ncbb¶

oop

Bindings for protocols::ncbb namespace

class pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::ncbb::NcbbDockDesignProtocol::apply(class core::pose::Pose &) –> void

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

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.ncbb.NcbbDockDesignProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::NcbbDockDesignProtocol::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.ncbb.NcbbDockDesignProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::NcbbDockDesignProtocol::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.ncbb.NcbbDockDesignProtocol) → str¶: C++: protocols::ncbb::NcbbDockDesignProtocol::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::ncbb::NcbbDockDesignProtocol::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::ncbb::NcbbDockDesignProtocol::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::ncbb::NcbbDockDesignProtocol::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.

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

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

Set the ‘type’ string

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

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.ncbb.NcbbDockDesignProtocolCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::NcbbDockDesignProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator) → str¶: C++: protocols::ncbb::NcbbDockDesignProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::ncbb::NcbbDockDesignProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover¶

Bases: Mover

A simple method to mutate a pose fairly destructively, and barely recover

apply(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::ncbb::ResidueReplacementRebuildMover::apply(class core::pose::Pose &) –> void

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

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.ncbb.ResidueReplacementRebuildMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::ncbb::ResidueReplacementRebuildMover::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.ncbb.ResidueReplacementRebuildMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::ncbb::ResidueReplacementRebuildMover::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.ncbb.ResidueReplacementRebuildMover) → str¶: C++: protocols::ncbb::ResidueReplacementRebuildMover::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

make_new_pose(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose¶: Mover Methods ///

C++: protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(const class core::pose::Pose &) const –> class core::pose::Pose

static mover_name() → str¶: C++: protocols::ncbb::ResidueReplacementRebuildMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

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

C++: protocols::ncbb::ResidueReplacementRebuildMover::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::ncbb::ResidueReplacementRebuildMover::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

score_function(*args, **kwargs)¶

Overloaded function.

score_function(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::ncbb::ResidueReplacementRebuildMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

score_function(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::ncbb::ResidueReplacementRebuildMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_resi_chosen(*args, **kwargs)¶

Overloaded function.

set_resi_chosen(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, setting: int) -> None

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resi_chosen(const unsigned long) –> void

set_resi_chosen(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> int

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resi_chosen() const –> unsigned long

set_resi_len(*args, **kwargs)¶

Overloaded function.

set_resi_len(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, setting: int) -> None

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resi_len(const unsigned long) –> void

set_resi_len(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> int

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resi_len() const –> unsigned long

set_resname(*args, **kwargs)¶

Overloaded function.

set_resname(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, setting: str) -> None

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resname(const std::string &) –> void

set_resname(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> str

C++: protocols::ncbb::ResidueReplacementRebuildMover::set_resname() const –> std::string

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.

show(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> None
show(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::ncbb::ResidueReplacementRebuildMover::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.

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

Set the ‘type’ string

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

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.ncbb.ResidueReplacementRebuildMoverCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::ResidueReplacementRebuildMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator) → str¶: C++: protocols::ncbb::ResidueReplacementRebuildMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::ncbb::ResidueReplacementRebuildMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ncbb.SecStructFinder¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ncbb.SecStructFinder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::ncbb::SecStructFinder::apply(class core::pose::Pose &) –> void

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

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.ncbb.SecStructFinder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructFinder::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.ncbb.SecStructFinder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructFinder::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.ncbb.SecStructFinder) → str¶: C++: protocols::ncbb::SecStructFinder::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 name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ncbb.SecStructFinder, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::ncbb::SecStructFinder::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.

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

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

Set the ‘type’ string

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

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.ncbb.SecStructFinderCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructFinderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator) → str¶: C++: protocols::ncbb::SecStructFinderCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::ncbb::SecStructFinderCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover¶

Bases: Mover

add_dihedral_constraints_to_pose(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose, number_dihedral_sets: int, uniqs: pyrosetta.rosetta.utility.vector1_char) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(class core::pose::Pose &, unsigned long, class utility::vector1<char, class std::allocator<char> >) –> void

apply(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::apply(class core::pose::Pose &) –> void

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

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.ncbb.SecStructMinimizeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructMinimizeMover::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.ncbb.SecStructMinimizeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructMinimizeMover::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_alpha_beta_pattern(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover) → str¶: C++: protocols::ncbb::SecStructMinimizeMover::get_alpha_beta_pattern() –> std::string

get_constrain(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover) → bool¶: C++: protocols::ncbb::SecStructMinimizeMover::get_constrain() –> bool

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_dihedral_pattern(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover) → str¶: C++: protocols::ncbb::SecStructMinimizeMover::get_dihedral_pattern() –> std::string

get_dihedrals(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::ncbb::SecStructMinimizeMover::get_dihedrals() –> class utility::vector1<double, class std::allocator<double> >

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.ncbb.SecStructMinimizeMover) → str¶: C++: protocols::ncbb::SecStructMinimizeMover::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_scorefunction(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::ncbb::SecStructMinimizeMover::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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::ncbb::SecStructMinimizeMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::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::ncbb::SecStructMinimizeMover::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_alpha_beta_pattern(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, alpha_beta_pattern: str) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::set_alpha_beta_pattern(const std::string &) –> void

set_constrain(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, constrain: bool) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::set_constrain(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_dihedral_pattern(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, dihedral_pattern: str) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::set_dihedral_pattern(const std::string &) –> void

set_dihedrals(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, dihedrals: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::set_dihedrals(const class utility::vector1<double, class std::allocator<double> > &) –> 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_scorefunction(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::ncbb::SecStructMinimizeMover::set_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> 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.

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

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

Set the ‘type’ string

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

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.ncbb.SecStructMinimizeMoverCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::ncbb::SecStructMinimizeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator) → str¶: C++: protocols::ncbb::SecStructMinimizeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::ncbb::SecStructMinimizeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc¶

Bases: Multifunc

class for fitting a length of secondary structure keeping the same dihedrals

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool¶

Christophe added the following to allow premature end of minimization: If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None¶

Calculate function value derivatives

C++: protocols::ncbb::SecStructMinimizeMultiFunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dofs_to_vars(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, dofs: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_double¶

give short set of torsions from full dofs

C++: protocols::ncbb::SecStructMinimizeMultiFunc::dofs_to_vars(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

dump(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None¶

Error state reached – derivative does not match gradient

C++: protocols::ncbb::SecStructMinimizeMultiFunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

vars_to_dofs(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_double¶

give full dofs from short set of torsions

C++: protocols::ncbb::SecStructMinimizeMultiFunc::vars_to_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

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

pyrosetta.rosetta.protocols.ncbb.calculate_statistics(pose: pyrosetta.rosetta.core.pose.Pose, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Calculate various statistics, and add them to the current JD2 job

C++: protocols::ncbb::calculate_statistics(const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

pyrosetta.rosetta.protocols.ncbb.count_uniq_char(pattern: str, num: int, uniqs: pyrosetta.rosetta.utility.vector1_char) → None¶: C++: protocols::ncbb::count_uniq_char(std::string, unsigned long &, class utility::vector1<char, class std::allocator<char> > &) –> void

pyrosetta.rosetta.protocols.ncbb.final_design_min(pose: pyrosetta.rosetta.core.pose.Pose, score_fxn_: pyrosetta.rosetta.core.scoring.ScoreFunction, desn_tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶: C++: protocols::ncbb::final_design_min(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

pyrosetta.rosetta.protocols.ncbb.get_number_dihedrals(uniqs: pyrosetta.rosetta.utility.vector1_char, dihedral_pattern: str, alpha_beta_pattern: str) → int¶: C++: protocols::ncbb::get_number_dihedrals(class utility::vector1<char, class std::allocator<char> >, const std::string &, const std::string &) –> unsigned long

pyrosetta.rosetta.protocols.ncbb.give_dihedral_index(n: int, uniqs: pyrosetta.rosetta.utility.vector1_char, dihedral_pattern: str, alpha_beta_pattern: str) → int¶: C++: protocols::ncbb::give_dihedral_index(unsigned long, class utility::vector1<char, class std::allocator<char> >, std::string, std::string) –> unsigned long

pyrosetta.rosetta.protocols.ncbb.init_common_options(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, score_fxn_: pyrosetta.rosetta.core.scoring.ScoreFunction, mc_temp_: float, pert_mc_temp_: float, pert_dock_rot_mag_: float, pert_dock_trans_mag_: float, pert_pep_small_temp_: float, pert_pep_small_H_: float, pert_pep_small_L_: float, pert_pep_small_E_: float, pert_pep_shear_temp_: float, pert_pep_shear_H_: float, pert_pep_shear_L_: float, pert_pep_shear_E_: float, pert_pep_num_rep_: int, pert_num_: int, dock_design_loop_num_: int, no_design_: bool, final_design_min_: bool, use_soft_rep_: bool, mc_initial_pose_: bool, pymol_: bool, keep_history_: bool) → None¶: C++: protocols::ncbb::init_common_options(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, class std::shared_ptr<class core::scoring::ScoreFunction>, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, unsigned long &, unsigned long &, unsigned long &, bool &, bool &, bool &, bool &, bool &, bool &) –> void

pyrosetta.rosetta.protocols.ncbb.ncbb_design_main_loop(loop_num: int, pert_num: int, pose: pyrosetta.rosetta.core.pose.Pose, pert_trial: pyrosetta.rosetta.protocols.moves.TrialMover, designable_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, pep_start: int, pep_end: int, desn_ta_min: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶: C++: protocols::ncbb::ncbb_design_main_loop(unsigned long, unsigned long, class core::pose::Pose, class std::shared_ptr<class protocols::moves::TrialMover>, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, unsigned long, unsigned long, class std::shared_ptr<class protocols::minimization_packing::TaskAwareMinMover>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

pyrosetta.rosetta.protocols.ncbb.setup_filter_stats() → None¶: C++: protocols::ncbb::setup_filter_stats() –> void

pyrosetta.rosetta.protocols.ncbb.setup_pert_foldtree(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::ncbb::setup_pert_foldtree(class core::pose::Pose &) –> void