observers_from(const class core::conformation::Conformation &) –> void

replace_residue(*args, **kwargs)

Overloaded function.

1. replace_residue(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, atom_pairs: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t) -> None

C++: protocols::environment::ProtectedConformation::replace_residue(const unsigned long, const class core::conformation::Residue &, const class utility::vector1<struct std::pair<std::string, std::string >, class std::allocator<struct std::pair<std::string, std::string > > > &) –> void

2. replace_residue(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, orient_backbone: bool) -> None

C++: protocols::environment::ProtectedConformation::replace_residue(const unsigned long, const class core::conformation::Residue &, const bool) –> void

reset_chain_endings(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → None

C++: protocols::environment::ProtectedConformation::reset_chain_endings() –> void

reset_move_data(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → None

C++: protocols::environment::ProtectedConformation::reset_move_data() –> void

reset_residue_type_set_for_conf(*args, **kwargs)

Overloaded function.

1. reset_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, new_set: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> None

2. reset_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, new_set: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> None

Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS.

(If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.)

NOTE: You’re potentially in for a bunch of trouble if the passed in set isn’t a modified version of the value returned by modifiable_residue_type_set_for_conf() from this conformation. Also, a clone of the RTS is made, so subsequent edits to the RTS will not be reflected in the Conformation’s RTS

C++: core::conformation::Conformation::reset_residue_type_set_for_conf(class std::shared_ptr<const class core::chemical::PoseResidueTypeSet>, enum core::chemical::TypeSetMode) –> void

reset_structure_moved(self: pyrosetta.rosetta.core.conformation.Conformation) → None

reset the structure_moved_ bool

C++: core::conformation::Conformation::reset_structure_moved() const –> void

residue(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue

access one of the residues

this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.

update coordinates and torsions for this and all other residues before allowing read access

C++: core::conformation::Conformation::residue(unsigned long) const –> const class core::conformation::Residue &

residue_cop(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue

access one of the residues, using COP

C++: core::conformation::Conformation::residue_cop(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

residue_data(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

Write access to the datacache array stored inside a Residue object. Although the Conformation

very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable.

The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a %Conformation) so that it can be used during scoring evaluation. Accessing the residue_data will trigger a coordinate (or torsion) update.

C++: core::conformation::Conformation::residue_data(unsigned long) –> class basic::datacache::BasicDataCache &

residue_type(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.ResidueType

access one of the residue’s types – avoids coord/torsion update

C++: core::conformation::Conformation::residue_type(unsigned long) const –> const class core::chemical::ResidueType &

residue_type_ptr(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.ResidueType

access one of the residue’s types as a COP – avoids coord/torsion update

C++: core::conformation::Conformation::residue_type_ptr(unsigned long) const –> class std::shared_ptr<const class core::chemical::ResidueType>

residue_type_set_for_conf(*args, **kwargs)

Overloaded function.

1. residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

2. residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

Return the appropriate ResidueTypeSet for the Conformation

If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn’t have a specific PoseResidueTypeSet

C++: core::conformation::Conformation::residue_type_set_for_conf(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

residue_typeset_mode(*args, **kwargs)

Overloaded function.

1. residue_typeset_mode(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.TypeSetMode

2. residue_typeset_mode(self: pyrosetta.rosetta.core.conformation.Conformation, majority: bool) -> pyrosetta.rosetta.core.chemical.TypeSetMode

What mode of ResidueTypeSet is this Conformation made of?

If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes

C++: core::conformation::Conformation::residue_typeset_mode(bool) const –> enum core::chemical::TypeSetMode

resolve_partial_atom_id(self: pyrosetta.rosetta.core.conformation.Conformation, partial_id: core::id::PartialAtomID) → pyrosetta.rosetta.core.id.AtomID

Resolve a partial atom ID into an AtomID that is specific for this %Conformation

C++: core::conformation::Conformation::resolve_partial_atom_id(const class core::id::PartialAtomID &) const –> class core::id::AtomID

resolver(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation) → pyrosetta.rosetta.core.environment.SequenceAnnotation

C++: protocols::environment::ProtectedConformation::resolver() const –> class std::shared_ptr<const class core::environment::SequenceAnnotation>

safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : bool) → None

C++: protocols::environment::ProtectedConformation::safely_append_polymer_residue_after_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void

safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.conformation.Residue, : int, : bool) → None

C++: protocols::environment::ProtectedConformation::safely_prepend_polymer_residue_before_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, other: pyrosetta.rosetta.core.conformation.Conformation, recurse: bool) → bool

C++: protocols::environment::ProtectedConformation::same_type_as_me(const class core::conformation::Conformation &, const bool) const –> bool

secstruct(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → str

Returns the secondary structure the position <seqpos>

character representing secondary structure; returns ‘L’ if the requested sequence position is larger than the length in the secondary structure array

C++: core::conformation::Conformation::secstruct(unsigned long) const –> char

sequence_matches(self: pyrosetta.rosetta.core.conformation.Conformation, other: pyrosetta.rosetta.core.conformation.Conformation) → bool

do the names of all residues in this and src match?

C++: core::conformation::Conformation::sequence_matches(const class core::conformation::Conformation &) const –> bool

set_bond_angle(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, setting: float) → None

C++: protocols::environment::ProtectedConformation::set_bond_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const double) –> void

set_bond_length(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, setting: float) → None

C++: protocols::environment::ProtectedConformation::set_bond_length(const class core::id::AtomID &, const class core::id::AtomID &, const double) –> void

set_dof(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, id: pyrosetta.rosetta.core.id.DOF_ID, setting: float) → None

C++: protocols::environment::ProtectedConformation::set_dof(const class core::id::DOF_ID &, const double) –> void

set_jump(*args, **kwargs)

Overloaded function.

1. set_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : pyrosetta.rosetta.core.id.AtomID, : pyrosetta.rosetta.core.kinematics.Jump) -> None

C++: protocols::environment::ProtectedConformation::set_jump(const class core::id::AtomID &, const class core::kinematics::Jump &) –> void

2. set_jump(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int, : pyrosetta.rosetta.core.kinematics.Jump) -> None

C++: protocols::environment::ProtectedConformation::set_jump(const int, const class core::kinematics::Jump &) –> void

set_jump_atom_stub_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.StubID) → None

C++: core::conformation::Conformation::set_jump_atom_stub_id(const class core::id::StubID &) –> void

set_membrane_info(self: pyrosetta.rosetta.core.conformation.Conformation, mem_info: core::conformation::membrane::MembraneInfo) → None

Setup a Membrane Info object in Conformation - pos & topology

Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.

C++: core::conformation::Conformation::set_membrane_info(class std::shared_ptr<class core::conformation::membrane::MembraneInfo>) –> void

set_noncanonical_connection(self: pyrosetta.rosetta.core.conformation.Conformation, res_id_lower: int, lr_conn_id: int, res_id_upper: int, ur_conn_id: int) → None

Create an arbitrary covalent connection between two residues.

C++: core::conformation::Conformation::set_noncanonical_connection(unsigned long, unsigned long, unsigned long, unsigned long) –> void

set_polymeric_connection(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, : int, : int) → None

C++: protocols::environment::ProtectedConformation::set_polymeric_connection(unsigned long, unsigned long) –> void

set_secstruct(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, seqpos: int, setting: str) → None

C++: protocols::environment::ProtectedConformation::set_secstruct(const unsigned long, const char) –> void

set_stub_transform(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, stub_id1: pyrosetta.rosetta.core.id.StubID, stub_id2: pyrosetta.rosetta.core.id.StubID, target_rt: pyrosetta.rosetta.core.kinematics.RT) → None

C++: protocols::environment::ProtectedConformation::set_stub_transform(const class core::id::StubID &, const class core::id::StubID &, const class core::kinematics::RT &) –> void

set_torsion(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, id: pyrosetta.rosetta.core.id.TorsionID, setting: float) → None

C++: protocols::environment::ProtectedConformation::set_torsion(const class core::id::TorsionID &, const double) –> void

set_torsion_angle(*args, **kwargs)

Overloaded function.

1. set_torsion_angle(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, setting: float) -> None

2. set_torsion_angle(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, setting: float, quiet: bool) -> None

C++: protocols::environment::ProtectedConformation::set_torsion_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const double, const bool) –> void

set_xyz(self: pyrosetta.rosetta.protocols.environment.ProtectedConformation, id: pyrosetta.rosetta.core.id.AtomID, position: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::environment::ProtectedConformation::set_xyz(const class core::id::AtomID &, const class numeric::xyzVector<double> &) –> void

setup_glycan_trees(self: pyrosetta.rosetta.core.conformation.Conformation) → None

Setup glycan trees and attach length observer.

C++: core::conformation::Conformation::setup_glycan_trees() –> void

sever_chemical_bond(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos1: int, res1_resconn_index: int, seqpos2: int, res2_resconn_index: int) → None

Sever the chemical bond between two residues by stating that the

connections for those residues are “incomplete” (i.e. in a state where these residues are not ready to be scored).

C++: core::conformation::Conformation::sever_chemical_bond(unsigned long, unsigned long, unsigned long, unsigned long) –> void

show_residue_connections(*args, **kwargs)

Overloaded function.

1. show_residue_connections(self: pyrosetta.rosetta.core.conformation.Conformation) -> None

Show residue connections for debugging purposes.

C++: core::conformation::Conformation::show_residue_connections() const –> void

2. show_residue_connections(self: pyrosetta.rosetta.core.conformation.Conformation, os: pyrosetta.rosetta.std.ostream) -> None

Show residue connections for debugging purposes.

C++: core::conformation::Conformation::show_residue_connections(std::ostream &) const –> void

size(self: pyrosetta.rosetta.core.conformation.Conformation) → int

Returns the number of residues in the Conformation

C++: core::conformation::Conformation::size() const –> unsigned long

structure_moved(self: pyrosetta.rosetta.core.conformation.Conformation) → bool

has the structure moved since the last call to reset_move_data or reset_structure_moved

C++: core::conformation::Conformation::structure_moved() const –> bool

stub_from_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.StubID) → core::kinematics::Stub

C++: core::conformation::Conformation::stub_from_id(const class core::id::StubID &) const –> class core::kinematics::Stub

torsion(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID) → float

Return the torsion angle OR rigid-body offset for <id>

C++: core::conformation::Conformation::torsion(const class core::id::TorsionID &) const –> double

torsion_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → float

Returns the torsion angle defined by <atom[1-4]> in Radians

C++: core::conformation::Conformation::torsion_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> double

unblock_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None

allow signals to be sent

C++: core::conformation::Conformation::unblock_signals() –> void

update_actcoord(self: pyrosetta.rosetta.core.conformation.Conformation, resid: int) → None

C++: core::conformation::Conformation::update_actcoord(unsigned long) –> void

update_actcoords(self: pyrosetta.rosetta.core.conformation.Conformation) → None

C++: core::conformation::Conformation::update_actcoords() –> void

update_domain_map(self: pyrosetta.rosetta.core.conformation.Conformation, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t) → None

Generate a domain_map from the current dof/xyz moved data

C++: core::conformation::Conformation::update_domain_map(class ObjexxFCL::FArray1D<int> &) const –> void

update_membrane_position(self: pyrosetta.rosetta.core.conformation.Conformation, center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Update Normal, Center in the Membrane

Sets the center and normal coordinates to the appropriate parameters and checks for a valid stub prior to returning.

C++: core::conformation::Conformation::update_membrane_position(class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> void

update_noncanonical_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int, lr_conn_id: int, upper_seqpos: int, ur_conn_id: int) → None

Update the connection status between the lower_seqpos residue’s lr_conn_id connection ID and

the upper_seqpos residue’s ur_conn_id connection ID.

C++: core::conformation::Conformation::update_noncanonical_connection(unsigned long, unsigned long, unsigned long, unsigned long) –> void

update_orbital_coords(*args, **kwargs)

Overloaded function.

1. update_orbital_coords(self: pyrosetta.rosetta.core.conformation.Conformation, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: core::conformation::Conformation::update_orbital_coords(class core::conformation::Residue &) const –> void

2. update_orbital_coords(self: pyrosetta.rosetta.core.conformation.Conformation, resid: int) -> None

C++: core::conformation::Conformation::update_orbital_coords(unsigned long) –> void

update_polymeric_connection(*args, **kwargs)

Overloaded function.

1. update_polymeric_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int) -> None

2. update_polymeric_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int, update_connection_dep_atoms: bool) -> None

Update the polymer connection status between lower_seqpos and lower_seqpos+1

based on chainID’s and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated.

C++: core::conformation::Conformation::update_polymeric_connection(unsigned long, bool) –> void

upstream_jump_stub(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → core::kinematics::Stub

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming

C++: core::conformation::Conformation::upstream_jump_stub(int) const –> class core::kinematics::Stub

xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.numeric.xyzVector_double_t

access xyz coordinates of an atom

C++: core::conformation::Conformation::xyz(const class core::id::AtomID &) const –> const class numeric::xyzVector<double> &

class pyrosetta.rosetta.protocols.environment.ScriptCM

Bases: ClientMover

apply(self: pyrosetta.rosetta.protocols.environment.ScriptCM, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::environment::ScriptCM::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.environment.ScriptCM, : pyrosetta.rosetta.protocols.environment.ScriptCM) → pyrosetta.rosetta.protocols.environment.ScriptCM

C++: protocols::environment::ScriptCM::operator=(const class protocols::environment::ScriptCM &) –> class protocols::environment::ScriptCM &

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.environment.ScriptCM) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::environment::ScriptCM::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.environment.ScriptCM) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::environment::ScriptCM::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.environment.ScriptCM) → str

C++: protocols::environment::ScriptCM::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_t

non-const accessor

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

initialize(self: pyrosetta.rosetta.protocols.environment.ScriptCM, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::environment::ScriptCM::initialize(class core::pose::Pose &) –> 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::environment::ScriptCM::mover_name() –> std::string

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.environment.ScriptCM) -> str

C++: protocols::environment::ScriptCM::name() const –> const std::string &

2. name(self: pyrosetta.rosetta.protocols.environment.ScriptCM, name: str) -> None

C++: protocols::environment::ScriptCM::name(const std::string &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.environment.ScriptCM, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::environment::ScriptCM::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::environment::ScriptCM::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

static scriptcm_group_name() → str

C++: protocols::environment::ScriptCM::scriptcm_group_name() –> std::string

static scriptcm_subelement_ct_namer(: str) → str

C++: protocols::environment::ScriptCM::scriptcm_subelement_ct_namer(std::string) –> std::string

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

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

Get the set ‘type’ string

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

yield_claims(self: pyrosetta.rosetta.protocols.environment.ScriptCM, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.basic.datacache.WriteableCacheableMap) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t

C++: protocols::environment::ScriptCM::yield_claims(const class core::pose::Pose &, class std::shared_ptr<class basic::datacache::WriteableCacheableMap>) –> class std::list<class std::shared_ptr<class protocols::environment::claims::EnvClaim>, class std::allocator<class std::shared_ptr<class protocols::environment::claims::EnvClaim> > >

yield_submovers(self: pyrosetta.rosetta.protocols.environment.ClientMover, : pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t) → None

this method is used to make sure any movers contained in this

mover (that want to make claims) also get registered with the environment.

C++: protocols::environment::ClientMover::yield_submovers(class std::set<class std::shared_ptr<class protocols::environment::ClientMover>, struct std::less<class std::shared_ptr<class protocols::environment::ClientMover> >, class std::allocator<class std::shared_ptr<class protocols::environment::ClientMover> > > &) const –> void

class pyrosetta.rosetta.protocols.environment.ScriptCMCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.environment.ScriptCMCreator, : pyrosetta.rosetta.protocols.environment.ScriptCMCreator) → pyrosetta.rosetta.protocols.environment.ScriptCMCreator

C++: protocols::environment::ScriptCMCreator::operator=(const class protocols::environment::ScriptCMCreator &) –> class protocols::environment::ScriptCMCreator &

create_mover(self: pyrosetta.rosetta.protocols.environment.ScriptCMCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.environment.ScriptCMCreator) → str

C++: protocols::environment::ScriptCMCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.environment.ScriptCMCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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