topology_broker

• claims
• weights

Bindings for protocols::topology_broker namespace

class pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.AsymFoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) → None

C++: protocols::topology_broker::AsymFoldandDockClaimer::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, : 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.AsymFoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) → pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer

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

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

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

docking_jump(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, pose: pyrosetta.rosetta.core.pose.Pose, chain_break_res: int) → int

C++: protocols::topology_broker::AsymFoldandDockClaimer::docking_jump(class core::pose::Pose &, unsigned long) –> unsigned long

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.AsymFoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::AsymFoldandDockClaimer::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.AsymFoldandDockClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::AsymFoldandDockClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

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

C++: protocols::topology_broker::AsymFoldandDockClaimer::read_tag(std::string, std::istream &) –> 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_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 std::string &) –> 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.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.AsymFoldandDockClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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, : 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.BasicJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer

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

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

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

end_label(*args, **kwargs)

Overloaded function.

1. end_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> str

C++: protocols::topology_broker::BasicJumpClaimer::end_label() const –> const std::string &

2. end_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, endLabel: str) -> None

C++: protocols::topology_broker::BasicJumpClaimer::end_label(const std::string &) –> void

end_position(*args, **kwargs)

Overloaded function.

1. end_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> int

C++: protocols::topology_broker::BasicJumpClaimer::end_position() const –> unsigned long

2. end_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, endPosition: int) -> None

C++: protocols::topology_broker::BasicJumpClaimer::end_position(unsigned long) –> void

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.BasicJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::BasicJumpClaimer::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.BasicJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::BasicJumpClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.BasicJumpClaimer) → pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer

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

start_label(*args, **kwargs)

Overloaded function.

1. start_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> str

C++: protocols::topology_broker::BasicJumpClaimer::start_label() const –> const std::string &

2. start_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, startLabel: str) -> None

C++: protocols::topology_broker::BasicJumpClaimer::start_label(const std::string &) –> void

start_position(*args, **kwargs)

Overloaded function.

1. start_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> int

C++: protocols::topology_broker::BasicJumpClaimer::start_position() const –> unsigned long

2. start_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, startPosition: int) -> None

C++: protocols::topology_broker::BasicJumpClaimer::start_position(unsigned long) –> void

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.BasicJumpClaimer) → str

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

class pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage

Bases: pybind11_object

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

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

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

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

matches(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, label: str) → bool

C++: protocols::topology_broker::ClaimerMessage::matches(const std::string &) –> bool

nr_recepients(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → int

C++: protocols::topology_broker::ClaimerMessage::nr_recepients() const –> unsigned long

received(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → bool

C++: protocols::topology_broker::ClaimerMessage::received() const –> bool

received_by_me(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, me: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) → None

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

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

C++: protocols::topology_broker::ClaimerMessage::set_label(const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, : pyrosetta.rosetta.std.ostream) → None

C++: protocols::topology_broker::ClaimerMessage::show(std::ostream &) const –> void

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

name of Claimer

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

class pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

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

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

C++: protocols::topology_broker::ConstraintClaimer::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, : 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.ConstraintClaimer, : pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer

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

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

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

combine_ratio(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → int

C++: protocols::topology_broker::ConstraintClaimer::combine_ratio() const –> unsigned long

drop_random_rate(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → float

C++: protocols::topology_broker::ConstraintClaimer::drop_random_rate() const –> double

filter_name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → str

C++: protocols::topology_broker::ConstraintClaimer::filter_name() const –> const std::string &

filter_weight(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → float

C++: protocols::topology_broker::ConstraintClaimer::filter_weight() const –> double

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.ConstraintClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::ConstraintClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → None

C++: protocols::topology_broker::ConstraintClaimer::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(std::istream &) –> 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(std::istream &) –> void

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

C++: protocols::topology_broker::ConstraintClaimer::read_tag(std::string, std::istream &) –> 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_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_centroid(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: bool) → None

C++: protocols::topology_broker::ConstraintClaimer::set_centroid(bool) –> void

set_combine_ratio(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: int) → None

C++: protocols::topology_broker::ConstraintClaimer::set_combine_ratio(unsigned long) –> void

set_cst_file(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : str) → None

C++: protocols::topology_broker::ConstraintClaimer::set_cst_file(const std::string &) –> void

set_filter_weight(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, weight: float) → None

C++: protocols::topology_broker::ConstraintClaimer::set_filter_weight(double) –> void

set_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: bool) → None

C++: protocols::topology_broker::ConstraintClaimer::set_fullatom(bool) –> void

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

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

set_skip_redundant(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: int) → None

C++: protocols::topology_broker::ConstraintClaimer::set_skip_redundant(unsigned long) –> void

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

tag(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) → str

C++: protocols::topology_broker::ConstraintClaimer::tag() const –> const std::string &

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

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper

Bases: PoseEvaluator

applicable(self: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, : pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

2. apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

C++: protocols::topology_broker::ConstraintEvaluatorWrapper::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

3. apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose: pyrosetta.rosetta.core.pose.Pose) -> float

C++: protocols::topology_broker::ConstraintEvaluatorWrapper::apply(class core::pose::Pose &) const –> double

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

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

name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, i: int) → str

C++: protocols::topology_broker::ConstraintEvaluatorWrapper::name(unsigned long) const –> std::string

size(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) → int

C++: protocols::topology_broker::ConstraintEvaluatorWrapper::size() const –> unsigned long

class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator

Bases: EvaluatorCreator

creator for the ConstraintsEvaluatorWrapperCreator class

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.CoordConstraintClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

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

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

C++: protocols::topology_broker::CoordConstraintClaimer::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, : 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.CoordConstraintClaimer, : pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) → pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer

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

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

C++: protocols::topology_broker::CoordConstraintClaimer::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.CoordConstraintClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::CoordConstraintClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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.CoordConstraintClaimer) -> None

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

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

C++: protocols::topology_broker::CoordConstraintClaimer::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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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

superimpose(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

superimpose xyz coords in constraints_ with pose

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

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.CoordConstraintClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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, : 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.CutBiasClaimer, : pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) → pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

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

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

C++: protocols::topology_broker::CutBiasClaimer::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.CutBiasClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::CutBiasClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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.CutBiasClaimer, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::topology_broker::CutBiasClaimer::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.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.CutBiasClaimer, : pyrosetta.rosetta.std.istream) → None

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

C++: protocols::topology_broker::CutBiasClaimer::read(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.CutBiasClaimer) → pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

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

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.CutBiasClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

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

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

C++: protocols::topology_broker::DensityScoringClaimer::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, : 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.DensityScoringClaimer, : pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) → pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

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

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

C++: protocols::topology_broker::DensityScoringClaimer::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.DensityScoringClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::DensityScoringClaimer::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.DensityScoringClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::DensityScoringClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.DensityScoringClaimer) → pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

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

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.DensityScoringClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer

Bases: 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

static _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, : 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) → 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: 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(std::istream &) –> 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(std::istream &) –> 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(std::string, std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.EXCN_FailedBroking

Bases: EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed

Bases: EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.topology_broker.EXCN_Input

Bases: BadInput

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker

Bases: Exception

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown

Bases: EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.FibrilModelingClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) → None

C++: protocols::topology_broker::FibrilModelingClaimer::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.FibrilModelingClaimer, : pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) → bool

has to decline foreign BB claims for slave regions

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

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

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

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

C++: protocols::topology_broker::FibrilModelingClaimer::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.FibrilModelingClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FibrilModelingClaimer::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.FibrilModelingClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FibrilModelingClaimer::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>

make_fibril(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::FibrilModelingClaimer::make_fibril(class core::pose::Pose &) –> void

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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.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.FibrilModelingClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.FoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) → None

C++: protocols::topology_broker::FoldandDockClaimer::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, : 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.FoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) → pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer

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

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

C++: protocols::topology_broker::FoldandDockClaimer::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.FoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FoldandDockClaimer::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.FoldandDockClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::FoldandDockClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.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.FoldandDockClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

Bases: TopologyClaimer

static _static_type_name() → str

C++: protocols::topology_broker::FragmentClaimer::_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, : 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.FragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

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

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

C++: protocols::topology_broker::FragmentClaimer::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(std::istream &) –> 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(std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.FragmentClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

Bases: 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

static _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, : 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) → 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: 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(std::istream &) –> 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(std::istream &) –> 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(std::string, std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.LoopFragmentClaimer

Bases: FragmentClaimer

static _static_type_name() → str

C++: protocols::topology_broker::LoopFragmentClaimer::_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, : 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.LoopFragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer) → pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer

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

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

C++: protocols::topology_broker::FragmentClaimer::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.LoopFragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::LoopFragmentClaimer::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.LoopFragmentClaimer, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::topology_broker::LoopFragmentClaimer::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(std::istream &) –> 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(std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.LoopFragmentClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

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

addVirtualResAsRootMembrane(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(class core::pose::Pose &) –> void

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.MembraneTopologyClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) → None

C++: protocols::topology_broker::MembraneTopologyClaimer::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, : 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.MembraneTopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer

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

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

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

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: 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.MembraneTopologyClaimer) → bool

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

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

C++: protocols::topology_broker::MembraneTopologyClaimer::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.MembraneTopologyClaimer, dof_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::MembraneTopologyClaimer::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.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::topology_broker::MembraneTopologyClaimer::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.MembraneTopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::MembraneTopologyClaimer::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_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.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::MembraneTopologyClaimer::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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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.MembraneTopologyClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

Bases: SequenceClaimer, FragmentJumpClaimer

static _static_type_name() → str

C++: protocols::topology_broker::MetalloClaimer::_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.MetalloClaimer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::MetalloClaimer::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, : 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.MetalloClaimer, : pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) → pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

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

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

C++: protocols::topology_broker::MetalloClaimer::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.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::MetalloClaimer::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.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::MetalloClaimer::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.MetalloClaimer, pose: 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::MetalloClaimer::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(std::istream &) –> 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(std::istream &) –> 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(std::string, std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.MetalloClaimer) → pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

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

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.MetalloClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController

Bases: TopologyClaimer

static _static_type_name() → str

return the type name

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PcsEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

This is called each time the stageID is changed

C++: protocols::topology_broker::PcsEnergyController::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, : 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.PcsEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) → pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController

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

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

C++: protocols::topology_broker::PcsEnergyController::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) → None

Called Each time END CLAIMER is processed

C++: protocols::topology_broker::PcsEnergyController::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

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

This is called to process each tag

C++: protocols::topology_broker::PcsEnergyController::read_tag(std::string, std::istream &) –> 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_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_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) → None

Called any time the CLAIMER is being read (before any tag is read)

C++: protocols::topology_broker::PcsEnergyController::set_defaults() –> void

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

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> 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.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.PcsEnergyController) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController::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, : 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.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) → pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController

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

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

C++: protocols::topology_broker::PseudocontactShiftEnergyController::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

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

C++: protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(std::string, std::istream &) –> 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_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 std::string &) –> 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.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.PseudocontactShiftEnergyController) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1

Bases: TopologyClaimer

static _static_type_name() → str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::_static_type_name() –> std::string

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PseudocontactShiftEnergyController_Ts1, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::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, : 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.PseudocontactShiftEnergyController_Ts1, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) → pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → 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: 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.PseudocontactShiftEnergyController_Ts1) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1, tag: str, : pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(std::string, std::istream &) –> 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_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_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::set_defaults() –> void

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

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> 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.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.PseudocontactShiftEnergyController_Ts1) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2

Bases: TopologyClaimer

static _static_type_name() → str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::_static_type_name() –> std::string

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PseudocontactShiftEnergyController_Ts2, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::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, : 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.PseudocontactShiftEnergyController_Ts2, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) → pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → 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: 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.PseudocontactShiftEnergyController_Ts2) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2, tag: str, : pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::read_tag(std::string, std::istream &) –> 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_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_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::set_defaults() –> void

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

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> 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.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.PseudocontactShiftEnergyController_Ts2) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3

Bases: TopologyClaimer

static _static_type_name() → str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::_static_type_name() –> std::string

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PseudocontactShiftEnergyController_Ts3, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::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, : 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.PseudocontactShiftEnergyController_Ts3, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) → pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → 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: 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.PseudocontactShiftEnergyController_Ts3) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3, tag: str, : pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(std::string, std::istream &) –> 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_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_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::set_defaults() –> void

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

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> 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.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.PseudocontactShiftEnergyController_Ts3) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4

Bases: TopologyClaimer

static _static_type_name() → str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::_static_type_name() –> std::string

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.PseudocontactShiftEnergyController_Ts4, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::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, : 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.PseudocontactShiftEnergyController_Ts4, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) → pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → 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: 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.PseudocontactShiftEnergyController_Ts4) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4, tag: str, : pyrosetta.rosetta.std.istream) → bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(std::string, std::istream &) –> 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_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_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) → None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::set_defaults() –> void

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

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> 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.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.PseudocontactShiftEnergyController_Ts4) → str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover

Bases: RigidBodyMover

apply(self: pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::RigidBodyRandomTMHMover::apply(class core::pose::Pose &) –> void

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

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None

C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover) → str

C++: protocols::topology_broker::RigidBodyRandomTMHMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

static name() → str

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

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

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

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

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool

C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

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

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

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

rb_jump(*args, **kwargs)

Overloaded function.

1. rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

2. rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> void

static register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> void

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

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

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

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

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

setter for poses contained for rms

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

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

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

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

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

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> None

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

C++: protocols::rigid::RigidBodyMover::show(std::ostream &) const –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None

C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer

Bases: 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.

class CM_SuggestFixResidue

Bases: ClaimerMessage

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

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

property good_fix_pos_

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

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

matches(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, label: str) → bool

C++: protocols::topology_broker::ClaimerMessage::matches(const std::string &) –> bool

nr_recepients(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → int

C++: protocols::topology_broker::ClaimerMessage::nr_recepients() const –> unsigned long

received(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → bool

C++: protocols::topology_broker::ClaimerMessage::received() const –> bool

received_by_me(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, me: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) → None

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

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

C++: protocols::topology_broker::ClaimerMessage::set_label(const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, : pyrosetta.rosetta.std.ostream) → None

C++: protocols::topology_broker::ClaimerMessage::show(std::ostream &) const –> void

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

name of Claimer

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

static _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) → 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: 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(std::istream &) –> 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(std::istream &) –> 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 std::string &) –> 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.SequenceClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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, : 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.SequenceClaimer, : pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer) → pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer

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

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

C++: protocols::topology_broker::SequenceClaimer::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.SequenceClaimer, : 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 if this Sequence has been moved from position 1 — needs to issue a fixed CUT in the fold-tree

C++: protocols::topology_broker::SequenceClaimer::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.SequenceClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::SequenceClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.SequenceClaimer) → pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer

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

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.SequenceClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver

Bases: pybind11_object

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

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

find_global_pose_number(*args, **kwargs)

Overloaded function.

1. find_global_pose_number(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, label: str, resid: int) -> int

Returns global position of element at position resid in sequence claim with the specified label.

C++: protocols::topology_broker::SequenceNumberResolver::find_global_pose_number(const std::string &, unsigned long) const –> unsigned long

2. find_global_pose_number(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, pos_pair: Tuple[str, int]) -> int

C++: protocols::topology_broker::SequenceNumberResolver::find_global_pose_number(struct std::pair<std::string, unsigned long>) const –> unsigned long

3. find_global_pose_number(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, label: str) -> int

Returns global position of first element of sequence claim with the specified label.

C++: protocols::topology_broker::SequenceNumberResolver::find_global_pose_number(const std::string &) const –> unsigned long

find_label(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, pose_number: int) → str

Returns label of sequence claim that corresponds to the global sequence position <pose_number>

C++: protocols::topology_broker::SequenceNumberResolver::find_label(unsigned long) const –> std::string

find_local_pose_number(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, pose_number: int) → int

Returns position of global <pose_number> in corresponding sequence claim.

C++: protocols::topology_broker::SequenceNumberResolver::find_local_pose_number(unsigned long) const –> unsigned long

offset(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, label: str) → int

Returns offset of a given label.

C++: protocols::topology_broker::SequenceNumberResolver::offset(const std::string &) const –> unsigned long

register_label_offset(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver, label: str, offset: int) → None

EXCN_BadInput if label or offset is already taken

C++: protocols::topology_broker::SequenceNumberResolver::register_label_offset(const std::string &, unsigned long) –> void

terminal_pair(self: pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver) → Tuple[int, str]

returns the map element with the largest offset = SequenceClaim at the end of the sequence

C++: protocols::topology_broker::SequenceNumberResolver::terminal_pair() const –> struct std::pair<unsigned long, std::string >

class pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer

Bases: FragmentClaimer

static _static_type_name() → str

C++: protocols::topology_broker::StartStructClaimer::_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, : 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.StartStructClaimer, : pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer) → pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer

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

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

C++: protocols::topology_broker::StartStructClaimer::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.StartStructClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

C++: protocols::topology_broker::StartStructClaimer::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.StartStructClaimer, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::StartStructClaimer::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.StartStructClaimer, : 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

overloaded to allow perturbation of start structure

C++: protocols::topology_broker::StartStructClaimer::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.StartStructClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

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

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

C++: protocols::topology_broker::StartStructClaimer::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(std::istream &) –> 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(std::istream &) –> void

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

C++: protocols::topology_broker::StartStructClaimer::read_tag(std::string, std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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.StartStructClaimer) → pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer

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

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.StartStructClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage

Bases: ClaimerMessage

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

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

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

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

matches(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, label: str) → bool

C++: protocols::topology_broker::ClaimerMessage::matches(const std::string &) –> bool

nr_recepients(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → int

C++: protocols::topology_broker::ClaimerMessage::nr_recepients() const –> unsigned long

received(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → bool

C++: protocols::topology_broker::ClaimerMessage::received() const –> bool

received_by_me(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, me: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) → None

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

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

C++: protocols::topology_broker::ClaimerMessage::set_label(const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, : pyrosetta.rosetta.std.ostream) → None

C++: protocols::topology_broker::ClaimerMessage::show(std::ostream &) const –> void

property some_claim_

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

name of Claimer

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

class pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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, : 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.SymmetryClaimer, : pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer) → pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer

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

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

C++: protocols::topology_broker::SymmetryClaimer::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.SymmetryClaimer) → pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer

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

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

symmetry_duplicate(self: pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(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 core::pose::Pose &) –> void

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

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

class pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer

Bases: TopologyClaimer

static _static_type_name() → str

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

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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.TMHTopologySamplerClaimer, : 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::TMHTopologySamplerClaimer::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, : 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.TMHTopologySamplerClaimer, : pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) → pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer

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

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

this claimer builds its own radial fold tree based on read-in spanfile

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

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: 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.TMHTopologySamplerClaimer) → bool

the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself

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

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

TMHTopologySamplerClaimer has virtual functions… use this to obtain a new instance

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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.TMHTopologySamplerClaimer, dof_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate DofClaims

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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.TMHTopologySamplerClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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.TMHTopologySamplerClaimer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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.TMHTopologySamplerClaimer, pose: pyrosetta.rosetta.core.pose.Pose, init_dofs: 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

make move_map and add the DoF claims from generate_claims() to the movemap. Now we can move certain parts with certain DOFs.

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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_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.TMHTopologySamplerClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

read in the pose’s spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc.

C++: protocols::topology_broker::TMHTopologySamplerClaimer::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(std::istream &) –> 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(std::istream &) –> void

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

read tag from topology broker file (setup.tpb)

C++: protocols::topology_broker::TMHTopologySamplerClaimer::read_tag(std::string, std::istream &) –> 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

static register_options() → None

register cmd-line options in option system ( call before core::init )

C++: protocols::topology_broker::TMHTopologySamplerClaimer::register_options() –> 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 std::string &) –> 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.TMHTopologySamplerClaimer, pose: pyrosetta.rosetta.core.pose.Pose) → None

get the pose from the boker and set it as this object’s pose

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

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.TMHTopologySamplerClaimer) → str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer

Bases: FragmentClaimer

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

static _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, : 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) → 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: 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(std::istream &) –> void

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

C++: protocols::topology_broker::TemplateFragmentClaimer::read_config_file(const std::string &) –> 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(std::istream &) –> 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 std::string &) –> 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 std::string &) –> 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: FragmentJumpClaimer

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

static _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, : 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) → 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: 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(std::istream &) –> void

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

C++: protocols::topology_broker::TemplateJumpClaimer::read_config_file(const std::string &) –> 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(std::istream &) –> 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(std::string, std::istream &) –> bool

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

C++: protocols::topology_broker::TemplateJumpClaimer::read_topol_file(const std::string &) –> 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 std::string &) –> 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 std::string &) –> 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.TopologyBroker

Bases: pybind11_object

add(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, cl: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → None

—————- Application Setup ————————————

add new Claimers to the broker —- useful before a job is started

C++: protocols::topology_broker::TopologyBroker::add(class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>) –> void

add_chainbreak_variants(*args, **kwargs)

Overloaded function.

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

2. add_chainbreak_variants(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, pose: pyrosetta.rosetta.core.pose.Pose, max_dist: int) -> None

3. add_chainbreak_variants(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, pose: pyrosetta.rosetta.core.pose.Pose, max_dist: int, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) -> None

add chainbreak variant residue to the unphysical chainbreaks

C++: protocols::topology_broker::TopologyBroker::add_chainbreak_variants(class core::pose::Pose &, unsigned long, class std::shared_ptr<const class core::kinematics::ShortestPathInFoldTree>) const –> void

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

if some claimer wants to influence the movemap for relax he can do it here:

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

apply(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, : pyrosetta.rosetta.core.pose.Pose) → None

———————– Job Setup ——————————————

at the start of a job this is called, e.g., by the AbrelaxMover it generates a pose with appropriate foldtree and initializes dofs, adds constraints, etc.

C++: protocols::topology_broker::TopologyBroker::apply(class core::pose::Pose &) –> void

apply_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, progress: float) → None

apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed

C++: protocols::topology_broker::TopologyBroker::apply_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double) const –> void

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

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

check_chainbreak_variants(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, pose: pyrosetta.rosetta.core.pose.Pose) → bool

check that each chainbreak residue has a chainbreak variant

C++: protocols::topology_broker::TopologyBroker::check_chainbreak_variants(class core::pose::Pose &) const –> bool

claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, i: int) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

Returns the ith topology claimer if it exists.

C++: protocols::topology_broker::TopologyBroker::claimer(unsigned long) const –> const class std::shared_ptr<class protocols::topology_broker::TopologyClaimer> &

current_pose(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyBroker::current_pose() const –> const class core::pose::Pose &

does_final_fold_tree_exist(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → bool

C++: protocols::topology_broker::TopologyBroker::does_final_fold_tree_exist() const –> bool

final_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → pyrosetta.rosetta.core.kinematics.FoldTree

access for hacky claimers

C++: protocols::topology_broker::TopologyBroker::final_fold_tree() const –> class core::kinematics::FoldTree &

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

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyBroker_t

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

has_chainbreaks_to_close(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → bool

do we need to close loops ( unphysical chainbreaks have been introduced? )

C++: protocols::topology_broker::TopologyBroker::has_chainbreaks_to_close() const –> bool

has_sequence_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → bool

/ ——————————- End Consulting ——————————————–

C++: protocols::topology_broker::TopologyBroker::has_sequence_claimer() –> bool

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

the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part

thus extra hook for this — > only some Claimers will answer

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

mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) → pyrosetta.rosetta.protocols.moves.Mover

return a set of Movers ( RandomMover, i.e. container of movers )

C++: protocols::topology_broker::TopologyBroker::mover(const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) const –> class std::shared_ptr<class protocols::moves::Mover>

num_claimers(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → int

Returns the number of claimers associated with the broker

C++: protocols::topology_broker::TopologyBroker::num_claimers() const –> unsigned long

relay_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, msg: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) → None

C++: protocols::topology_broker::TopologyBroker::relay_message(class protocols::topology_broker::ClaimerMessage &) const –> void

resolve_sequence_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, label: str) → protocols::topology_broker::claims::SequenceClaim

get the sequence claim that is consistent with the label,

throws EXCN_Unknown_SequenceLabel if not found

C++: protocols::topology_broker::TopologyBroker::resolve_sequence_label(const std::string &) const –> class protocols::topology_broker::claims::SequenceClaim &

sequence_number_resolver(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) → pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver

C++: protocols::topology_broker::TopologyBroker::sequence_number_resolver() const –> const class protocols::topology_broker::SequenceNumberResolver &

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

switch to fullatom — some Claimers might help by providing template based side-chain information

C++: protocols::topology_broker::TopologyBroker::switch_to_fullatom(class core::pose::Pose &) –> void

use_job_pose(*args, **kwargs)

Overloaded function.

1. use_job_pose(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker, setting: bool) -> None

use the input pose from the job (i.e., call new_decoy( pose ) )

C++: protocols::topology_broker::TopologyBroker::use_job_pose(bool) –> void

2. use_job_pose(self: pyrosetta.rosetta.protocols.topology_broker.TopologyBroker) -> bool

Returns true if we are using the input pose from the job

(i.e. new_decoy(pose)), false otherwise.

C++: protocols::topology_broker::TopologyBroker::use_job_pose() const –> bool

class pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

Bases: pybind11_object

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

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::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, : 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.TopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) → pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

clone it!

C++: protocols::topology_broker::TopologyClaimer::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.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) → None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::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.TopologyClaimer, : 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 dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::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_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(std::istream &) –> 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(std::istream &) –> 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_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 std::string &) –> 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.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.TopologyClaimer) → str

name of Claimer

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

class pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory

Bases: 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?

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 std::string &, 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

static 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 std::string &) 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