movers

Bindings for protocols::denovo_design::movers namespace

class pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Adds a segment to the structuredata

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::AddSegmentDataMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover

C++: protocols::denovo_design::movers::AddSegmentDataMover::operator=(const class protocols::denovo_design::movers::AddSegmentDataMover &) –> class protocols::denovo_design::movers::AddSegmentDataMover &

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.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMover) str

C++: protocols::denovo_design::movers::AddSegmentDataMover::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::denovo_design::movers::AddSegmentDataMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, 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::denovo_design::movers::AddSegmentDataMover::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::denovo_design::movers::AddSegmentDataMover::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_abego(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, abego: str) None

Sets the abego of the segment to be created

C++: protocols::denovo_design::movers::AddSegmentDataMover::set_abego(const std::string &) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

set_secstruct(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, secstruct: str) None

Sets the secondary structure of the segment to be created

C++: protocols::denovo_design::movers::AddSegmentDataMover::set_secstruct(const std::string &) –> void

set_segment_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, name: str) None

Sets the name of the segment which will be created

C++: protocols::denovo_design::movers::AddSegmentDataMover::set_segment_name(const std::string &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::AddSegmentDataMover::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.denovo_design.movers.AddSegmentDataMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator

C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::operator=(const class protocols::denovo_design::movers::AddSegmentDataMoverCreator &) –> class protocols::denovo_design::movers::AddSegmentDataMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator) str

C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::AddSegmentDataMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Aligns one residue onto another

add_target_selector(*args, **kwargs)

Overloaded function.

  1. add_target_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)

Clones the residue selector

C++: protocols::denovo_design::movers::AlignResiduesMover::add_target_selector(const class core::select::residue_selector::ResidueSelector &) –> void

  1. add_target_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)

Directly stores the ResidueSelectorCOP

C++: protocols::denovo_design::movers::AlignResiduesMover::add_target_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

add_template_selector(*args, **kwargs)

Overloaded function.

  1. add_template_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)

Clones the residue selector

C++: protocols::denovo_design::movers::AlignResiduesMover::add_template_selector(const class core::select::residue_selector::ResidueSelector &) –> void

  1. add_template_selector(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)

Directly stores the ResidueSelectorCOP

C++: protocols::denovo_design::movers::AlignResiduesMover::add_template_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::AlignResiduesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, : pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover

C++: protocols::denovo_design::movers::AlignResiduesMover::operator=(const class protocols::denovo_design::movers::AlignResiduesMover &) –> class protocols::denovo_design::movers::AlignResiduesMover &

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

clear_target_selectors(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) None

clears the list of target residue selectors

C++: protocols::denovo_design::movers::AlignResiduesMover::clear_target_selectors() –> void

clear_template_selectors(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) None

clears the list of template residue selectors

C++: protocols::denovo_design::movers::AlignResiduesMover::clear_template_selectors() –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMover) str

C++: protocols::denovo_design::movers::AlignResiduesMover::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::denovo_design::movers::AlignResiduesMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, 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::denovo_design::movers::AlignResiduesMover::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::denovo_design::movers::AlignResiduesMover::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_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, id: str) None

Sets the ID of this mover

C++: protocols::denovo_design::movers::AlignResiduesMover::set_id(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.denovo_design.movers.AlignResiduesMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::AlignResiduesMover::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.denovo_design.movers.AlignResiduesMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator

C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::operator=(const class protocols::denovo_design::movers::AlignResiduesMoverCreator &) –> class protocols::denovo_design::movers::AlignResiduesMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator) str

C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::AlignResiduesMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator

C++: protocols::denovo_design::movers::BridgeChainsCreator::operator=(const class protocols::denovo_design::movers::BridgeChainsCreator &) –> class protocols::denovo_design::movers::BridgeChainsCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::BridgeChainsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator) str

C++: protocols::denovo_design::movers::BridgeChainsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::BridgeChainsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Creates a bridge connection between two chains using remodel

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::BridgeChainsMover::apply(class core::pose::Pose &) –> void

architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect

C++: protocols::denovo_design::movers::BridgeChainsMover::architect() const –> const class protocols::denovo_design::connection::ConnectionArchitect &

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover

C++: protocols::denovo_design::movers::BridgeChainsMover::operator=(const class protocols::denovo_design::movers::BridgeChainsMover &) –> class protocols::denovo_design::movers::BridgeChainsMover &

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.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::BridgeChainsMover::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>

dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) bool

C++: protocols::denovo_design::movers::BridgeChainsMover::dry_run() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::BridgeChainsMover::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.denovo_design.movers.BridgeChainsMover) str

C++: protocols::denovo_design::movers::BridgeChainsMover::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::denovo_design::movers::BridgeChainsMover::mover_name() –> std::string

static name() str

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

overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) int

C++: protocols::denovo_design::movers::BridgeChainsMover::overlap() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, 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::denovo_design::movers::BridgeChainsMover::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::denovo_design::movers::BridgeChainsMover::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

scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::denovo_design::movers::BridgeChainsMover::scorefxn() const –> 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_dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, dry_run: bool) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_dry_run(const bool) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, my_id: str) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_id(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_iterations(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, iterations: int) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_iterations(const unsigned long) –> void

set_motifs(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, motifs_str: str, cut_resis_str: str) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_motifs(const std::string &, const std::string &) –> void

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

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

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

set_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, overlap_val: int) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_overlap(const unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

set_segment1_ids(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, segments: str) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_segment1_ids(const std::string &) –> void

set_segment2_ids(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, segments: str) None

C++: protocols::denovo_design::movers::BridgeChainsMover::set_segment2_ids(const std::string &) –> void

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

Set the ‘type’ string

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

static setup_attlist_for_derived_classes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

C++: protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::BridgeChainsMover::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.denovo_design.movers.BridgeChainsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator

C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::operator=(const class protocols::denovo_design::movers::BridgeChainsMoverCreator &) –> class protocols::denovo_design::movers::BridgeChainsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator) str

C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::BridgeChainsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover

Bases: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover

add_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt

C++: protocols::denovo_design::movers::FoldArchitectMover::add_filter(const class protocols::filters::Filter &) –> void

add_postfold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Adds a mover to the list of postfold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover(const class protocols::moves::Mover &) –> void

add_prefold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Adds a mover to the list of prefold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover(const class protocols::moves::Mover &) –> void

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::FoldArchitectMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover, : pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover) pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMover::operator=(const class protocols::denovo_design::movers::BuildDeNovoBackboneMover &) –> class protocols::denovo_design::movers::BuildDeNovoBackboneMover &

clear_filters(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of filters used to indicate whether a given folding attempt is successful

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_filters() –> void

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

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

clear_info is called by jd2 before calling apply

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

clear_postfold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of postfold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers() –> void

clear_prefold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of prefold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers() –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.BuildDeNovoBackboneMover) str

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMover::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

id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) str

C++: protocols::denovo_design::movers::FoldArchitectMover::id() const –> 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::denovo_design::movers::BuildDeNovoBackboneMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, 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::denovo_design::movers::FoldArchitectMover::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::denovo_design::movers::BuildDeNovoBackboneMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static provide_xml_schema_with_name(xsd: utility::tag::XMLSchemaDefinition, mover_name: str) None

C++: protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name(class utility::tag::XMLSchemaDefinition &, const std::string &) –> 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_architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, architect: pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect) None

Sets the architect that will be used to build blueprints dynamically

C++: protocols::denovo_design::movers::FoldArchitectMover::set_architect(const class protocols::denovo_design::architects::DeNovoArchitect &) –> void

set_build_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, overlap_val: int) None

Sets the number of residues of overlap to use between build phases

C++: protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap(const unsigned long) –> void

set_builder(*args, **kwargs)

Overloaded function.

  1. set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None

Sets the pose builder that will be used to create the extended-chain pose

Clones the provided PoseBuilder

C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(const class protocols::denovo_design::components::PoseBuilder &) –> void

  1. set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None

Sets the pose builder that will be used to create the extended-chain pose

Uses/stores the provided PoseBuilder pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>) –> 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_debug(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, debug: bool) None

The debug value of the poseBuilder will be set based on this

C++: protocols::denovo_design::movers::FoldArchitectMover::set_debug(const bool) –> void

set_dump_pdbs(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, dump: bool) None

If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted

C++: protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs(const bool) –> void

set_folder(*args, **kwargs)

Overloaded function.

  1. set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None

Sets the pose folder that will be used to sample conformations.

Clones the PoseFolder

C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(const class protocols::denovo_design::components::PoseFolder &) –> void

  1. set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None

Sets the pose folder that will be used to sample conformations

Uses the provided PoseFolder pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, id_value: str) None

Sets the ID of this mover

C++: protocols::denovo_design::movers::FoldArchitectMover::set_id(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_iterations_per_phase(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, niter: int) None

Sets the number of folding attempts for each build phase

C++: protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase(const unsigned long) –> 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_perturber(*args, **kwargs)

Overloaded function.

  1. set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None

Sets the perturber that will be used to change the plans of the architects

Clones the provided Perturber

C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(const class protocols::denovo_design::components::StructureDataPerturber &) –> void

  1. set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None

Sets the perturber that will be used to change the plans of the architects

Uses/stores the provided Perturber pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>) –> void

set_score_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false

C++: protocols::denovo_design::movers::FoldArchitectMover::set_score_filter(const class protocols::filters::Filter &) –> void

set_start_segments(*args, **kwargs)

Overloaded function.

  1. set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None

sets names of segments to be included in the starting build phase

Comma-separated string containing segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const std::string &) –> void

  1. set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None

sets names of segments to be included in the starting build phase

Set of segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

set_stop_segments(*args, **kwargs)

Overloaded function.

  1. set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None

sets names of segments to be included in the final build phase

Comma-separated string containing segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const std::string &) –> void

  1. set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None

sets names of segments to be included in the final build phase

Set of segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

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

Set the ‘type’ string

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

setup_from_xml_file(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_file: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses an XML file and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file(const std::string &, class basic::datacache::DataMap &) –> void

setup_from_xml_string(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_string: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses an XML string and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string(const std::string &, class basic::datacache::DataMap &) –> void

setup_from_xml_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses a Tag object and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> 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.denovo_design.movers.BuildDeNovoBackboneMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::operator=(const class protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator &) –> class protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator) str

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.CutAndJump

Bases: pybind11_builtins.pybind11_object

property cutpoint
property jump
class pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

declares covalent bond

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, : pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::operator=(const class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover &) –> class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover &

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.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMover) str

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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::denovo_design::movers::DeclareStructureDataCovalentBondMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, 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::denovo_design::movers::DeclareStructureDataCovalentBondMover::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::denovo_design::movers::DeclareStructureDataCovalentBondMover::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_atom1(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, atom: str) None

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::set_atom1(const std::string &) –> void

set_atom2(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, atom: str) None

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::set_atom2(const std::string &) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover, output: pyrosetta.rosetta.std.ostream) -> None

Show the contents of the Mover

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::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.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::operator=(const class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator &) –> class protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator) str

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed

Bases: pyrosetta.rosetta.utility.excn.Exception

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

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

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed, : pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed

C++: protocols::denovo_design::movers::EXCN_FilterFailed::operator=(const class protocols::denovo_design::movers::EXCN_FilterFailed &) –> class protocols::denovo_design::movers::EXCN_FilterFailed &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

filter_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) str

C++: protocols::denovo_design::movers::EXCN_FilterFailed::filter_name() const –> const std::string &

filter_num(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed) int

C++: protocols::denovo_design::movers::EXCN_FilterFailed::filter_num() const –> unsigned long

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold

Bases: pyrosetta.rosetta.utility.excn.Exception

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

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

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold, : pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold) pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold

C++: protocols::denovo_design::movers::EXCN_NothingToFold::operator=(const class protocols::denovo_design::movers::EXCN_NothingToFold &) –> class protocols::denovo_design::movers::EXCN_NothingToFold &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::ExtendChainMover::apply(class core::pose::Pose &) –> void

architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect

C++: protocols::denovo_design::movers::ExtendChainMover::architect() const –> const class protocols::denovo_design::architects::DeNovoArchitect &

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, : pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover

C++: protocols::denovo_design::movers::ExtendChainMover::operator=(const class protocols::denovo_design::movers::ExtendChainMover &) –> class protocols::denovo_design::movers::ExtendChainMover &

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.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::ExtendChainMover::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.denovo_design.movers.ExtendChainMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::ExtendChainMover::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.denovo_design.movers.ExtendChainMover) str

C++: protocols::denovo_design::movers::ExtendChainMover::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::denovo_design::movers::ExtendChainMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the ExtendChainTags

C++: protocols::denovo_design::movers::ExtendChainMover::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::denovo_design::movers::ExtendChainMover::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_chain(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, chain: int) None

C++: protocols::denovo_design::movers::ExtendChainMover::set_chain(const unsigned long) –> 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_dry_run(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, dry_run: bool) None

C++: protocols::denovo_design::movers::ExtendChainMover::set_dry_run(const bool) –> 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_prepend(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, prepend: bool) None

C++: protocols::denovo_design::movers::ExtendChainMover::set_prepend(const bool) –> void

set_segment_names(*args, **kwargs)

Overloaded function.

  1. set_segment_names(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, segment_names_str: str) -> None

C++: protocols::denovo_design::movers::ExtendChainMover::set_segment_names(const std::string &) –> void

  1. set_segment_names(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover, seg_names: pyrosetta.rosetta.std.vector_std_string) -> None

C++: protocols::denovo_design::movers::ExtendChainMover::set_segment_names(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator

C++: protocols::denovo_design::movers::ExtendChainMoverCreator::operator=(const class protocols::denovo_design::movers::ExtendChainMoverCreator &) –> class protocols::denovo_design::movers::ExtendChainMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::ExtendChainMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator) str

C++: protocols::denovo_design::movers::ExtendChainMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::ExtendChainMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign

Bases: pyrosetta.rosetta.protocols.relax.FastRelax

add_constraint_generator(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, generator: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) None

Adds a constraint generator. Currently only used if ramp_down_constraints is set. If constraint generators are present, each time the constraint weights are changed, the constraint generators will be used to selectively remove constraint-generated constraints and add new ones

C++: protocols::denovo_design::movers::FastDesign::add_constraint_generator(class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator>) –> void

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the FastDesign. Overloaded apply function from mover base class.

C++: protocols::denovo_design::movers::FastDesign::apply(class core::pose::Pose &) –> void

apply_disulfides(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::relax::RelaxProtocolBase::apply_disulfides(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, : pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign

C++: protocols::denovo_design::movers::FastDesign::operator=(const class protocols::denovo_design::movers::FastDesign &) –> class protocols::denovo_design::movers::FastDesign &

batch_apply(*args, **kwargs)

Overloaded function.

  1. batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t) -> None

  2. batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, input_csts: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None

  3. batch_apply(self: pyrosetta.rosetta.protocols.relax.FastRelax, input_structs: pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, input_csts: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, decay_rate: float) -> None

Batch Relax, a new even faster way to relax entire batches of structures.

C++: protocols::relax::FastRelax::batch_apply(class std::vector<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet>, double) –> void

cartesian(*args, **kwargs)

Overloaded function.

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::cartesian() const –> bool

  1. cartesian(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, newval: bool) -> None

Use cartesian (minimization step)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.

C++: protocols::relax::RelaxProtocolBase::cartesian(bool) –> void

clear_constraint_generators(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) None

Clears the list of constraint generators

C++: protocols::denovo_design::movers::FastDesign::clear_constraint_generators() –> void

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.moves.Mover

return a copy of this class in an owning pointer

C++: protocols::denovo_design::movers::FastDesign::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

static complex_type_generator_for_fast_relax(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::relax::FastRelax::complex_type_generator_for_fast_relax(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

constrain_coords(*args, **kwargs)

Overloaded function.

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_coords() const –> bool

  1. constrain_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_coords(bool) –> void

constrain_relax_segments(*args, **kwargs)

Overloaded function.

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments() const –> bool

  1. constrain_relax_segments(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_segments: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_segments(bool) –> void

constrain_relax_to_native_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords() const –> bool

  1. constrain_relax_to_native_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_native_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords(bool) –> void

constrain_relax_to_start_coords(*args, **kwargs)

Overloaded function.

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords() const –> bool

  1. constrain_relax_to_start_coords(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, constrain_relax_to_start_coords: bool) -> None

C++: protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords(bool) –> void

coord_constrain_sidechains(*args, **kwargs)

Overloaded function.

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains() const –> bool

  1. coord_constrain_sidechains(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, coord_constrain_sidechains: bool) -> None

C++: protocols::relax::RelaxProtocolBase::coord_constrain_sidechains(bool) –> void

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>

default_repeats(self: pyrosetta.rosetta.protocols.relax.FastRelax) int

Return the number of repeats

C++: protocols::relax::FastRelax::default_repeats() const –> unsigned long

dry_run(*args, **kwargs)

Overloaded function.

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::dry_run() const –> bool

  1. dry_run(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, setting: bool) -> None

C++: protocols::relax::RelaxProtocolBase::dry_run(bool) –> void

dualspace(*args, **kwargs)

Overloaded function.

  1. dualspace(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) -> None

Use the dualspace (Dihedral + Cartesian) relax protocol (Default false)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Recommended to set minimize_bond_angles to true as well. Requires scorefunction setup for non-ideal minimization.

C++: protocols::relax::FastRelax::dualspace(bool) –> void

  1. dualspace(self: pyrosetta.rosetta.protocols.relax.FastRelax) -> bool

C++: protocols::relax::FastRelax::dualspace() –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) pyrosetta.rosetta.protocols.moves.Mover

return a fresh instance of this class in an owning pointer

C++: protocols::denovo_design::movers::FastDesign::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_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::relax::RelaxProtocolBase::get_movemap() –> class std::shared_ptr<class core::kinematics::MoveMap>

get_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) str

C++: protocols::denovo_design::movers::FastDesign::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_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::relax::RelaxProtocolBase::get_scorefxn() const –> const class std::shared_ptr<const 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_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::relax::RelaxProtocolBase::get_task_factory() const –> const class std::shared_ptr<class core::pack::task::TaskFactory> &

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

max_iter(*args, **kwargs)

Overloaded function.

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> int

C++: protocols::relax::RelaxProtocolBase::max_iter() const –> unsigned long

  1. max_iter(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, max_iter: int) -> None

C++: protocols::relax::RelaxProtocolBase::max_iter(unsigned long) –> void

min_type(*args, **kwargs)

Overloaded function.

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> str

C++: protocols::relax::RelaxProtocolBase::min_type() const –> std::string

  1. min_type(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, min_type: str) -> None

C++: protocols::relax::RelaxProtocolBase::min_type(std::string) –> void

minimize_bond_angles(*args, **kwargs)

Overloaded function.

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles() const –> bool

  1. minimize_bond_angles(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_angles: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_angles(bool) –> void

minimize_bond_lengths(*args, **kwargs)

Overloaded function.

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths() const –> bool

  1. minimize_bond_lengths(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, minimize_bond_lengths: bool) -> None

C++: protocols::relax::RelaxProtocolBase::minimize_bond_lengths(bool) –> void

movemap_disables_packing_of_fixed_chi_positions(self: pyrosetta.rosetta.protocols.relax.FastRelax) bool
Get whether the MoveMap can automatically disable packing of positions

where sidechain minimization is prohibited. Default false.

C++: protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions() const –> bool

static mover_name() str

C++: protocols::denovo_design::movers::FastDesign::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the FastDesignTags

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

provide_citation_info(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::denovo_design::movers::FastDesign::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::denovo_design::movers::FastDesign::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

ramp_down_constraints(*args, **kwargs)

Overloaded function.

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) -> bool

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints() const –> bool

  1. ramp_down_constraints(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, ramp_down_constraints: bool) -> None

C++: protocols::relax::RelaxProtocolBase::ramp_down_constraints(bool) –> void

static register_options() None

C++: protocols::relax::RelaxProtocolBase::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_clear_designable_residues(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign, clear_res: bool) None

If set, residues that are designable will be mutated to alanine before design

C++: protocols::denovo_design::movers::FastDesign::set_clear_designable_residues(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_default_coordinate_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None

C++: protocols::relax::RelaxProtocolBase::set_default_coordinate_settings() –> void

set_default_minimization_settings(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None

C++: protocols::relax::RelaxProtocolBase::set_default_minimization_settings() –> void

set_default_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None

C++: protocols::relax::RelaxProtocolBase::set_default_movemap() –> void

set_defaults(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase) None

C++: protocols::relax::RelaxProtocolBase::set_defaults() –> void

set_enable_design(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) None
sets the enable_design option.

Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.)

C++: protocols::relax::FastRelax::set_enable_design(const bool) –> void

set_force_nonideal(self: pyrosetta.rosetta.protocols.relax.FastRelax, val: bool) None

Force us to batchrelax with nonideal geometry (using additional memory)

C++: protocols::relax::FastRelax::set_force_nonideal(bool) –> 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_movemap(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::relax::RelaxProtocolBase::set_movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

set_movemap_disables_packing_of_fixed_chi_positions(self: pyrosetta.rosetta.protocols.relax.FastRelax, setting: bool) None
Set whether the MoveMap can automatically disable packing of positions

where sidechain minimization is prohibited. Default false.

C++: protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(const bool) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, mm_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None

C++: protocols::relax::RelaxProtocolBase::set_movemap_factory(class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::relax::RelaxProtocolBase::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_script_from_lines(self: pyrosetta.rosetta.protocols.relax.FastRelax, filelines: pyrosetta.rosetta.std.vector_std_string) None

replace schedule by providing lines of commands explicitly

C++: protocols::relax::FastRelax::set_script_from_lines(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

set_script_to_batchrelax_default(*args, **kwargs)

Overloaded function.

  1. set_script_to_batchrelax_default(self: pyrosetta.rosetta.protocols.relax.FastRelax) -> None

  2. set_script_to_batchrelax_default(self: pyrosetta.rosetta.protocols.relax.FastRelax, standard_repeats: int) -> None

Override the stored script with the default script for batchrelax

Ignores ‘-default_repeat’ value

C++: protocols::relax::FastRelax::set_script_to_batchrelax_default(unsigned long) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.relax.RelaxProtocolBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::relax::RelaxProtocolBase::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

set_to_default(self: pyrosetta.rosetta.protocols.relax.FastRelax) None

Initializes class using option system. This is called by the constructors

C++: protocols::relax::FastRelax::set_to_default() –> void

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

Set the ‘type’ string

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

set_up_default_task_factory(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign) None

Create the default task factory. Must be called before design can occur.

C++: protocols::denovo_design::movers::FastDesign::set_up_default_task_factory() –> 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.denovo_design.movers.FastDesignCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator

C++: protocols::denovo_design::movers::FastDesignCreator::operator=(const class protocols::denovo_design::movers::FastDesignCreator &) –> class protocols::denovo_design::movers::FastDesignCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::FastDesignCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator) str

C++: protocols::denovo_design::movers::FastDesignCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::FastDesignCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover that builds and folds a structure via fragment insertion

add_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt

C++: protocols::denovo_design::movers::FoldArchitectMover::add_filter(const class protocols::filters::Filter &) –> void

add_postfold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Adds a mover to the list of postfold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover(const class protocols::moves::Mover &) –> void

add_prefold_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Adds a mover to the list of prefold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover(const class protocols::moves::Mover &) –> void

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::FoldArchitectMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover

C++: protocols::denovo_design::movers::FoldArchitectMover::operator=(const class protocols::denovo_design::movers::FoldArchitectMover &) –> class protocols::denovo_design::movers::FoldArchitectMover &

clear_filters(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of filters used to indicate whether a given folding attempt is successful

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_filters() –> void

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

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

clear_info is called by jd2 before calling apply

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

clear_postfold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of postfold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers() –> void

clear_prefold_movers(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) None

Clears the list of prefold movers

C++: protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers() –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldArchitectMover::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.denovo_design.movers.FoldArchitectMover) str

C++: protocols::denovo_design::movers::FoldArchitectMover::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

id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover) str

C++: protocols::denovo_design::movers::FoldArchitectMover::id() const –> 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::denovo_design::movers::FoldArchitectMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, 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::denovo_design::movers::FoldArchitectMover::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::denovo_design::movers::FoldArchitectMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static provide_xml_schema_with_name(xsd: utility::tag::XMLSchemaDefinition, mover_name: str) None

C++: protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name(class utility::tag::XMLSchemaDefinition &, const std::string &) –> 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_architect(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, architect: pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect) None

Sets the architect that will be used to build blueprints dynamically

C++: protocols::denovo_design::movers::FoldArchitectMover::set_architect(const class protocols::denovo_design::architects::DeNovoArchitect &) –> void

set_build_overlap(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, overlap_val: int) None

Sets the number of residues of overlap to use between build phases

C++: protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap(const unsigned long) –> void

set_builder(*args, **kwargs)

Overloaded function.

  1. set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None

Sets the pose builder that will be used to create the extended-chain pose

Clones the provided PoseBuilder

C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(const class protocols::denovo_design::components::PoseBuilder &) –> void

  1. set_builder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, builder: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) -> None

Sets the pose builder that will be used to create the extended-chain pose

Uses/stores the provided PoseBuilder pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_builder(class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>) –> 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_debug(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, debug: bool) None

The debug value of the poseBuilder will be set based on this

C++: protocols::denovo_design::movers::FoldArchitectMover::set_debug(const bool) –> void

set_dump_pdbs(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, dump: bool) None

If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted

C++: protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs(const bool) –> void

set_folder(*args, **kwargs)

Overloaded function.

  1. set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None

Sets the pose folder that will be used to sample conformations.

Clones the PoseFolder

C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(const class protocols::denovo_design::components::PoseFolder &) –> void

  1. set_folder(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, folder: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> None

Sets the pose folder that will be used to sample conformations

Uses the provided PoseFolder pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_folder(class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, id_value: str) None

Sets the ID of this mover

C++: protocols::denovo_design::movers::FoldArchitectMover::set_id(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_iterations_per_phase(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, niter: int) None

Sets the number of folding attempts for each build phase

C++: protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase(const unsigned long) –> 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_perturber(*args, **kwargs)

Overloaded function.

  1. set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None

Sets the perturber that will be used to change the plans of the architects

Clones the provided Perturber

C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(const class protocols::denovo_design::components::StructureDataPerturber &) –> void

  1. set_perturber(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) -> None

Sets the perturber that will be used to change the plans of the architects

Uses/stores the provided Perturber pointer directly

C++: protocols::denovo_design::movers::FoldArchitectMover::set_perturber(class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>) –> void

set_score_filter(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false

C++: protocols::denovo_design::movers::FoldArchitectMover::set_score_filter(const class protocols::filters::Filter &) –> void

set_start_segments(*args, **kwargs)

Overloaded function.

  1. set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None

sets names of segments to be included in the starting build phase

Comma-separated string containing segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const std::string &) –> void

  1. set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None

sets names of segments to be included in the starting build phase

Set of segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_start_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

set_stop_segments(*args, **kwargs)

Overloaded function.

  1. set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments_csv: str) -> None

sets names of segments to be included in the final build phase

Comma-separated string containing segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const std::string &) –> void

  1. set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, segments: pyrosetta.rosetta.std.set_std_string_t) -> None

sets names of segments to be included in the final build phase

Set of segment names

C++: protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

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

Set the ‘type’ string

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

setup_from_xml_file(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_file: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses an XML file and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file(const std::string &, class basic::datacache::DataMap &) –> void

setup_from_xml_string(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, xml_string: str, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses an XML string and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string(const std::string &, class basic::datacache::DataMap &) –> void

setup_from_xml_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Reads/parses a Tag object and uses it to set up the mover

C++: protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> 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.denovo_design.movers.FoldArchitectMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator

C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::operator=(const class protocols::denovo_design::movers::FoldArchitectMoverCreator &) –> class protocols::denovo_design::movers::FoldArchitectMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator) str

C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::FoldArchitectMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Creates and sets a new fold tree for the pose by traversing a FoldGraph

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::operator=(const class protocols::denovo_design::movers::FoldTreeFromFoldGraphMover &) –> class protocols::denovo_design::movers::FoldTreeFromFoldGraphMover &

static class_name() str

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::class_name() –> std::string

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover) str

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMover, 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::denovo_design::movers::FoldTreeFromFoldGraphMover::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_roots(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, roots: pyrosetta.rosetta.std.vector_std_string) None

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::set_roots(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::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.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::operator=(const class protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator &) –> class protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator) str

C++: protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator::keyname() const –> 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.denovo_design.movers.MakeAsymmetricStructureDataMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Converts a StructureData for a symmetric pose into an asymmetric representation

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::operator=(const class protocols::denovo_design::movers::MakeAsymmetricStructureDataMover &) –> class protocols::denovo_design::movers::MakeAsymmetricStructureDataMover &

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.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) str

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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::denovo_design::movers::MakeAsymmetricStructureDataMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, 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::denovo_design::movers::MakeAsymmetricStructureDataMover::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::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::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.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::operator=(const class protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator &) –> class protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator) str

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand, : pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand) pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand

C++: protocols::denovo_design::movers::RelaxScriptCommand::operator=(const struct protocols::denovo_design::movers::RelaxScriptCommand &) –> struct protocols::denovo_design::movers::RelaxScriptCommand &

property command
property nparams
property param1
property param2
property param3
property param4
class pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Rotates a segment in the pose

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::denovo_design::movers::RotateSegmentMover::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, random: float) -> None

C++: protocols::denovo_design::movers::RotateSegmentMover::apply(class core::pose::Pose &, const double) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, : pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover

C++: protocols::denovo_design::movers::RotateSegmentMover::operator=(const class protocols::denovo_design::movers::RotateSegmentMover &) –> class protocols::denovo_design::movers::RotateSegmentMover &

static class_name() str

C++: protocols::denovo_design::movers::RotateSegmentMover::class_name() –> std::string

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover) str

C++: protocols::denovo_design::movers::RotateSegmentMover::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.denovo_design.movers.RotateSegmentMover, 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::denovo_design::movers::RotateSegmentMover::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_rotation_range(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover, start: float, stop: float) None

C++: protocols::denovo_design::movers::RotateSegmentMover::set_rotation_range(const double, const double) –> 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.denovo_design.movers.RotateSegmentMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator

C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::operator=(const class protocols::denovo_design::movers::RotateSegmentMoverCreator &) –> class protocols::denovo_design::movers::RotateSegmentMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator) str

C++: protocols::denovo_design::movers::RotateSegmentMoverCreator::keyname() const –> 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.denovo_design.movers.RotationRange

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange, : pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange) pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange

C++: protocols::denovo_design::movers::RotationRange::operator=(const class protocols::denovo_design::movers::RotationRange &) –> class protocols::denovo_design::movers::RotationRange &

property start
property stop
class pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Creates a sealed foldtree, and removes all cutpoints from the pose

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::SealFoldTreeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover

C++: protocols::denovo_design::movers::SealFoldTreeMover::operator=(const class protocols::denovo_design::movers::SealFoldTreeMover &) –> class protocols::denovo_design::movers::SealFoldTreeMover &

static class_name() str

C++: protocols::denovo_design::movers::SealFoldTreeMover::class_name() –> std::string

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) str

C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover, 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::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::SealFoldTreeMover::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.denovo_design.movers.SealFoldTreeMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator

C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::operator=(const class protocols::denovo_design::movers::SealFoldTreeMoverCreator &) –> class protocols::denovo_design::movers::SealFoldTreeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator) str

C++: protocols::denovo_design::movers::SealFoldTreeMoverCreator::keyname() const –> 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.denovo_design.movers.SetPoseSecstructFromStructureDataMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover) pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover

C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::operator=(const class protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover &) –> class protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover &

static class_name() str

C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::class_name() –> const std::string

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover) str

C++: protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::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.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

  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.denovo_design.movers.SetResidueAliasMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Sets a residue alias in the StructureData

apply(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::movers::SetResidueAliasMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, : pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover

C++: protocols::denovo_design::movers::SetResidueAliasMover::operator=(const class protocols::denovo_design::movers::SetResidueAliasMover &) –> class protocols::denovo_design::movers::SetResidueAliasMover &

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.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMover) str

C++: protocols::denovo_design::movers::SetResidueAliasMover::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::denovo_design::movers::SetResidueAliasMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, 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::denovo_design::movers::SetResidueAliasMover::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::denovo_design::movers::SetResidueAliasMover::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_alias_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, alias: str) None

Sets the name of the alias

C++: protocols::denovo_design::movers::SetResidueAliasMover::set_alias_name(const std::string &) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

set_resid(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, resid: int) None

Sets the residue within the segment to which the alias refers

C++: protocols::denovo_design::movers::SetResidueAliasMover::set_resid(const unsigned long) –> void

set_segment_name(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, segment: str) None

Sets the name of the segment that contains the residue to which the alias refers

C++: protocols::denovo_design::movers::SetResidueAliasMover::set_segment_name(const std::string &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::denovo_design::movers::SetResidueAliasMover::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.denovo_design.movers.SetResidueAliasMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator

C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::operator=(const class protocols::denovo_design::movers::SetResidueAliasMoverCreator &) –> class protocols::denovo_design::movers::SetResidueAliasMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator) str

C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::movers::SetResidueAliasMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.denovo_design.movers.add_overlap_to_loops(loops: pyrosetta.rosetta.protocols.loops.Loops, overlap: int, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.select.residue_selector.ResidueVector

goes through loops and adds overlapping residues

C++: protocols::denovo_design::movers::add_overlap_to_loops(class protocols::loops::Loops &, const unsigned long, const class core::pose::Pose &) –> class core::select::residue_selector::ResidueVector

pyrosetta.rosetta.protocols.denovo_design.movers.calc_dihedral(p1: pyrosetta.rosetta.numeric.xyzVector_double_t, p2: pyrosetta.rosetta.numeric.xyzVector_double_t, p3: pyrosetta.rosetta.numeric.xyzVector_double_t, p4: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: protocols::denovo_design::movers::calc_dihedral(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double