grafting

Bindings for protocols::grafting namespace

class pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover

Bases: pyrosetta.rosetta.protocols.grafting.GraftMoverBase

Grafting class adapted from Steven Lewis’ pose_into_pose algorithm.

  1. Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the insertion will occur between.

  2. Connects the left side of the piece to the scaffold by inserting ideal geometry

    (aka superposition of terminal overhangs is not needed)

  3. Cycles of:
    1. SmallMover for sampling

    2. CCD to close right (Nter) side of the graft.

    The insert is included as dihedral-inflexible residues in the CCD arm. Residues on either side of the scaffold are used by default to close the loop. A Moevemap can be given to include more residues for CCD to use, such as loops connecting secondary structural elements

    1. MinMover to help close the graft through chainbreak terms

    d) Closure check - will stop if closed (This can be overridden) d) MonteCarlo Boltzmann criterion

  1. Repack flexible residues, insert residues, connecting residues between scaffold and insert, and neighbors

example:

mover = AnchoredGraftMover(start, end, piece, cter_overhang, nter_overhang); mover.apply(pose);

see also: grafting/util.hh.

Uses a single arm to close the loop by default. **Nter_loop_start—->Piece—-> | Cter_loop_end** Default movemap keeps insert Frozen in dihedral angle space, But think of the insert as part of a CCD giant arm. Default flexibility on Nter and Cter is only two residues (–> part of diagram). Will delete any residues between start and end, and any overhang residues from the insert.

Algorithm originally from pose_into_pose: The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Internally, apply performs the insertion, idealizes the loop residues (omegas to 180, peptide bonds idealized) and the newly made polymer connections at the insert point, and then attempts to close the loop(s). It is intended, but not guaranteed, to produce a graft with good rama, omega, and chainbreak/peptide_bond scores. All-atom minimization of graft or pose after insertion is recommended.

apply(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Grafts the piece into the pose, uses CCD to close the connection. Insert does not change dihedral space, but DOES change cartesian space by default. Does not repack any sidechains. Deletes overhang and region between start and end if residues are present.

C++: protocols::grafting::AnchoredGraftMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, : pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover)pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover

C++: protocols::grafting::AnchoredGraftMover::operator=(const class protocols::grafting::AnchoredGraftMover &) –> class protocols::grafting::AnchoredGraftMover &

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.grafting.AnchoredGraftMover)pyrosetta.rosetta.protocols.moves.Mover

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

static complex_type_generator_for_anchored_graft_mover(: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition)pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

copy_pdbinfo(*args, **kwargs)

Overloaded function.

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, copy_pdbinfo: bool) -> None

Copy PDBInfo from the pose piece into pose during graft. If false(default), PDBInfo will be obsoleted.

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo(bool) –> void

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) -> bool

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo() const –> bool

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>

end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::end() –> unsigned long

final_repack(*args, **kwargs)

Overloaded function.

  1. final_repack(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, final_repack: bool) -> None

Pack sidechains of flexible residues, insert and neighbors at end?

Default True.

C++: protocols::grafting::AnchoredGraftMover::final_repack(bool) –> void

  1. final_repack(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

Pack sidechains of flexible residues, insert and neighbors at end?

C++: protocols::grafting::AnchoredGraftMover::final_repack() –> bool

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

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

get_Cter_loop_end(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

the Cterminal loop end (Last flexible residue). Useful to use after insertion.

C++: protocols::grafting::AnchoredGraftMover::get_Cter_loop_end() –> unsigned long

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_cterm_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_cterm_insert_flexibility() –> unsigned long

get_cterm_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility() –> unsigned long

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_loops(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover)pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::grafting::AnchoredGraftMover::get_loops() –> const class protocols::loops::Loops &

get_name(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → str

C++: protocols::grafting::AnchoredGraftMover::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_nterm_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_nterm_insert_flexibility() –> unsigned long

get_nterm_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility() –> unsigned long

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

graft_is_closed(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → bool

C++: protocols::grafting::AnchoredGraftMover::graft_is_closed() const –> bool

idealize_insert(*args, **kwargs)

Overloaded function.

  1. idealize_insert(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, idealize: bool) -> None

C++: protocols::grafting::AnchoredGraftMover::idealize_insert(bool) –> void

  1. idealize_insert(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

C++: protocols::grafting::AnchoredGraftMover::idealize_insert() const –> bool

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 > > &

insertion_length(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::insertion_length() –> unsigned long

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::grafting::AnchoredGraftMover::mover_name() –> std::string

static name() → str

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

neighbor_dis(*args, **kwargs)

Overloaded function.

  1. neighbor_dis(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, dis: float) -> None

Neighbor distance for any repacking of side-chains.

C++: protocols::grafting::AnchoredGraftMover::neighbor_dis(double) –> void

  1. neighbor_dis(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> float

C++: protocols::grafting::AnchoredGraftMover::neighbor_dis() const –> double

original_end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::original_end() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::grafting::AnchoredGraftMover::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_cen_scorefunction(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::grafting::AnchoredGraftMover::set_cen_scorefunction(class std::shared_ptr<const 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_cycles(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, cycles: int) → None

C++: protocols::grafting::AnchoredGraftMover::set_cycles(unsigned long) –> void

set_defaults(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → None

C++: protocols::grafting::AnchoredGraftMover::set_defaults() –> void

set_fa_scorefunction(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::grafting::AnchoredGraftMover::set_fa_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, Nter_insert_flexibility: int, Cter_insert_flexibility: int) → None

Sets insert flexibility on either end of insert

C++: protocols::grafting::AnchoredGraftMover::set_insert_flexibility(const unsigned long, const unsigned long) –> void

set_insert_region(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, start: int, end: int) → None

C++: protocols::grafting::GraftMoverBase::set_insert_region(const unsigned long, const unsigned long) –> void

set_mintype(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, mintype: str) → None

Sets the mintype for the MinMover

C++: protocols::grafting::AnchoredGraftMover::set_mintype(std::string) –> void

set_movemaps(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, scaffold_mm: pyrosetta.rosetta.core.kinematics.MoveMap, insert_mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

Advanced way to set flexibility and residues used for CCD

Will combine the movemaps for apply, and renumber everything. Flexible residues in multiple chains not recommended. From the first bb flexible residue to the last will act as one giant CCD arm,

using those residues for minimization and CCD that have bb true in movemap. This can be amazing as you can use loop regions in various parts of your protein to help the graft complete.

Note: Will disregard flexibility settings, as the movemaps will be used as primary way to define flexibility. May want to consider turning off the sampling step when passing crazy movemaps.

C++: protocols::grafting::AnchoredGraftMover::set_movemaps(const class std::shared_ptr<const class core::kinematics::MoveMap>, const class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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_piece(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, piece: pyrosetta.rosetta.core.pose.Pose, Nter_overhang_length: int, Cter_overhang_length: int) → None

Sets the piece that will be inserted, and any overhang residues.

Overhang residues are residues not being inserted into the scaffold. These residues are deleted before insertion and are used by classes usually for superposition or Initial orientation of the insert relative to the scaffold.

C++: protocols::grafting::GraftMoverBase::set_piece(const class core::pose::Pose &, unsigned long, unsigned long) –> void

set_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, Nter_scaffold_flexibility: int, Cter_scaffold_flexibility: int) → None

Sets scaffold flexiblity on either end of scaffold

C++: protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility(const unsigned long, const unsigned long) –> void

set_skip_sampling(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, skip_sampling: bool) → None

Sets the mover to skip the small mover sampling step.

C++: protocols::grafting::AnchoredGraftMover::set_skip_sampling(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

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

start(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::start() –> unsigned long

stop_at_closure(*args, **kwargs)

Overloaded function.

  1. stop_at_closure(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, stop_at_closure: bool) -> None

Stop at closure of both ends?

Default True.

C++: protocols::grafting::AnchoredGraftMover::stop_at_closure(bool) –> void

  1. stop_at_closure(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

Stop at closure of both ends?

C++: protocols::grafting::AnchoredGraftMover::stop_at_closure() –> bool

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.grafting.AnchoredGraftMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator, : pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator)pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator

C++: protocols::grafting::AnchoredGraftMoverCreator::operator=(const class protocols::grafting::AnchoredGraftMoverCreator &) –> class protocols::grafting::AnchoredGraftMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator)pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator) → str

C++: protocols::grafting::AnchoredGraftMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover

Bases: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover

General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of:

  1. SmallMover for sampling (Can be disabled))

  2. CCDs both terminal ends of the scaffold using flexibility settings or movemap

    To close the graft.

  3. MinMover to help close the graft through chainbreak terms

d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion

  1. Repacks flexible residues and insert residues

Differs from AnchoredGraftMover in that the insert is held fixed in space after the superposition

example:

mover = CCDEndsGraftMover(start, end, piece, cter_overhang, nter_overhang) mover.apply(pose)

see also: grafting/util.hh.

Uses two CCD arms on either side of the scaffold to close graft. Insert is held fixed in cartesian space after superposition of any overhang residues by default.

**Nter_loop_start—–> | Piece | <—-Nter_loop_end** (Note that Nter_loop_start and Nter_loop_end points to redidue BEFORE loop and AFTER loop) Default flexibility on Nter and Cter is only two residues (–> part of diagram). Will delete any residues between start and end of the scaffold, and any overhang residues from the insert.

Internally, apply performs the insertion, idealizes the loop residues (omegas to 180, peptide bonds idealized) and the newly made polymer connections at the insert point, and then attempts to close the loop(s). Repacks sidechains of insert and overhang residues after insertion is complete By default, will stop apply once graft is closed. Closure is measured as all bond lengths and angles of loop being acceptable.

apply(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::grafting::CCDEndsGraftMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover, : pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover)pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover

C++: protocols::grafting::CCDEndsGraftMover::operator=(const class protocols::grafting::CCDEndsGraftMover &) –> class protocols::grafting::CCDEndsGraftMover &

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.grafting.CCDEndsGraftMover)pyrosetta.rosetta.protocols.moves.Mover

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

static complex_type_generator_for_anchored_graft_mover(: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition)pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

copy_pdbinfo(*args, **kwargs)

Overloaded function.

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, copy_pdbinfo: bool) -> None

Copy PDBInfo from the pose piece into pose during graft. If false(default), PDBInfo will be obsoleted.

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo(bool) –> void

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) -> bool

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo() const –> bool

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>

end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::end() –> unsigned long

final_repack(*args, **kwargs)

Overloaded function.

  1. final_repack(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, final_repack: bool) -> None

Pack sidechains of flexible residues, insert and neighbors at end?

Default True.

C++: protocols::grafting::AnchoredGraftMover::final_repack(bool) –> void

  1. final_repack(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

Pack sidechains of flexible residues, insert and neighbors at end?

C++: protocols::grafting::AnchoredGraftMover::final_repack() –> bool

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

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

get_Cter_loop_end(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

the Cterminal loop end (Last flexible residue). Useful to use after insertion.

C++: protocols::grafting::AnchoredGraftMover::get_Cter_loop_end() –> unsigned long

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_cterm_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_cterm_insert_flexibility() –> unsigned long

get_cterm_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility() –> unsigned long

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_loops(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover)pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::grafting::AnchoredGraftMover::get_loops() –> const class protocols::loops::Loops &

get_name(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover) → str

C++: protocols::grafting::CCDEndsGraftMover::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_nterm_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_nterm_insert_flexibility() –> unsigned long

get_nterm_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → int

C++: protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility() –> unsigned long

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

graft_is_closed(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover) → bool

C++: protocols::grafting::CCDEndsGraftMover::graft_is_closed() const –> bool

idealize_insert(*args, **kwargs)

Overloaded function.

  1. idealize_insert(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, idealize: bool) -> None

C++: protocols::grafting::AnchoredGraftMover::idealize_insert(bool) –> void

  1. idealize_insert(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

C++: protocols::grafting::AnchoredGraftMover::idealize_insert() const –> bool

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 > > &

insertion_length(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::insertion_length() –> unsigned long

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::grafting::CCDEndsGraftMover::mover_name() –> std::string

static name() → str

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

neighbor_dis(*args, **kwargs)

Overloaded function.

  1. neighbor_dis(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, dis: float) -> None

Neighbor distance for any repacking of side-chains.

C++: protocols::grafting::AnchoredGraftMover::neighbor_dis(double) –> void

  1. neighbor_dis(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> float

C++: protocols::grafting::AnchoredGraftMover::neighbor_dis() const –> double

original_end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::original_end() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::grafting::CCDEndsGraftMover::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_cen_scorefunction(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::grafting::AnchoredGraftMover::set_cen_scorefunction(class std::shared_ptr<const 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_cycles(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, cycles: int) → None

C++: protocols::grafting::AnchoredGraftMover::set_cycles(unsigned long) –> void

set_defaults(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) → None

C++: protocols::grafting::AnchoredGraftMover::set_defaults() –> void

set_fa_scorefunction(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, score: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::grafting::AnchoredGraftMover::set_fa_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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_insert_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, Nter_insert_flexibility: int, Cter_insert_flexibility: int) → None

Sets insert flexibility on either end of insert

C++: protocols::grafting::AnchoredGraftMover::set_insert_flexibility(const unsigned long, const unsigned long) –> void

set_insert_region(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, start: int, end: int) → None

C++: protocols::grafting::GraftMoverBase::set_insert_region(const unsigned long, const unsigned long) –> void

set_mintype(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, mintype: str) → None

Sets the mintype for the MinMover

C++: protocols::grafting::AnchoredGraftMover::set_mintype(std::string) –> void

set_movemaps(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, scaffold_mm: pyrosetta.rosetta.core.kinematics.MoveMap, insert_mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

Advanced way to set flexibility and residues used for CCD

Will combine the movemaps for apply, and renumber everything. Flexible residues in multiple chains not recommended. From the first bb flexible residue to the last will act as one giant CCD arm,

using those residues for minimization and CCD that have bb true in movemap. This can be amazing as you can use loop regions in various parts of your protein to help the graft complete.

Note: Will disregard flexibility settings, as the movemaps will be used as primary way to define flexibility. May want to consider turning off the sampling step when passing crazy movemaps.

C++: protocols::grafting::AnchoredGraftMover::set_movemaps(const class std::shared_ptr<const class core::kinematics::MoveMap>, const class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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_piece(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, piece: pyrosetta.rosetta.core.pose.Pose, Nter_overhang_length: int, Cter_overhang_length: int) → None

Sets the piece that will be inserted, and any overhang residues.

Overhang residues are residues not being inserted into the scaffold. These residues are deleted before insertion and are used by classes usually for superposition or Initial orientation of the insert relative to the scaffold.

C++: protocols::grafting::GraftMoverBase::set_piece(const class core::pose::Pose &, unsigned long, unsigned long) –> void

set_scaffold_flexibility(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, Nter_scaffold_flexibility: int, Cter_scaffold_flexibility: int) → None

Sets scaffold flexiblity on either end of scaffold

C++: protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility(const unsigned long, const unsigned long) –> void

set_skip_sampling(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, skip_sampling: bool) → None

Sets the mover to skip the small mover sampling step.

C++: protocols::grafting::AnchoredGraftMover::set_skip_sampling(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

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

start(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::start() –> unsigned long

stop_at_closure(*args, **kwargs)

Overloaded function.

  1. stop_at_closure(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover, stop_at_closure: bool) -> None

Stop at closure of both ends?

Default True.

C++: protocols::grafting::AnchoredGraftMover::stop_at_closure(bool) –> void

  1. stop_at_closure(self: pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover) -> bool

Stop at closure of both ends?

C++: protocols::grafting::AnchoredGraftMover::stop_at_closure() –> bool

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.grafting.CCDEndsGraftMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator, : pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator)pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator

C++: protocols::grafting::CCDEndsGraftMoverCreator::operator=(const class protocols::grafting::CCDEndsGraftMoverCreator &) –> class protocols::grafting::CCDEndsGraftMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator)pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator) → str

C++: protocols::grafting::CCDEndsGraftMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.grafting.GraftMoverBase

Bases: pyrosetta.rosetta.protocols.moves.Mover

Fairly abstract base class for GraftMover classes

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

Main Method

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

assign(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, : pyrosetta.rosetta.protocols.grafting.GraftMoverBase)pyrosetta.rosetta.protocols.grafting.GraftMoverBase

C++: protocols::grafting::GraftMoverBase::operator=(const class protocols::grafting::GraftMoverBase &) –> class protocols::grafting::GraftMoverBase &

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.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>

copy_pdbinfo(*args, **kwargs)

Overloaded function.

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, copy_pdbinfo: bool) -> None

Copy PDBInfo from the pose piece into pose during graft. If false(default), PDBInfo will be obsoleted.

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo(bool) –> void

  1. copy_pdbinfo(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) -> bool

C++: protocols::grafting::GraftMoverBase::copy_pdbinfo() const –> bool

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>

end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::end() –> unsigned long

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.grafting.GraftMoverBase) → str

Return the name of the Mover.

C++: protocols::grafting::GraftMoverBase::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 > > &

insertion_length(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::insertion_length() –> unsigned long

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

original_end(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::original_end() –> unsigned long

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_insert_region(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, start: int, end: int) → None

C++: protocols::grafting::GraftMoverBase::set_insert_region(const unsigned long, 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_piece(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase, piece: pyrosetta.rosetta.core.pose.Pose, Nter_overhang_length: int, Cter_overhang_length: int) → None

Sets the piece that will be inserted, and any overhang residues.

Overhang residues are residues not being inserted into the scaffold. These residues are deleted before insertion and are used by classes usually for superposition or Initial orientation of the insert relative to the scaffold.

C++: protocols::grafting::GraftMoverBase::set_piece(const class core::pose::Pose &, unsigned long, unsigned long) –> 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

start(self: pyrosetta.rosetta.protocols.grafting.GraftMoverBase) → int

C++: protocols::grafting::GraftMoverBase::start() –> unsigned long

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 &

pyrosetta.rosetta.protocols.grafting.add_cutpoint_variants_for_ccd(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

Adds cutpoint varients above and below cutpoint

C++: protocols::grafting::add_cutpoint_variants_for_ccd(class core::pose::Pose &, const class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.grafting.combine_movemaps_post_insertion(*args, **kwargs)

Overloaded function.

  1. combine_movemaps_post_insertion(scaffold_mm: pyrosetta.rosetta.core.kinematics.MoveMap, insert_mm: pyrosetta.rosetta.core.kinematics.MoveMap, start: int, original_end: int, insertion_length: int) -> pyrosetta.rosetta.core.kinematics.MoveMap

  2. combine_movemaps_post_insertion(scaffold_mm: pyrosetta.rosetta.core.kinematics.MoveMap, insert_mm: pyrosetta.rosetta.core.kinematics.MoveMap, start: int, original_end: int, insertion_length: int, cter_overhang_start: int) -> pyrosetta.rosetta.core.kinematics.MoveMap

combines the two main movemaps to use after the insertion.

Start + End denote residue number before and after the insert. original_end denotes the end residue number before insertion occurred

C++: protocols::grafting::combine_movemaps_post_insertion(class std::shared_ptr<const class core::kinematics::MoveMap>, class std::shared_ptr<const class core::kinematics::MoveMap>, unsigned long, unsigned long, unsigned long, unsigned long) –> class std::shared_ptr<class core::kinematics::MoveMap>

pyrosetta.rosetta.protocols.grafting.delete_overhang_residues(piece: pyrosetta.rosetta.core.pose.Pose, Nter_overhang_len: int, Cter_overhang_length_len: int) → None
deletes overhang residues of the pose piece.

Recommended use is within apply method

C++: protocols::grafting::delete_overhang_residues(class core::pose::Pose &, unsigned long, unsigned long) –> void

pyrosetta.rosetta.protocols.grafting.delete_region(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → None

Deletes a region of the pose. Starting from and including ‘start’ and ‘end’ residue.

C++: protocols::grafting::delete_region(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.grafting.graft_closed(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops) → bool
Uses has_severe_peptide_bond_issues with stringent geometry values to

determine graft closure at cutpoint.

C++: protocols::grafting::graft_closed(class core::pose::Pose &, class protocols::loops::Loops &) –> bool

pyrosetta.rosetta.protocols.grafting.idealize_combined_pose(*args, **kwargs)

Overloaded function.

  1. idealize_combined_pose(combined: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, start: int, insert_start: int, insert_end: int, Nter_loop_start: int, Cter_loop_end: int) -> None

  2. idealize_combined_pose(combined: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, start: int, insert_start: int, insert_end: int, Nter_loop_start: int, Cter_loop_end: int, idealize_insert: bool) -> None

Idealize loop residues and residues in movemap.

C++: protocols::grafting::idealize_combined_pose(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, bool) –> void

pyrosetta.rosetta.protocols.grafting.insert_pose_into_pose(*args, **kwargs)

Overloaded function.

  1. insert_pose_into_pose(scaffold_pose: pyrosetta.rosetta.core.pose.Pose, insert_pose: pyrosetta.rosetta.core.pose.Pose, insert_point: int, insert_point_end: int) -> pyrosetta.rosetta.core.pose.Pose

  2. insert_pose_into_pose(scaffold_pose: pyrosetta.rosetta.core.pose.Pose, insert_pose: pyrosetta.rosetta.core.pose.Pose, insert_point: int, insert_point_end: int, copy_pdbinfo: bool) -> pyrosetta.rosetta.core.pose.Pose

Steven Lewis smlewi.com, Jared Adolf-Bryfogle

inserts one pose into another pose, returning the product as a new value.

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point.

C++: protocols::grafting::insert_pose_into_pose(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long, bool) –> class core::pose::Pose

  1. insert_pose_into_pose(scaffold_pose: pyrosetta.rosetta.core.pose.Pose, insert_pose: pyrosetta.rosetta.core.pose.Pose, insert_point: int) -> pyrosetta.rosetta.core.pose.Pose

  2. insert_pose_into_pose(scaffold_pose: pyrosetta.rosetta.core.pose.Pose, insert_pose: pyrosetta.rosetta.core.pose.Pose, insert_point: int, copy_pdbinfo: bool) -> pyrosetta.rosetta.core.pose.Pose

inserts one pose into another pose, returning the product as a new value.

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point. insert_point_end is assumed to be insert_point+1.

C++: protocols::grafting::insert_pose_into_pose(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, bool) –> class core::pose::Pose

pyrosetta.rosetta.protocols.grafting.perturb_backbone_for_test(pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → float
Uses a small mover at high KT to perturb residues in the movemap for testing.

Returns bb_RMS_including_o

C++: protocols::grafting::perturb_backbone_for_test(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> double

pyrosetta.rosetta.protocols.grafting.remove_cutpoint_variants_for_ccd(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

Removes cutpoint variants above and below cutpoint

C++: protocols::grafting::remove_cutpoint_variants_for_ccd(class core::pose::Pose &, const class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.grafting.repack_connection_and_residues_in_movemap(pose: pyrosetta.rosetta.core.pose.Pose, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, start: int, end: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the first and last residue of the insert.

C++: protocols::grafting::repack_connection_and_residues_in_movemap(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const unsigned long, const unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

pyrosetta.rosetta.protocols.grafting.repack_connection_and_residues_in_movemap_and_piece(pose: pyrosetta.rosetta.core.pose.Pose, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, start: int, end: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the entire insert.

C++: protocols::grafting::repack_connection_and_residues_in_movemap_and_piece(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const unsigned long, const unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

pyrosetta.rosetta.protocols.grafting.repack_connection_and_residues_in_movemap_and_piece_and_neighbors(*args, **kwargs)

Overloaded function.

  1. repack_connection_and_residues_in_movemap_and_piece_and_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, start: int, end: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

  2. repack_connection_and_residues_in_movemap_and_piece_and_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, start: int, end: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, neighbor_dis: float) -> None

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the entire insert and neighbors.

C++: protocols::grafting::repack_connection_and_residues_in_movemap_and_piece_and_neighbors(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const unsigned long, const unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>, double) –> void

pyrosetta.rosetta.protocols.grafting.replace_region(*args, **kwargs)

Overloaded function.

  1. replace_region(from_pose: pyrosetta.rosetta.core.pose.Pose, to_pose: pyrosetta.rosetta.core.pose.Pose, from_pose_start_residue: int, to_pose_start_residue: int, insertion_length: int) -> pyrosetta.rosetta.core.pose.Pose

  2. replace_region(from_pose: pyrosetta.rosetta.core.pose.Pose, to_pose: pyrosetta.rosetta.core.pose.Pose, from_pose_start_residue: int, to_pose_start_residue: int, insertion_length: int, copy_pdbinfo: bool) -> pyrosetta.rosetta.core.pose.Pose

replaces residues from from_pose to to_pose into pose where insertion region is defined. Returns product as a new value.

C++: protocols::grafting::replace_region(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, bool) –> class core::pose::Pose

pyrosetta.rosetta.protocols.grafting.return_region(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int)pyrosetta.rosetta.core.pose.Pose

Returns a region of the pose including start and end as a new pose. Has a simple foldtree.

C++: protocols::grafting::return_region(class core::pose::Pose &, const unsigned long, const unsigned long) –> class core::pose::Pose

pyrosetta.rosetta.protocols.grafting.setup_single_loop_double_arm_remodeling_foldtree(*args, **kwargs)

Overloaded function.

  1. setup_single_loop_double_arm_remodeling_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, Nter_loop_start: int, Cter_loop_end: int, end: int) -> None

  2. setup_single_loop_double_arm_remodeling_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, Nter_loop_start: int, Cter_loop_end: int, end: int, loop_modeling: bool) -> None

**Nter_loop_start—->Piece | <—-Nter_loop_end** Insert will move in cartesian space

for CCD and loops is end_-1

C++: protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(class core::pose::Pose &, const unsigned long, const unsigned long, unsigned long, bool) –> void

pyrosetta.rosetta.protocols.grafting.setup_single_loop_single_arm_remodeling_foldtree(*args, **kwargs)

Overloaded function.

  1. setup_single_loop_single_arm_remodeling_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, Nter_loop_start: int, Cter_loop_end: int) -> None

  2. setup_single_loop_single_arm_remodeling_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, Nter_loop_start: int, Cter_loop_end: int, loop_modeling: bool) -> None

**Nter_loop_start—->Piece—-> | Cter_loop_end**

Default FoldTree used by AnchoredGraftMover.

for CCD and loops is Cter_loop_end-1

C++: protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(class core::pose::Pose &, const unsigned long, const unsigned long, bool) –> void

pyrosetta.rosetta.protocols.grafting.superimpose_overhangs_heavy(*args, **kwargs)

Overloaded function.

  1. superimpose_overhangs_heavy(pose: pyrosetta.rosetta.core.pose.Pose, piece: pyrosetta.rosetta.core.pose.Pose, ca_only: bool, start: int, end: int) -> None

  2. superimpose_overhangs_heavy(pose: pyrosetta.rosetta.core.pose.Pose, piece: pyrosetta.rosetta.core.pose.Pose, ca_only: bool, start: int, end: int, Nter_overhang_len: int) -> None

  3. superimpose_overhangs_heavy(pose: pyrosetta.rosetta.core.pose.Pose, piece: pyrosetta.rosetta.core.pose.Pose, ca_only: bool, start: int, end: int, Nter_overhang_len: int, Cter_overhang_length_len: int) -> None

uses rms_util to superimpose overhang residues of piece onto pose.

Start + End denote residue number before and after the insert will be. For example, start = 10, end = 11 for a scaffold where the previous residues are already deleted or a scaffold where you are superposimposing a linker between two domains - one that ends at start and the other that begins at end

C++: protocols::grafting::superimpose_overhangs_heavy(const class core::pose::Pose &, class core::pose::Pose &, bool, unsigned long, unsigned long, unsigned long, unsigned long) –> void