topology_broker

• claims
• weights

Bindings for protocols::topology_broker namespace

class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator

Bases: pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator

creator for the ConstraintsEvaluatorWrapperCreator class

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_evaluators(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void

assign(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator, : pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) → pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator

C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::operator=(const class protocols::topology_broker::ConstraintEvaluatorWrapperCreator &) –> class protocols::topology_broker::ConstraintEvaluatorWrapperCreator &

register_options(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) → None

C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::register_options() –> void

type_name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) → str

C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, arg0: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

_static_type_name() → str

C++: protocols::topology_broker::DisulfJumpClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer

C++: protocols::topology_broker::DisulfJumpClaimer::operator=(const class protocols::topology_broker::DisulfJumpClaimer &) –> class protocols::topology_broker::DisulfJumpClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::DisulfJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::DisulfJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, lib: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, all_frames: pyrosetta.rosetta.core.fragment.FrameList) → None

C++: protocols::topology_broker::DisulfJumpClaimer::generate_jump_frags(const class protocols::jumping::DisulfPairingLibrary &, class core::fragment::FrameList &) const –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::DisulfJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) → None

multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::DisulfJumpClaimer::new_decoy(const class core::pose::Pose &) –> void

2. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) -> None

C++: protocols::topology_broker::DisulfJumpClaimer::new_decoy() –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) → bool

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) → None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(class std::basic_istream<char> &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) → None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(class std::basic_istream<char> &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, tag: str, is: pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::DisulfJumpClaimer::read_tag(class std::basic_string<char>, class std::basic_istream<char> &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) → None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) → None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) → None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) → None

C++: protocols::topology_broker::TopologyClaimer::set_label(const class std::basic_string<char> &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const class std::basic_string<char> &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) → None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) → None

has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::DisulfJumpClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, arg0: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, arg0: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, arg1: str) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, jump_def: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, mover_tag: str, weight: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> None
5. __init__(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, arg0: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

_static_type_name() → str

C++: protocols::topology_broker::FragmentJumpClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::operator=(const class protocols::topology_broker::FragmentJumpClaimer &) –> class protocols::topology_broker::FragmentJumpClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) → None

multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void

2. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) → bool

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) → None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(class std::basic_istream<char> &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) → None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(class std::basic_istream<char> &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, tag: str, is: pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::FragmentJumpClaimer::read_tag(class std::basic_string<char>, class std::basic_istream<char> &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) → None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) → None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) → None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) → None

C++: protocols::topology_broker::TopologyClaimer::set_label(const class std::basic_string<char> &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const class std::basic_string<char> &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) → None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) → None

has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

defines a rigid part of structure… imagine a loop-relax application core structure is fixed via jumps and loops can move

the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in “bExclusive_ mode” the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates )

e.g., a hole in the structure shouldn’t pose a problem, since we basically copy the atom-tree.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, input_pose: pyrosetta.rosetta.core.pose.Pose, rigid: pyrosetta.rosetta.protocols.loops.Loops) -> None
3. __init__(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, arg0: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

_static_type_name() → str

C++: protocols::topology_broker::RigidChunkClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

will fail if a BB torsion claim of the rigid region has been declined

C++: protocols::topology_broker::RigidChunkClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → None

disallow torsion moves in relax if bRigidInRelax

C++: protocols::topology_broker::RigidChunkClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate

C++: protocols::topology_broker::RigidChunkClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) → pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer

C++: protocols::topology_broker::RigidChunkClaimer::operator=(const class protocols::topology_broker::RigidChunkClaimer &) –> class protocols::topology_broker::RigidChunkClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::RigidChunkClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

issue jump-claims for jumps yet missing to keep rigid regions fixed

C++: protocols::topology_broker::RigidChunkClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate DofClaims for BB

C++: protocols::topology_broker::RigidChunkClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

initialize BB residues and rigid-internal jumps from starting structure — copying atom-tree dofs

C++: protocols::topology_broker::RigidChunkClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, cut_bias: pyrosetta.rosetta.utility.vector1_double) → None

multiply your bias to this – if its zero don’t change that, i.e., multiply only

C++: protocols::topology_broker::RigidChunkClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) -> None

C++: protocols::topology_broker::RigidChunkClaimer::new_decoy() –> void

2. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::RigidChunkClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) → bool

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) → None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(class std::basic_istream<char> &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) → None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(class std::basic_istream<char> &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, cm: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → None

C++: protocols::topology_broker::RigidChunkClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) → None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) → None

C++: protocols::topology_broker::TopologyClaimer::set_label(const class std::basic_string<char> &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) → None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, : pyrosetta.rosetta.core.pose.Pose, bNeedToRepack: pyrosetta.rosetta.utility.vector1_bool) → None

rigid-chunk can probably provide some side-chain info from full-length model

C++: protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::RigidChunkClaimer::type() const –> std::string

use_loops_from_threading_job(*args, **kwargs)

Overloaded function.

1. use_loops_from_threading_job(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer) -> bool

Returns true if we are using loop definitions from ThreadingJob

C++: protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job() const –> bool

2. use_loops_from_threading_job(self: pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer, setting: bool) -> None

Sets whether we should use loop definitions from ThreadingJob

C++: protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job(bool) –> void

class pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer, arg0: str, arg1: int) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer, config_file: str, fragsize: int, weight: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> None
4. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer, arg0: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

_static_type_name() → str

C++: protocols::topology_broker::TemplateFragmentClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer

C++: protocols::topology_broker::TemplateFragmentClaimer::operator=(const class protocols::topology_broker::TemplateFragmentClaimer &) –> class protocols::topology_broker::TemplateFragmentClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TemplateFragmentClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) → None

multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

2. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) → bool

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) → None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(class std::basic_istream<char> &) –> void

read_config_file(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer, file: str) → None

C++: protocols::topology_broker::TemplateFragmentClaimer::read_config_file(const class std::basic_string<char> &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) → None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(class std::basic_istream<char> &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) → None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) → None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) → None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) → None

C++: protocols::topology_broker::TopologyClaimer::set_label(const class std::basic_string<char> &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const class std::basic_string<char> &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) → None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) → None

has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::TemplateFragmentClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, arg0: str) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, config_file: str, weight: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> None
4. __init__(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, arg0: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

_static_type_name() → str

C++: protocols::topology_broker::TemplateJumpClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer

C++: protocols::topology_broker::TemplateJumpClaimer::operator=(const class protocols::topology_broker::TemplateJumpClaimer &) –> class protocols::topology_broker::TemplateJumpClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TemplateJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) → None

multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void

2. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) → bool

claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) → None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(class std::basic_istream<char> &) –> void

read_config_file(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, file: str) → None

C++: protocols::topology_broker::TemplateJumpClaimer::read_config_file(const class std::basic_string<char> &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) → None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(class std::basic_istream<char> &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, tag: str, is: pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::FragmentJumpClaimer::read_tag(class std::basic_string<char>, class std::basic_istream<char> &) –> bool

read_topol_file(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer, file: str) → None

C++: protocols::topology_broker::TemplateJumpClaimer::read_topol_file(const class std::basic_string<char> &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) → None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) → None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) → None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) → None

C++: protocols::topology_broker::TopologyClaimer::set_label(const class std::basic_string<char> &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) → None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const class std::basic_string<char> &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) → None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) → None

has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::TemplateJumpClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_topology_broker_TopologyClaimerFactory_t

A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method. APL Question: Should this be one-instance-per-program (singleton) or one-instance-per-job?

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_type(*args, **kwargs)

Overloaded function.

1. add_type(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory, name: str, claimer: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

Registers the TopologyClaimer with name <name>. Instances of this

class can be retrieved by calling newTopologyClaimer(<name>).

C++: protocols::topology_broker::TopologyClaimerFactory::add_type(const class std::basic_string<char> &, class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>) –> void

2. add_type(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory, claimer: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

Registers the TopologyClaimer using the name returned by

claimer->type(). Instances of this class can be retrieved by calling newTopologyClaimer(<name>).

C++: protocols::topology_broker::TopologyClaimerFactory::add_type(class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>) –> void

get_instance() → protocols::topology_broker::TopologyClaimerFactory

C++: utility::SingletonBase<protocols::topology_broker::TopologyClaimerFactory>::get_instance() –> class protocols::topology_broker::TopologyClaimerFactory *

newTopologyClaimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory, name: str) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

Returns a new instance of the TopologyClaimer identified by <name>

C++: protocols::topology_broker::TopologyClaimerFactory::newTopologyClaimer(const class std::basic_string<char> &) const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

pyrosetta.rosetta.protocols.topology_broker.add_cmdline_claims(*args, **kwargs)

Overloaded function.

1. add_cmdline_claims(: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) -> None
2. add_cmdline_claims(: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, do_I_need_frags: bool) -> None

read broker::setup flag and add all claims to Broker

C++: protocols::topology_broker::add_cmdline_claims(class protocols::topology_broker::TopologyBroker &, bool) –> void