struct_fragment

Bindings for protocols::struct_fragment namespace

class pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply Mover

C++: protocols::struct_fragment::StructFragmentMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, : pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover

C++: protocols::struct_fragment::StructFragmentMover::operator=(const class protocols::struct_fragment::StructFragmentMover &) –> class protocols::struct_fragment::StructFragmentMover &

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.struct_fragment.StructFragmentMover) pyrosetta.rosetta.protocols.moves.Mover

Create clone of this mover

C++: protocols::struct_fragment::StructFragmentMover::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.struct_fragment.StructFragmentMover) pyrosetta.rosetta.protocols.moves.Mover

Create a fresh instance of this mover

C++: protocols::struct_fragment::StructFragmentMover::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_frag_weight_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the path to the fragment weight file

C++: protocols::struct_fragment::StructFragmentMover::get_frag_weight_file() 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_large_frag_size(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) int

Get the size of large fragments

C++: protocols::struct_fragment::StructFragmentMover::get_large_frag_size() const –> unsigned long

get_large_frage_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the parth to the large fragment file

C++: protocols::struct_fragment::StructFragmentMover::get_large_frage_file() const –> std::string

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_loop_angle_conf(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) float

Get the confidence for phi and psi angles

C++: protocols::struct_fragment::StructFragmentMover::get_loop_angle_conf() const –> double

get_n_candidates(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) int

Get the number of fragment candidates per position

C++: protocols::struct_fragment::StructFragmentMover::get_n_candidates() const –> unsigned long

get_n_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) int

Get the number of fragments per position

C++: protocols::struct_fragment::StructFragmentMover::get_n_frags() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get mover name

C++: protocols::struct_fragment::StructFragmentMover::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_output_frag_files(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) bool

Check if fragment files should be outputted

C++: protocols::struct_fragment::StructFragmentMover::get_output_frag_files() const –> bool

get_prefix(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the prefix for the fragment file output

C++: protocols::struct_fragment::StructFragmentMover::get_prefix() const –> std::string

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_sequence_profile(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the path to a sequence profile

C++: protocols::struct_fragment::StructFragmentMover::get_sequence_profile() const –> std::string

get_small_frag_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the path to the small fragment file

C++: protocols::struct_fragment::StructFragmentMover::get_small_frag_file() const –> std::string

get_small_frag_size(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) int

Get the size of small fragments

C++: protocols::struct_fragment::StructFragmentMover::get_small_frag_size() const –> unsigned long

get_steal_large_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) bool

Check if large fragments are being stolen

C++: protocols::struct_fragment::StructFragmentMover::get_steal_large_frags() const –> bool

get_steal_small_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) bool

Check if small fragments are being stolen

C++: protocols::struct_fragment::StructFragmentMover::get_steal_small_frags() const –> bool

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

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

get_vall_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover) str

Get the path to the vall file

C++: protocols::struct_fragment::StructFragmentMover::get_vall_file() 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

Return mover name

C++: protocols::struct_fragment::StructFragmentMover::mover_name() –> std::string

static name() str

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

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

Parse RosettaScripts options for this mover

C++: protocols::struct_fragment::StructFragmentMover::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::struct_fragment::StructFragmentMover::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_frag_weight_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, frag_weight_file: str) None

Set the path to the fragment weight file

C++: protocols::struct_fragment::StructFragmentMover::set_frag_weight_file(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_large_frag_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, large_frag_file: str) None

Set the parth to the large fragment file

C++: protocols::struct_fragment::StructFragmentMover::set_large_frag_file(std::string) –> void

set_large_frag_size(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, large_frag_size: int) None

Set the size of large fragments

C++: protocols::struct_fragment::StructFragmentMover::set_large_frag_size(unsigned long) –> void

set_loop_angle_conf(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, loop_angle_conf: float) None

Set the confidence for phi and psi angles

C++: protocols::struct_fragment::StructFragmentMover::set_loop_angle_conf(double) –> void

set_n_candidates(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, n_candidates: int) None

Set the number of fragment candidates per position

C++: protocols::struct_fragment::StructFragmentMover::set_n_candidates(unsigned long) –> void

set_n_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, n_frags: int) None

Set the number of fragments per position

C++: protocols::struct_fragment::StructFragmentMover::set_n_frags(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_output_frag_files(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, output_frag_files: bool) None

Set whether fragment files should be outputted

C++: protocols::struct_fragment::StructFragmentMover::set_output_frag_files(bool) –> void

set_prefix(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, prefix: str) None

Set the prefix for the fragment file output

C++: protocols::struct_fragment::StructFragmentMover::set_prefix(std::string) –> void

set_secstruct(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, ss: str) None

sets the secondary structure to be used for constraint generation

C++: protocols::struct_fragment::StructFragmentMover::set_secstruct(const std::string &) –> void

set_sequence_profile(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, sequence_profile: str) None

Set the path to a sequence profile

C++: protocols::struct_fragment::StructFragmentMover::set_sequence_profile(std::string) –> void

set_small_frag_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, small_frag_file: str) None

Set the path to the small fragment file

C++: protocols::struct_fragment::StructFragmentMover::set_small_frag_file(std::string) –> void

set_small_frag_size(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, small_frag_size: int) None

Set the size of small fragments

C++: protocols::struct_fragment::StructFragmentMover::set_small_frag_size(unsigned long) –> void

set_steal_large_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, steal_large_frags: bool) None

Set whether large fragments are being stolen

C++: protocols::struct_fragment::StructFragmentMover::set_steal_large_frags(bool) –> void

set_steal_small_frags(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, steal_small_frags: bool) None

Set whether small fragments are being stolen

C++: protocols::struct_fragment::StructFragmentMover::set_steal_small_frags(bool) –> 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_dssp(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, use_dssp: bool) None
If true, and no secstruct is specified, DSSP will be used to determine the pose

secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used.

Desired value

C++: protocols::struct_fragment::StructFragmentMover::set_use_dssp(const bool) –> void

set_vall_file(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover, vall_file: str) None

Set the path to the vall file

C++: protocols::struct_fragment::StructFragmentMover::set_vall_file(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.struct_fragment.StructFragmentMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

RosettaScripts factory for StructFragmentMover.

assign(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator, : pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator) pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator

C++: protocols::struct_fragment::StructFragmentMoverCreator::operator=(const class protocols::struct_fragment::StructFragmentMoverCreator &) –> class protocols::struct_fragment::StructFragmentMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator) str

C++: protocols::struct_fragment::StructFragmentMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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