#include <FibrilModelingClaimer.hh>
Public Member Functions | |
| FibrilModelingClaimer () | |
| FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, int shift=0) | |
| FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, loops::Loops input_rigid) | |
| void | make_fibril (core::pose::Pose &pose) |
| TopologyClaimerOP | clone () const override |
| clone it! More... | |
| std::string | type () const override |
| type() is specifying the output name of the TopologyClaimer More... | |
| void | add_mover (moves::RandomMover &random_mover, core::pose::Pose const &pose, abinitio::StageID stageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress) override |
| 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_ More... | |
| void | initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, claims::DofClaims &) override |
| initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this More... | |
| void | generate_claims (claims::DofClaims &new_claims) override |
| generate first round of DOF claims More... | |
| bool | allow_claim (claims::DofClaim const &) override |
| has to decline foreign BB claims for slave regions More... | |
 Public Member Functions inherited from protocols::topology_broker::TopologyClaimer | |
| ~TopologyClaimer () override=default | |
| Automatically generated virtual destructor for class deriving directly from VirtualBase. More... | |
| TopologyClaimer () | |
| TopologyClaimer (weights::AbinitioMoverWeightOP weight) | |
| construct with weight-set ( how important is mover for different abinitio stages ? ) More... | |
| TopologyClaimerCOP | get_self_ptr () const |
| self pointers More... | |
| TopologyClaimerOP | get_self_ptr () |
| TopologyClaimerCAP | get_self_weak_ptr () const |
| TopologyClaimerAP | get_self_weak_ptr () |
| virtual bool | claimer_builds_own_fold_tree () |
| virtual core::kinematics::FoldTreeOP | get_fold_tree (core::pose::Pose &) |
| in case a claimer has its own fold_tree. get_fold_tree() is called by the broker More... | |
| virtual void | build_fold_tree (core::pose::Pose &, core::kinematics::FoldTree &) |
| virtual void | set_pose_from_broker (core::pose::Pose &) |
| virtual void | read (std::istream &) |
| read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block More... | |
| virtual void | pre_process (core::pose::Pose &) |
| virtual void | generate_sequence_claims (claims::DofClaims &) |
| generate claims that affect the sequence of the pose More... | |
| virtual void | generate_symmetry_claims (claims::SymmetryClaims &) |
| generate claims that affect the sequence of the pose More... | |
| virtual void | finalize_claims (claims::DofClaims &) |
| is called after all round1 claims have been approved or retracted – additional claims can be issued in this round More... | |
| virtual void | switch_to_fullatom (core::pose::Pose &, utility::vector1< bool >) const |
| 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 More... | |
| virtual void | manipulate_cut_bias (utility::vector1< core::Real > &) |
| 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 More... | |
| virtual bool | accept_declined_claim (claims::DofClaim const &) |
| 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 ... ) More... | |
| virtual void | claim_accepted (claims::DofClaimOP my_claim) |
| this claim of yours was accepted.... I so far haven't done anything with this... might go away. More... | |
| virtual void | add_constraints (core::pose::Pose &) const |
| add constraints to pose... might make this stage dependent as with movers... More... | |
| virtual core::fragment::FragSetCOP | loop_frags (core::kinematics::MoveMap &) const |
| 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 More... | |
| virtual bool | passes_filter (core::pose::Pose const &, abinitio::StageID, core::Real, std::ostringstream &) |
| 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_ More... | |
| void | set_mover_weight (weights::AbinitioMoverWeightOP wset) |
| weights::AbinitioMoverWeight & | mover_weight () |
| void | read_mover_weight (std::istream &is) |
| read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage More... | |
| virtual void | adjust_relax_movemap (core::kinematics::MoveMap &) const |
| void | set_broker (TopologyBrokerCAP ptr) |
| don't use this — it is called by TopologyBroker add_claim only More... | |
| TopologyBroker const & | broker () const |
| return the broker we are collaborating with More... | |
| virtual void | new_decoy () |
| a new decoy — random choices to be made ? make them here More... | |
| virtual void | new_decoy (core::pose::Pose const &) |
| an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose More... | |
| std::string const & | label () const |
| void | set_label (std::string const &str) |
| virtual void | receive_message (ClaimerMessage &) |
| virtual core::pose::PoseOP | get_pose_from_claimer () |
Static Public Member Functions | |
| static std::string | _static_type_name () |
Protected Member Functions | |
| bool | read_tag (std::string tag, std::istream &is) override |
| Protected Member Functions inherited from protocols::topology_broker::TopologyClaimer | |
| virtual moves::MoverOP | get_mover (core::pose::Pose const &) const |
| what is your mover ... called by add_mover — overload this or add_mover if you have movers too supply More... | |
| virtual void | set_defaults () |
| virtual void | init_after_reading () |
Private Types | |
| typedef TopologyClaimer | Parent |
Private Attributes | |
| core::pose::Pose | input_pose_ |
| monomer pose More... | |
| loops::Loops | rigid_core_ |
| regions that can be used for rigid core More... | |
| loops::Loops | input_rigid_core_ |
| bool | bAlign_ |
| align to the monomer before create symmetry More... | |
| int | sequence_shift_ |
| core::conformation::symmetry::SymmetryInfoOP | symminfo_ |
| symmetry information More... | |
Member Typedef Documentation
◆ Parent
Constructor & Destructor Documentation
◆ FibrilModelingClaimer() [1/3]
| protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer | ( | ) |
◆ FibrilModelingClaimer() [2/3]
| protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer | ( | core::pose::Pose const & | input_pose, |
| loops::Loops | rigid, | ||
| int | shift = 0 |
||
| ) |
References bAlign_, input_rigid_core_, protocols::loops::Loops::make_sequence_shift(), rigid_core_, and sequence_shift_.
◆ FibrilModelingClaimer() [3/3]
| protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer | ( | core::pose::Pose const & | input_pose, |
| loops::Loops | rigid, | ||
| loops::Loops | input_rigid | ||
| ) |
References bAlign_, input_rigid_core_, rigid_core_, and sequence_shift_.
Member Function Documentation
◆ _static_type_name()
|
inlinestatic |
Referenced by type().
◆ add_mover()
|
overridevirtual |
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_
Reimplemented from protocols::topology_broker::TopologyClaimer.
References protocols::moves::MoverContainer::add_mover(), and core::scoring::ScoreFunction::get_self_ptr().
◆ allow_claim()
|
overridevirtual |
has to decline foreign BB claims for slave regions
Reimplemented from protocols::topology_broker::TopologyClaimer.
References core::conformation::symmetry::is_symmetric(), protocols::topology_broker::claims::DofClaim::owner(), and symminfo_.
◆ clone()
|
inlineoverridevirtual |
clone it!
Implements protocols::topology_broker::TopologyClaimer.
◆ generate_claims()
|
overridevirtual |
generate first round of DOF claims
Reimplemented from protocols::topology_broker::TopologyClaimer.
References core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::conformation::Conformation::fold_tree(), protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), protocols::topology_broker::claims::DofClaim::INIT, input_pose_, and protocols::topology_broker::TopologyClaimer::label().
◆ initialize_dofs()
|
overridevirtual |
initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this
initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this
Reimplemented from protocols::topology_broker::TopologyClaimer.
References protocols::symmetry::SymDockingInitialPerturbation::apply(), make_fibril(), and core::pose::symmetry::make_symmetric_movemap().
◆ make_fibril()
| void protocols::topology_broker::FibrilModelingClaimer::make_fibril | ( | core::pose::Pose & | pose | ) |
References bAlign_, input_pose_, input_rigid_core_, core::pose::symmetry::is_symmetric(), rigid_core_, core::pose::symmetry::symmetry_info(), and symminfo_.
Referenced by initialize_dofs().
◆ read_tag()
|
overrideprotectedvirtual |
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bAlign_, protocols::loops::Loops::clear(), core::chemical::FA_STANDARD, protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), input_pose_, input_rigid_core_, core::pose::Pose::is_fullatom(), protocols::loops::Loops::make_sequence_shift(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::topology_broker::TopologyClaimer::read_tag(), rigid_core_, sequence_shift_, and type().
◆ type()
|
inlineoverridevirtual |
type() is specifying the output name of the TopologyClaimer
Implements protocols::topology_broker::TopologyClaimer.
References _static_type_name().
Referenced by read_tag().
Member Data Documentation
◆ bAlign_
|
private |
align to the monomer before create symmetry
Referenced by FibrilModelingClaimer(), make_fibril(), and read_tag().
◆ input_pose_
|
private |
monomer pose
Referenced by generate_claims(), make_fibril(), and read_tag().
◆ input_rigid_core_
|
private |
Referenced by FibrilModelingClaimer(), make_fibril(), and read_tag().
◆ rigid_core_
|
private |
regions that can be used for rigid core
Referenced by FibrilModelingClaimer(), make_fibril(), and read_tag().
◆ sequence_shift_
|
private |
Referenced by FibrilModelingClaimer(), and read_tag().
◆ symminfo_
|
private |
symmetry information
Referenced by allow_claim(), and make_fibril().
The documentation for this class was generated from the following files:
- src/protocols/topology_broker/FibrilModelingClaimer.hh
- src/protocols/topology_broker/FibrilModelingClaimer.cc
