calc_taskop_movers

Bindings for protocols::calc_taskop_movers namespace

class pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed

apply(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::calc_taskop_movers::ConsensusDesignMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, : pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover) pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover

C++: protocols::calc_taskop_movers::ConsensusDesignMover::operator=(const class protocols::calc_taskop_movers::ConsensusDesignMover &) –> class protocols::calc_taskop_movers::ConsensusDesignMover &

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.calc_taskop_movers.ConsensusDesignMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::calc_taskop_movers::ConsensusDesignMover::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>

create_consensus_design_task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(const class core::pose::Pose &) –> class std::shared_ptr<const class core::pack::task::PackerTask>

create_sequence_profile_constraints(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::calc_taskop_movers::ConsensusDesignMover::create_sequence_profile_constraints(const class core::pose::Pose &, const class core::pack::task::PackerTask &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

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

C++: protocols::calc_taskop_movers::ConsensusDesignMover::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.calc_taskop_movers.ConsensusDesignMover) str

C++: protocols::calc_taskop_movers::ConsensusDesignMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::calc_taskop_movers::ConsensusDesignMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::calc_taskop_movers::ConsensusDesignMover::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::calc_taskop_movers::ConsensusDesignMover::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_invert_task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, setting: bool) None

C++: protocols::calc_taskop_movers::ConsensusDesignMover::set_invert_task(bool) –> void

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

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

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

set_sasa_cutoff(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, cutoff: float) None

C++: protocols::calc_taskop_movers::ConsensusDesignMover::set_sasa_cutoff(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

set_use_seqprof_constraints(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover, setting: bool) None

C++: protocols::calc_taskop_movers::ConsensusDesignMover::set_use_seqprof_constraints(bool) –> void

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator, : pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator) pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator

C++: protocols::calc_taskop_movers::ConsensusDesignMoverCreator::operator=(const class protocols::calc_taskop_movers::ConsensusDesignMoverCreator &) –> class protocols::calc_taskop_movers::ConsensusDesignMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator) str

C++: protocols::calc_taskop_movers::ConsensusDesignMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Simple mover to Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif.

Simply calls the packer using the operation, optionally packing neighbor residues as it does so. If you need something more complex, use the SequenceMotifTaskOperation directly.

MOTIF:

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.

  • An X indicates it can be anything, and that we are designing here.

  • An AA Letter, like V, indicates that that position will be designed to a V.

  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.

  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine

  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.

  • RESFILE commands are accepted as well. FOr example [POLAR] is totally cool. Separate these by commas.

EXAMPLE:

Glycosylation N-Linked motif design: N[^P][ST]

apply(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, : pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover) pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::operator=(const class protocols::calc_taskop_movers::CreateSequenceMotifMover &) –> class protocols::calc_taskop_movers::CreateSequenceMotifMover &

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.calc_taskop_movers.CreateSequenceMotifMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::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.calc_taskop_movers.CreateSequenceMotifMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::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.calc_taskop_movers.CreateSequenceMotifMover) str

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, 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::calc_taskop_movers::CreateSequenceMotifMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

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

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::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_design_neighbors(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, design_neighbors: bool) None

Should we design neighbors? Default False.

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_design_neighbors(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_motif(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, motif: str) None

Set a string that tells this operation how to design.

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.

  • An X indicates it can be anything, and that we are designing here.

  • An AA Letter, like V, indicates that that position will be designed to a V.

  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.

  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine

  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.

  • RESFILE commands are accepted as well. A % is required in front of them. For example [%POLAR] is totally cool. These are the same as in a resfile line.

EXAMPLE:

Glycosylation N-Linked motif design: N[^P][ST]

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_motif(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_neighbor_distance(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, neighbor_distance: float) None
Set the distance for any neighbor packing set.

Default is 6A

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_neighbor_distance(double) –> void

set_pack_neighbors(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, pack_neighbors: bool) None

Should we pack neighbors? Default True.

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_pack_neighbors(bool) –> void

set_pack_rounds(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, pack_rounds: int) None

Set the number of packing/design rounds. Default is 5!

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_pack_rounds(unsigned long) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector where each position returned from the selector is a place in which we create the motif.

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

set_score_function(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::set_score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover) -> None

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

C++: protocols::calc_taskop_movers::CreateSequenceMotifMover::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.calc_taskop_movers.CreateSequenceMotifMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator, : pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator) pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator

C++: protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator::operator=(const class protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator &) –> class protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator) str

C++: protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a pure virtual base class for movers which redesign and repack the interface

apply(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, : pyrosetta.rosetta.core.pose.Pose) None

a dummy apply so that instantiation of this baseclass would be possible.

C++: protocols::calc_taskop_movers::DesignRepackMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, : pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover

C++: protocols::calc_taskop_movers::DesignRepackMover::operator=(const class protocols::calc_taskop_movers::DesignRepackMover &) –> class protocols::calc_taskop_movers::DesignRepackMover &

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_task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) None
after fiddling with a task from outside this mover, clear it, or else, on the next iteration through

the mover the changes will be remembered

C++: protocols::calc_taskop_movers::DesignRepackMover::clear_task() –> void

clear_task_factory(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) None

C++: protocols::calc_taskop_movers::DesignRepackMover::clear_task_factory() –> void

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

Return a clone of the Mover object.

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

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

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

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, des: bool) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::design(const bool) –> void

  1. design(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> bool

C++: protocols::calc_taskop_movers::DesignRepackMover::design() const –> bool

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.calc_taskop_movers.DesignRepackMover) str

C++: protocols::calc_taskop_movers::DesignRepackMover::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

static get_xsd_complex_type() utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

non-const accessor

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

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

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

min_bb(*args, **kwargs)

Overloaded function.

  1. min_bb(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, min_bb: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::min_bb(class std::shared_ptr<class core::select::residue_selector::ResidueSelector>) –> void

  1. min_bb(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_bb(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

min_bb_set(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_bb_set() const –> bool

min_rb(*args, **kwargs)

Overloaded function.

  1. min_rb(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, min_rb: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::min_rb(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

  1. min_rb(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, min_rb: bool) -> None

in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code.

C++: protocols::calc_taskop_movers::DesignRepackMover::min_rb(const bool) –> void

  1. min_rb(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_rb() const –> const class utility::vector1<bool, class std::allocator<bool> > &

min_rb_set(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_rb_set() const –> bool

min_sc(*args, **kwargs)

Overloaded function.

  1. min_sc(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, min_sc: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::min_sc(class std::shared_ptr<class core::select::residue_selector::ResidueSelector>) –> void

  1. min_sc(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_sc(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

min_sc_set(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) bool

C++: protocols::calc_taskop_movers::DesignRepackMover::min_sc_set() const –> bool

static name() str

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

optimize_foldtree(*args, **kwargs)

Overloaded function.

  1. optimize_foldtree(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> bool

C++: protocols::calc_taskop_movers::DesignRepackMover::optimize_foldtree() const –> bool

  1. optimize_foldtree(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, opt: bool) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::optimize_foldtree(const bool) –> void

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

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

prevent_repacking(*args, **kwargs)

Overloaded function.

  1. prevent_repacking(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, p: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. prevent_repacking(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

restrict_to_repacking(*args, **kwargs)

Overloaded function.

  1. restrict_to_repacking(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, p: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. restrict_to_repacking(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

scorefxn_minimize(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::calc_taskop_movers::DesignRepackMover::scorefxn_minimize() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn_repack(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::calc_taskop_movers::DesignRepackMover::scorefxn_repack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

set_scorefxn_minimize(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::calc_taskop_movers::DesignRepackMover::set_scorefxn_minimize(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_scorefxn_repack(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::calc_taskop_movers::DesignRepackMover::set_scorefxn_repack(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

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

Set the ‘type’ string

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

setup_packer_and_movemap(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(const class core::pose::Pose &) –> 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

target_residues(*args, **kwargs)

Overloaded function.

  1. target_residues(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Replace the current target_residue setting with the passed residue selector

C++: protocols::calc_taskop_movers::DesignRepackMover::target_residues(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

  1. target_residues(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::calc_taskop_movers::DesignRepackMover::target_residues() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

  1. target_residues(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::calc_taskop_movers::DesignRepackMover::target_residues(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::calc_taskop_movers::DesignRepackMover::task() –> class std::shared_ptr<class core::pack::task::PackerTask> &

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, p: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

  1. task_factory(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::calc_taskop_movers::DesignRepackMover::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &

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 &

use_preset_task(*args, **kwargs)

Overloaded function.

  1. use_preset_task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover, bt: bool) -> None

C++: protocols::calc_taskop_movers::DesignRepackMover::use_preset_task(const bool) –> void

  1. use_preset_task(self: pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover) -> bool

C++: protocols::calc_taskop_movers::DesignRepackMover::use_preset_task() const –> bool

class pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue.

apply(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, : pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover) pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::operator=(const class protocols::calc_taskop_movers::ForceDisulfidesMover &) –> class protocols::calc_taskop_movers::ForceDisulfidesMover &

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.calc_taskop_movers.ForceDisulfidesMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::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>

disulfides(*args, **kwargs)

Overloaded function.

  1. disulfides(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, : pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >) –> void

  1. disulfides(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::disulfides(const class core::pose::Pose &) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

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

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::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.calc_taskop_movers.ForceDisulfidesMover) str

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::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::calc_taskop_movers::ForceDisulfidesMover::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

remove_existing(*args, **kwargs)

Overloaded function.

  1. remove_existing(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, setting: bool) -> None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::remove_existing(bool) –> void

  1. remove_existing(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover) -> bool

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::remove_existing() const –> bool

repack(*args, **kwargs)

Overloaded function.

  1. repack(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, setting: bool) -> None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::repack(bool) –> void

  1. repack(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover) -> bool

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::repack() 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(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

  1. scorefxn(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::calc_taskop_movers::ForceDisulfidesMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.calc_taskop_movers.ForceDisulfidesMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator, : pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator) pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator

C++: protocols::calc_taskop_movers::ForceDisulfidesMoverCreator::operator=(const class protocols::calc_taskop_movers::ForceDisulfidesMoverCreator &) –> class protocols::calc_taskop_movers::ForceDisulfidesMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator) str

C++: protocols::calc_taskop_movers::ForceDisulfidesMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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