topology_broker

Bindings for protocols::topology_broker namespace

class pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

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

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

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

end_label(*args, **kwargs)

Overloaded function.

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

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

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

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

end_position(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer

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

start_label(*args, **kwargs)

Overloaded function.

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

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

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

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

start_position(*args, **kwargs)

Overloaded function.

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

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

  1. 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_builtins.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: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) None

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

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

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

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

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper

Bases: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator

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

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

apply(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.protocols.evaluation.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: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer, : pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

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

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

superimpose xyz coords in constraints_ with pose

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

type(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer, : pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

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

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

type(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, : pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

type(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

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

static _static_type_name() str

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

allow a claim from a foreign Claimer

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

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

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

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

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking

Bases: pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.utility.excn.BadInput

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.utility.excn.Exception

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker

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

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

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

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

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

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

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

  1. 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: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None

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

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

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

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

has to decline foreign BB claims for slave regions

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

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

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

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

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

type(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer) str

type() is specifying the output name of the TopologyClaimer

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

class pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

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

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

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

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

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

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

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

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None

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

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

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

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

allow a claim from a foreign Claimer

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

assign(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer

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

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

return the broker we are collaborating with

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

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

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

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

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

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

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

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

clone(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

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

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

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

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

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

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

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

generate claims that affect the sequence of the pose

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

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

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

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

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

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

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

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

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

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

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

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

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

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

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

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

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

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

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

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

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

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

new_decoy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

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

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::FoldandDockClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

C++: protocols::topology_broker::FragmentClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::operator=(const class protocols::topology_broker::FragmentClaimer &) –> class protocols::topology_broker::FragmentClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::FragmentClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::FragmentClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore

static _static_type_name() str

C++: protocols::topology_broker::FragmentJumpClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::operator=(const class protocols::topology_broker::FragmentJumpClaimer &) –> class protocols::topology_broker::FragmentJumpClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, tag: str, is: pyrosetta.rosetta.std.istream) bool

C++: protocols::topology_broker::FragmentJumpClaimer::read_tag(std::string, std::istream &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::FragmentJumpClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

static _static_type_name() str

C++: protocols::topology_broker::LoopFragmentClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer

C++: protocols::topology_broker::LoopFragmentClaimer::operator=(const class protocols::topology_broker::LoopFragmentClaimer &) –> class protocols::topology_broker::LoopFragmentClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::FragmentClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::LoopFragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::FragmentClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::topology_broker::LoopFragmentClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer

C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::LoopFragmentClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

C++: protocols::topology_broker::MembraneTopologyClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

addVirtualResAsRootMembrane(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(class core::pose::Pose &) –> void

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None

C++: protocols::topology_broker::MembraneTopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer

C++: protocols::topology_broker::MembraneTopologyClaimer::operator=(const class protocols::topology_broker::MembraneTopologyClaimer &) –> class protocols::topology_broker::MembraneTopologyClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose, fold_tree_in: pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::MembraneTopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) bool

C++: protocols::topology_broker::MembraneTopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::MembraneTopologyClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, dof_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::MembraneTopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::topology_broker::MembraneTopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::MembraneTopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::MembraneTopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::MembraneTopologyClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

Bases: pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer, pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer

static _static_type_name() str

C++: protocols::topology_broker::MetalloClaimer::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool

C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::MetalloClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, : pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

C++: protocols::topology_broker::MetalloClaimer::operator=(const class protocols::topology_broker::MetalloClaimer &) –> class protocols::topology_broker::MetalloClaimer &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::MetalloClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::MetalloClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::MetalloClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None

C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, pose: pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

C++: protocols::topology_broker::MetalloClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str

C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None

C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, tag: str, is: pyrosetta.rosetta.std.istream) bool

C++: protocols::topology_broker::FragmentJumpClaimer::read_tag(std::string, std::istream &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_bInitDofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, set: bool) None

C++: protocols::topology_broker::FragmentClaimer::set_bInitDofs(bool) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, mover: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) None

C++: protocols::topology_broker::FragmentClaimer::set_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

set_mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, str: str) None

C++: protocols::topology_broker::FragmentClaimer::set_mover_tag(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer

C++: protocols::topology_broker::MetalloClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::MetalloClaimer>

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::MetalloClaimer::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

return the type name

C++: protocols::topology_broker::PcsEnergyController::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None

This is called each time the stageID is changed

C++: protocols::topology_broker::PcsEnergyController::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController

C++: protocols::topology_broker::PcsEnergyController::operator=(const class protocols::topology_broker::PcsEnergyController &) –> class protocols::topology_broker::PcsEnergyController &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PcsEnergyController::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) None

Called Each time END CLAIMER is processed

C++: protocols::topology_broker::PcsEnergyController::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, tag: str, : pyrosetta.rosetta.std.istream) bool

This is called to process each tag

C++: protocols::topology_broker::PcsEnergyController::read_tag(std::string, std::istream &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) None

Called any time the CLAIMER is being read (before any tag is read)

C++: protocols::topology_broker::PcsEnergyController::set_defaults() –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PcsEnergyController::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

C++: protocols::topology_broker::PseudocontactShiftEnergyController::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController

C++: protocols::topology_broker::PseudocontactShiftEnergyController::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController &) –> class protocols::topology_broker::PseudocontactShiftEnergyController &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController, tag: str, : pyrosetta.rosetta.std.istream) bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(std::string, std::istream &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str

C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &

loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers

(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>

manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None
multiply your bias to this – if its zero don’t change that, i.e., multiply only

this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void

mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight

C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &

new_decoy(*args, **kwargs)

Overloaded function.

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None

a new decoy — random choices to be made ? make them here

C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void

  1. new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None

an input pose is given, i.e., a starting structure for resampling

don’t make random choices, base choices on given pose

C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool
claimers can add movers to the RandomMover (Container).

add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool

pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void

read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None

read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block

C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void

read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void

read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1, tag: str, : pyrosetta.rosetta.std.istream) bool

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(std::string, std::istream &) –> bool

receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None

C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void

set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None

don’t use this — it is called by TopologyBroker add_claim only

C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void

set_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::set_defaults() –> void

set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None

C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void

set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None

C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void

set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void

switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None
has this Claimer some side chain conformations to add?

starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void

type(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) str

type() is specifying the output name of the TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::type() const –> std::string

class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2

Bases: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

static _static_type_name() str

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::_static_type_name() –> std::string

accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )

C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None

add constraints to pose… might make this stage dependent as with movers…

C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void

add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void

adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void

allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool

allow a claim from a foreign Claimer

C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool

assign(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 &) –> class protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 &

broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker

return the broker we are collaborating with

C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &

build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void

claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None

this claim of yours was accepted…. I so far haven’t done anything with this… might go away.

C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void

claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool

C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool

clone(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate first round of DOF claims

C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None

generate claims that affect the sequence of the pose

C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void

get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>

get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose

C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer

C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t

C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>

init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) None

C++: protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::init_after_reading() –> void

initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer,