topology_broker¶
Bindings for protocols::topology_broker namespace
- class pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::operator=(const class protocols::topology_broker::AsymFoldandDockClaimer &) –> class protocols::topology_broker::AsymFoldandDockClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- docking_jump(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, pose: pyrosetta.rosetta.core.pose.Pose, chain_break_res: int) int ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::docking_jump(class core::pose::Pose &, unsigned long) –> unsigned long
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- read_tag(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer, tag: str, is: pyrosetta.rosetta.std.istream) bool ¶
C++: protocols::topology_broker::AsymFoldandDockClaimer::read_tag(std::string, std::istream &) –> bool
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::AsymFoldandDockClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::BasicJumpClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
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.
end_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> str
C++: protocols::topology_broker::BasicJumpClaimer::end_label() const –> const std::string &
end_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, endLabel: str) -> None
C++: protocols::topology_broker::BasicJumpClaimer::end_label(const std::string &) –> void
- end_position(*args, **kwargs)¶
Overloaded function.
end_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> int
C++: protocols::topology_broker::BasicJumpClaimer::end_position() const –> unsigned long
end_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, endPosition: int) -> None
C++: protocols::topology_broker::BasicJumpClaimer::end_position(unsigned long) –> void
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
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.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- 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
C++: protocols::topology_broker::BasicJumpClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::BasicJumpClaimer>
- start_label(*args, **kwargs)¶
Overloaded function.
start_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> str
C++: protocols::topology_broker::BasicJumpClaimer::start_label() const –> const std::string &
start_label(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, startLabel: str) -> None
C++: protocols::topology_broker::BasicJumpClaimer::start_label(const std::string &) –> void
- start_position(*args, **kwargs)¶
Overloaded function.
start_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) -> int
C++: protocols::topology_broker::BasicJumpClaimer::start_position() const –> unsigned long
start_position(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer, startPosition: int) -> None
C++: protocols::topology_broker::BasicJumpClaimer::start_position(unsigned long) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer) str ¶
C++: protocols::topology_broker::BasicJumpClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, : pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage ¶
C++: protocols::topology_broker::ClaimerMessage::operator=(const class protocols::topology_broker::ClaimerMessage &) –> class protocols::topology_broker::ClaimerMessage &
- label(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) str ¶
C++: protocols::topology_broker::ClaimerMessage::label() const –> const std::string &
- matches(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, label: str) bool ¶
C++: protocols::topology_broker::ClaimerMessage::matches(const std::string &) –> bool
- nr_recepients(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) int ¶
C++: protocols::topology_broker::ClaimerMessage::nr_recepients() const –> unsigned long
- received(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) bool ¶
C++: protocols::topology_broker::ClaimerMessage::received() const –> bool
- received_by_me(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, me: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) None ¶
C++: protocols::topology_broker::ClaimerMessage::received_by_me(class std::weak_ptr<const class protocols::topology_broker::TopologyClaimer>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, str: str) None ¶
C++: protocols::topology_broker::ClaimerMessage::set_label(const std::string &) –> void
- show(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage, : pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::topology_broker::ClaimerMessage::show(std::ostream &) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage) str ¶
name of Claimer
C++: protocols::topology_broker::ClaimerMessage::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::ConstraintClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::ConstraintClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer ¶
C++: protocols::topology_broker::ConstraintClaimer::operator=(const class protocols::topology_broker::ConstraintClaimer &) –> class protocols::topology_broker::ConstraintClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::ConstraintClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- combine_ratio(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) int ¶
C++: protocols::topology_broker::ConstraintClaimer::combine_ratio() const –> unsigned long
- drop_random_rate(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) float ¶
C++: protocols::topology_broker::ConstraintClaimer::drop_random_rate() const –> double
- filter_name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) str ¶
C++: protocols::topology_broker::ConstraintClaimer::filter_name() const –> const std::string &
- filter_weight(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) float ¶
C++: protocols::topology_broker::ConstraintClaimer::filter_weight() const –> double
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::ConstraintClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this
C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) None ¶
C++: protocols::topology_broker::ConstraintClaimer::new_decoy() –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- read_tag(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, tag: str, : pyrosetta.rosetta.std.istream) bool ¶
C++: protocols::topology_broker::ConstraintClaimer::read_tag(std::string, std::istream &) –> bool
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_centroid(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: bool) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_centroid(bool) –> void
- set_combine_ratio(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: int) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_combine_ratio(unsigned long) –> void
- set_cst_file(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, : str) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_cst_file(const std::string &) –> void
- set_filter_weight(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, weight: float) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_filter_weight(double) –> void
- set_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: bool) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_fullatom(bool) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- set_skip_redundant(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer, setting: int) None ¶
C++: protocols::topology_broker::ConstraintClaimer::set_skip_redundant(unsigned long) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- tag(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) str ¶
C++: protocols::topology_broker::ConstraintClaimer::tag() const –> const std::string &
- type(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::ConstraintClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper¶
Bases:
PoseEvaluator
- applicable(self: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, : pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
C++: protocols::topology_broker::ConstraintEvaluatorWrapper::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void
apply(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose: pyrosetta.rosetta.core.pose.Pose) -> float
C++: protocols::topology_broker::ConstraintEvaluatorWrapper::apply(class core::pose::Pose &) const –> double
- assign(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, : pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapper::operator=(const class protocols::topology_broker::ConstraintEvaluatorWrapper &) –> class protocols::topology_broker::ConstraintEvaluatorWrapper &
- name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, i: int) str ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapper::name(unsigned long) const –> std::string
- size(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) int ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapper::size() const –> unsigned long
- class pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator¶
Bases:
EvaluatorCreator
creator for the ConstraintsEvaluatorWrapperCreator class
- add_evaluators(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator, : pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::operator=(const class protocols::topology_broker::ConstraintEvaluatorWrapperCreator &) –> class protocols::topology_broker::ConstraintEvaluatorWrapperCreator &
- register_options(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) None ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::register_options() –> void
- type_name(self: pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) str ¶
C++: protocols::topology_broker::ConstraintEvaluatorWrapperCreator::type_name() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::CoordConstraintClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
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.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) -> None
C++: protocols::topology_broker::CoordConstraintClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::topology_broker::CoordConstraintClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- superimpose(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
superimpose xyz coords in constraints_ with pose
C++: protocols::topology_broker::CoordConstraintClaimer::superimpose(const class core::pose::Pose &) const –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::CoordConstraintClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::CutBiasClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer, : pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer ¶
C++: protocols::topology_broker::CutBiasClaimer::operator=(const class protocols::topology_broker::CutBiasClaimer &) –> class protocols::topology_broker::CutBiasClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::CutBiasClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::CutBiasClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this
C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::topology_broker::CutBiasClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.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
C++: protocols::topology_broker::CutBiasClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::CutBiasClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::CutBiasClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::DensityScoringClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, was_declined: protocols::topology_broker::claims::DofClaim) bool ¶
C++: protocols::topology_broker::DensityScoringClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::DensityScoringClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, : pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer ¶
C++: protocols::topology_broker::DensityScoringClaimer::operator=(const class protocols::topology_broker::DensityScoringClaimer &) –> class protocols::topology_broker::DensityScoringClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::DensityScoringClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::DensityScoringClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::DensityScoringClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this
C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- 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
C++: protocols::topology_broker::DensityScoringClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::DensityScoringClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::DensityScoringClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer¶
Bases:
FragmentClaimer
Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore
- static _static_type_name() str ¶
C++: protocols::topology_broker::DisulfJumpClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool ¶
C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer ¶
C++: protocols::topology_broker::DisulfJumpClaimer::operator=(const class protocols::topology_broker::DisulfJumpClaimer &) –> class protocols::topology_broker::DisulfJumpClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::DisulfJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::DisulfJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_jump_frags(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, lib: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, all_frames: pyrosetta.rosetta.core.fragment.FrameList) None ¶
C++: protocols::topology_broker::DisulfJumpClaimer::generate_jump_frags(const class protocols::jumping::DisulfPairingLibrary &, class core::fragment::FrameList &) const –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::DisulfJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::topology_broker::DisulfJumpClaimer::new_decoy(const class core::pose::Pose &) –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) -> None
C++: protocols::topology_broker::DisulfJumpClaimer::new_decoy() –> void
- 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
C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::DisulfJumpClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking¶
Bases:
EXCN_TopologyBroker
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking, : pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking) pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking ¶
C++: protocols::topology_broker::EXCN_FailedBroking::operator=(const class protocols::topology_broker::EXCN_FailedBroking &) –> class protocols::topology_broker::EXCN_FailedBroking &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed¶
Bases:
EXCN_TopologyBroker
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed, : pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed) pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed ¶
C++: protocols::topology_broker::EXCN_FilterFailed::operator=(const class protocols::topology_broker::EXCN_FilterFailed &) –> class protocols::topology_broker::EXCN_FilterFailed &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.topology_broker.EXCN_Input¶
Bases:
BadInput
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.EXCN_Input, : pyrosetta.rosetta.protocols.topology_broker.EXCN_Input) pyrosetta.rosetta.protocols.topology_broker.EXCN_Input ¶
C++: protocols::topology_broker::EXCN_Input::operator=(const class protocols::topology_broker::EXCN_Input &) –> class protocols::topology_broker::EXCN_Input &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker¶
Bases:
Exception
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker, : pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker) pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker ¶
C++: protocols::topology_broker::EXCN_TopologyBroker::operator=(const class protocols::topology_broker::EXCN_TopologyBroker &) –> class protocols::topology_broker::EXCN_TopologyBroker &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown¶
Bases:
EXCN_TopologyBroker
- add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::add_msg(const std::string &) –> void
- assign(self: pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown, : pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown) pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown ¶
C++: protocols::topology_broker::EXCN_Unknown::operator=(const class protocols::topology_broker::EXCN_Unknown &) –> class protocols::topology_broker::EXCN_Unknown &
- crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Invoke a crash log for throwing this exception.
If your exception is one which is a “non-error” exception, override this function to do nothing.
C++: utility::excn::Exception::crash_log() const –> void
- display(self: pyrosetta.rosetta.utility.excn.Exception) None ¶
- Present this exception to the user.
Will invoke crash log reporting, if applicable
C++: utility::excn::Exception::display() const –> void
- file(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::file() –> const std::string &
- line(self: pyrosetta.rosetta.utility.excn.Exception) int ¶
C++: utility::excn::Exception::line() –> int
- msg(*args, **kwargs)¶
Overloaded function.
msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str
Will return a formatted message (with file/line information)
C++: utility::excn::Exception::msg() const –> std::string
msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None
Will set the raw message.
C++: utility::excn::Exception::msg(const std::string &) –> void
- prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None ¶
C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void
- raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
Will return the raw message (without file/line information)
C++: utility::excn::Exception::raw_msg() const –> std::string
- show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None ¶
C++: utility::excn::Exception::show(std::ostream &) const –> void
- traceback(self: pyrosetta.rosetta.utility.excn.Exception) str ¶
C++: utility::excn::Exception::traceback() –> const std::string &
- what(self: pyrosetta.rosetta.std.exception) str ¶
C++: std::exception::what() const –> const char *
- class pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::FibrilModelingClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
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.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::FibrilModelingClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::FoldandDockClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None ¶
C++: protocols::topology_broker::FoldandDockClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, : pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer ¶
C++: protocols::topology_broker::FoldandDockClaimer::operator=(const class protocols::topology_broker::FoldandDockClaimer &) –> class protocols::topology_broker::FoldandDockClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::FoldandDockClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, new_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FoldandDockClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FoldandDockClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::FoldandDockClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::FragmentClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool ¶
C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer ¶
C++: protocols::topology_broker::FragmentClaimer::operator=(const class protocols::topology_broker::FragmentClaimer &) –> class protocols::topology_broker::FragmentClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::FragmentClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- 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
C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::FragmentClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer¶
Bases:
FragmentClaimer
Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore
- static _static_type_name() str ¶
C++: protocols::topology_broker::FragmentJumpClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool ¶
C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer ¶
C++: protocols::topology_broker::FragmentJumpClaimer::operator=(const class protocols::topology_broker::FragmentJumpClaimer &) –> class protocols::topology_broker::FragmentJumpClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::FragmentJumpClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentJumpClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None
C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void
- 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
C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::FragmentJumpClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer¶
Bases:
FragmentClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::LoopFragmentClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool ¶
C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, : pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer ¶
C++: protocols::topology_broker::LoopFragmentClaimer::operator=(const class protocols::topology_broker::LoopFragmentClaimer &) –> class protocols::topology_broker::LoopFragmentClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::FragmentClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_mover(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::topology_broker::LoopFragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
C++: protocols::topology_broker::LoopFragmentClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- 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
C++: protocols::topology_broker::FragmentClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::FragmentClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::LoopFragmentClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- addVirtualResAsRootMembrane(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(class core::pose::Pose &) –> void
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, random_mover: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose, stageID: pyrosetta.rosetta.protocols.abinitio.StageID, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, : pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::operator=(const class protocols::topology_broker::MembraneTopologyClaimer &) –> class protocols::topology_broker::MembraneTopologyClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose, fold_tree_in: pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) bool ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, dof_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::MembraneTopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::MembraneTopologyClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer¶
Bases:
SequenceClaimer
,FragmentJumpClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::MetalloClaimer::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, was_declined: pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim) bool ¶
C++: protocols::topology_broker::FragmentClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::MetalloClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, : pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer ¶
C++: protocols::topology_broker::MetalloClaimer::operator=(const class protocols::topology_broker::MetalloClaimer &) –> class protocols::topology_broker::MetalloClaimer &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::MetalloClaimer::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::MetalloClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, dc: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::MetalloClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_mover(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::topology_broker::FragmentClaimer::get_mover(const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::moves::Mover>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- get_sequence_region(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer, start_region: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::topology_broker::FragmentClaimer::get_sequence_region(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) const –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer, pose: pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
C++: protocols::topology_broker::MetalloClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_tag(self: pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer) str ¶
C++: protocols::topology_broker::FragmentClaimer::mover_tag() const –> const std::string &
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy(const class core::pose::Pose &) –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer) -> None
C++: protocols::topology_broker::FragmentJumpClaimer::new_decoy() –> void
- 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
C++: protocols::topology_broker::MetalloClaimer::shared_from_this() –> class std::shared_ptr<class protocols::topology_broker::MetalloClaimer>
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::MetalloClaimer::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
return the type name
C++: protocols::topology_broker::PcsEnergyController::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
This is called each time the stageID is changed
C++: protocols::topology_broker::PcsEnergyController::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController ¶
C++: protocols::topology_broker::PcsEnergyController::operator=(const class protocols::topology_broker::PcsEnergyController &) –> class protocols::topology_broker::PcsEnergyController &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::PcsEnergyController::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate first round of DOF claims
C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate claims that affect the sequence of the pose
C++: protocols::topology_broker::TopologyClaimer::generate_sequence_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- get_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
in case a claimer has its own fold_tree. get_fold_tree() is called by the broker
C++: protocols::topology_broker::TopologyClaimer::get_fold_tree(class core::pose::Pose &) –> class std::shared_ptr<class core::kinematics::FoldTree>
- get_pose_from_claimer(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::topology_broker::TopologyClaimer::get_pose_from_claimer() –> class std::shared_ptr<class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_ptr() –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t ¶
C++: protocols::topology_broker::TopologyClaimer::get_self_weak_ptr() –> class std::weak_ptr<class protocols::topology_broker::TopologyClaimer>
- init_after_reading(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) None ¶
Called Each time END CLAIMER is processed
C++: protocols::topology_broker::PcsEnergyController::init_after_reading() –> void
- initialize_dofs(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, init_claims: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this
C++: protocols::topology_broker::TopologyClaimer::initialize_dofs(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &, class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) str ¶
C++: protocols::topology_broker::TopologyClaimer::label() const –> const std::string &
- loop_frags(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet ¶
- return fragments that can be used for loop-sampling… unfortunately some loop-samplers need fragments, rather then fragmovers
(e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling
C++: protocols::topology_broker::TopologyClaimer::loop_frags(class core::kinematics::MoveMap &) const –> class std::shared_ptr<const class core::fragment::FragSet>
- manipulate_cut_bias(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_double) None ¶
- multiply your bias to this – if its zero don’t change that, i.e., multiply only
this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction
C++: protocols::topology_broker::TopologyClaimer::manipulate_cut_bias(class utility::vector1<double, class std::allocator<double> > &) –> void
- mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight ¶
C++: protocols::topology_broker::TopologyClaimer::mover_weight() –> class protocols::topology_broker::weights::AbinitioMoverWeight &
- new_decoy(*args, **kwargs)¶
Overloaded function.
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) -> None
a new decoy — random choices to be made ? make them here
C++: protocols::topology_broker::TopologyClaimer::new_decoy() –> void
new_decoy(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) -> None
- an input pose is given, i.e., a starting structure for resampling
don’t make random choices, base choices on given pose
C++: protocols::topology_broker::TopologyClaimer::new_decoy(const class core::pose::Pose &) –> void
- passes_filter(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : float, : pyrosetta.rosetta.std.ostringstream) bool ¶
- claimers can add movers to the RandomMover (Container).
add your moves, make it dependent on stage if you want to. So far this is called only by abinitio… if you don’t want to do anything special — don’t overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_
C++: protocols::topology_broker::TopologyClaimer::passes_filter(const class core::pose::Pose &, enum protocols::abinitio::StageID, double, class std::basic_ostringstream<char> &) –> bool
- pre_process(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::pre_process(class core::pose::Pose &) –> void
- read(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.std.istream) None ¶
read definition of Claimer from setup file, i.e., a CLAIMER <type> … END_CLAIMER block
C++: protocols::topology_broker::TopologyClaimer::read(std::istream &) –> void
- read_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, is: pyrosetta.rosetta.std.istream) None ¶
read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage
C++: protocols::topology_broker::TopologyClaimer::read_mover_weight(std::istream &) –> void
- read_tag(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController, tag: str, : pyrosetta.rosetta.std.istream) bool ¶
This is called to process each tag
C++: protocols::topology_broker::PcsEnergyController::read_tag(std::string, std::istream &) –> bool
- receive_message(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::ClaimerMessage) None ¶
C++: protocols::topology_broker::TopologyClaimer::receive_message(class protocols::topology_broker::ClaimerMessage &) –> void
- set_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, ptr: pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) None ¶
don’t use this — it is called by TopologyBroker add_claim only
C++: protocols::topology_broker::TopologyClaimer::set_broker(class std::weak_ptr<const class protocols::topology_broker::TopologyBroker>) –> void
- set_defaults(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) None ¶
Called any time the CLAIMER is being read (before any tag is read)
C++: protocols::topology_broker::PcsEnergyController::set_defaults() –> void
- set_label(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, str: str) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_label(const std::string &) –> void
- set_mover_weight(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, wset: pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_mover_weight(class std::shared_ptr<class protocols::topology_broker::weights::AbinitioMoverWeight>) –> void
- set_pose_from_broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::topology_broker::TopologyClaimer::set_pose_from_broker(class core::pose::Pose &) –> void
- switch_to_fullatom(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- has this Claimer some side chain conformations to add?
starts with bNeedToRepack true for all residues… if you have a sidechain —> copy it to pose and set needtoRepack false for this residue
C++: protocols::topology_broker::TopologyClaimer::switch_to_fullatom(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) const –> void
- type(self: pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController) str ¶
type() is specifying the output name of the TopologyClaimer
C++: protocols::topology_broker::PcsEnergyController::type() const –> std::string
- class pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController¶
Bases:
TopologyClaimer
- static _static_type_name() str ¶
C++: protocols::topology_broker::PseudocontactShiftEnergyController::_static_type_name() –> std::string
- accept_declined_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can’t live without this claim being accepted. ( e.g., RigidChunks … )
C++: protocols::topology_broker::TopologyClaimer::accept_declined_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- add_constraints(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose) None ¶
add constraints to pose… might make this stage dependent as with movers…
C++: protocols::topology_broker::TopologyClaimer::add_constraints(class core::pose::Pose &) const –> void
- add_mover(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.abinitio.StageID, : pyrosetta.rosetta.core.scoring.ScoreFunction, : float) None ¶
C++: protocols::topology_broker::PseudocontactShiftEnergyController::add_mover(class protocols::moves::RandomMover &, const class core::pose::Pose &, enum protocols::abinitio::StageID, const class core::scoring::ScoreFunction &, double) –> void
- adjust_relax_movemap(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.kinematics.MoveMap) None ¶
C++: protocols::topology_broker::TopologyClaimer::adjust_relax_movemap(class core::kinematics::MoveMap &) const –> void
- allow_claim(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : protocols::topology_broker::claims::DofClaim) bool ¶
allow a claim from a foreign Claimer
C++: protocols::topology_broker::TopologyClaimer::allow_claim(const class protocols::topology_broker::claims::DofClaim &) –> bool
- assign(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController, : pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController ¶
C++: protocols::topology_broker::PseudocontactShiftEnergyController::operator=(const class protocols::topology_broker::PseudocontactShiftEnergyController &) –> class protocols::topology_broker::PseudocontactShiftEnergyController &
- broker(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) protocols::topology_broker::TopologyBroker ¶
return the broker we are collaborating with
C++: protocols::topology_broker::TopologyClaimer::broker() const –> const class protocols::topology_broker::TopologyBroker &
- build_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.kinematics.FoldTree) None ¶
C++: protocols::topology_broker::TopologyClaimer::build_fold_tree(class core::pose::Pose &, class core::kinematics::FoldTree &) –> void
- claim_accepted(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, my_claim: protocols::topology_broker::claims::DofClaim) None ¶
this claim of yours was accepted…. I so far haven’t done anything with this… might go away.
C++: protocols::topology_broker::TopologyClaimer::claim_accepted(class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>) –> void
- claimer_builds_own_fold_tree(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer) bool ¶
C++: protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree() –> bool
- clone(self: pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer ¶
C++: protocols::topology_broker::PseudocontactShiftEnergyController::clone() const –> class std::shared_ptr<class protocols::topology_broker::TopologyClaimer>
- finalize_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
is called after all round1 claims have been approved or retracted – additional claims can be issued in this round
C++: protocols::topology_broker::TopologyClaimer::finalize_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) None ¶
generate first round of DOF claims
C++: protocols::topology_broker::TopologyClaimer::generate_claims(class utility::vector1<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim>, class std::allocator<class std::shared_ptr<class protocols::topology_broker::claims::DofClaim> > > &) –> void
- generate_sequence_claims(self: pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer,