topology_broker¶

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.

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

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¶

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.

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

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

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.

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

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

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

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 claims that affect the sequence of the pose

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.

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

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

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.

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

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

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.

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

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

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¶

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

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_

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

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 claims that affect the sequence of the pose

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

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.

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

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¶

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

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_

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

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 claims that affect the sequence of the pose

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 – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

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.

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

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

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

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¶

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

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_

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

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 claims that affect the sequence of the pose

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 – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

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.

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

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

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

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_

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

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 – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

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.

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

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

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

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_

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

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 claims that affect the sequence of the pose

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.

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

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

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

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.

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

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.

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

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.

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

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.

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

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.

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

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¶

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

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 claims that affect the sequence of the pose

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.

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

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

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¶

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

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 claims that affect the sequence of the pose

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.

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

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

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

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_

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

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 claims that affect the sequence of the pose

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.

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

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

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

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

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_

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

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 claims that affect the sequence of the pose

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.

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

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

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

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

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_

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

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 claims that affect the sequence of the pose

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.

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

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

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¶

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

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 claims that affect the sequence of the pose

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.

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

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

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

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_

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

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.

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

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

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

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¶

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

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 claims that affect the sequence of the pose

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 – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

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.

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

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

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¶

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

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

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer,