ncbb

Bindings for protocols::ncbb namespace

class pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

static mover_name() str

C++: protocols::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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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.

  1. 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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

  1. show(self: pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover) -> None

  2. 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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

static 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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

static mover_name() str

C++: protocols::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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.core.optimization.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