#include <CoordConstraintClaimer.hh>
Public Member Functions | |
| CoordConstraintClaimer () | |
| ~CoordConstraintClaimer () override | |
| CoordConstraintClaimer (std::string const &pdb_file) | |
| TopologyClaimerOP | clone () const override |
| clone it! More... | |
| void | generate_claims (claims::DofClaims &) override |
| generate first round of DOF claims More... | |
| std::string | type () const override |
| type() is specifying the output name of the TopologyClaimer More... | |
| void | add_constraints (core::pose::Pose &) const override |
| add constraints to pose... might make this stage dependent as with movers... More... | |
| void | new_decoy () override |
| a new decoy — random choices to be made ? make them here More... | |
| void | new_decoy (core::pose::Pose const &) override |
| an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose More... | |
| void | superimpose (core::pose::Pose const &) const |
| superimpose xyz coords in constraints_ with pose 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 bool | allow_claim (claims::DofClaim const &) |
| allow a claim from a foreign Claimer More... | |
| virtual void | initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, claims::DofClaims &failed_to_init) |
| initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this 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 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... | |
| virtual void | add_mover (moves::RandomMover &, core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &, core::Real) |
| 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... | |
| 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 &) override |
| virtual functions for IO More... | |
| void | set_defaults () override |
| @detail read setup file More... | |
| void | init_after_reading () 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... | |
Private Types | |
| typedef TopologyClaimer | Parent |
Private Member Functions | |
| void | read_cst_pose () |
| void | set_cst_root () |
| void | generate_constraints (core::pose::Pose const &cst_pose) const |
| void | read_constraints_from_file (core::pose::Pose const &cst_pose) const |
Private Attributes | |
| std::string | filename_ = "NoFile" |
| std::string | cst_filename_ = "NoFile" |
| loops::Loops | rigid_ |
| core::scoring::constraints::ConstraintSetOP | constraints_ |
| std::string | sequence_ |
| core::scoring::func::FuncOP | cst_func_ |
| core::Size | root_ = 1 |
| std::string | root_from_label_ = "ALL" |
| bool | bRegenerateFromInputPose_ = false |
| bool | bUseXYZ_in_cstfile_ = false |
| core::pose::PoseOP | cst_pose_ |
| bool | bCentroid_ = true |
| true if constraints are active in centroid mode More... | |
| bool | bFullatom_ = false |
| true if constraints are active in full-atom mode More... | |
| bool | bLocal_ = false |
| tmp for backwards compatibility More... | |
| core::Real | perturb_ = 0 |
| add 0..perturb_ random number to xyz-coords. More... | |
| bool | bSuperimpose_ = false |
| superimpose xyz coordinates with pose in add_constraints() More... | |
| loops::Loops | superimpose_regions_ |
| superimpose on these residues More... | |
Member Typedef Documentation
◆ Parent
Constructor & Destructor Documentation
◆ CoordConstraintClaimer() [1/2]
| protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer | ( | ) |
◆ ~CoordConstraintClaimer()
|
overridedefault |
◆ CoordConstraintClaimer() [2/2]
| protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer | ( | std::string const & | pdb_file | ) |
Member Function Documentation
◆ _static_type_name()
|
inlinestatic |
Referenced by type().
◆ add_constraints()
|
overridevirtual |
add constraints to pose... might make this stage dependent as with movers...
Reimplemented from protocols::topology_broker::TopologyClaimer.
References core::pose::Pose::add_constraints(), core::pose::Pose::annotated_sequence(), bCentroid_, bFullatom_, bSuperimpose_, bUseXYZ_in_cstfile_, constraints_, cst_pose_, core::pose::Pose::is_fullatom(), protocols::topology_broker::TopologyClaimer::label(), sequence_, superimpose(), and tr().
◆ clone()
|
inlineoverridevirtual |
clone it!
Implements protocols::topology_broker::TopologyClaimer.
◆ generate_claims()
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overridevirtual |
generate first round of DOF claims
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bLocal_, protocols::topology_broker::TopologyClaimer::broker(), bUseXYZ_in_cstfile_, constraints_, cst_pose_, protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue::good_fix_pos_, protocols::topology_broker::TopologyClaimer::label(), protocols::topology_broker::claims::DofClaim::NEED_TO_KNOW, read_constraints_from_file(), protocols::topology_broker::ClaimerMessage::received(), protocols::topology_broker::TopologyBroker::relay_message(), root_, root_from_label_, set_cst_root(), and tr().
◆ generate_constraints()
|
private |
References protocols::loops::Loops::add_loop(), core::chemical::ResidueType::atom_index(), core::id::AtomID::atomno(), bLocal_, constraints_, cst_func_, core::conformation::named_stub_id_to_stub_id(), perturb_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, rigid_, root_, core::pose::Pose::size(), protocols::loops::Loops::size(), tr(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().
Referenced by init_after_reading(), and new_decoy().
◆ init_after_reading()
|
overrideprotectedvirtual |
Reimplemented from protocols::topology_broker::TopologyClaimer.
References cst_filename_, cst_func_, cst_pose_, generate_constraints(), read_constraints_from_file(), sequence_, and type().
◆ new_decoy() [1/2]
|
overridevirtual |
a new decoy — random choices to be made ? make them here
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bUseXYZ_in_cstfile_, constraints_, cst_pose_, and generate_constraints().
Referenced by new_decoy().
◆ new_decoy() [2/2]
|
overridevirtual |
an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bRegenerateFromInputPose_, bSuperimpose_, cst_pose_, new_decoy(), and sequence_.
◆ read_constraints_from_file()
|
private |
References constraints_, cst_filename_, and tr().
Referenced by generate_claims(), and init_after_reading().
◆ read_cst_pose()
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private |
References core::chemical::CENTROID, cst_pose_, filename_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and sequence_.
Referenced by read_tag().
◆ read_tag()
|
overrideprotectedvirtual |
virtual functions for IO
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bCentroid_, bFullatom_, bLocal_, bRegenerateFromInputPose_, bSuperimpose_, bUseXYZ_in_cstfile_, cst_filename_, cst_func_, filename_, core::scoring::constraints::ConstraintIO::get_func_factory(), protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), core::scoring::func::FuncFactory::new_func(), perturb_, read_cst_pose(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::topology_broker::TopologyClaimer::read_tag(), rigid_, root_, root_from_label_, superimpose_regions_, and type().
◆ set_cst_root()
|
private |
References constraints_, cst_pose_, core::pose::named_stub_id_to_stub_id(), and root_.
Referenced by generate_claims().
◆ set_defaults()
|
overrideprotectedvirtual |
@detail read setup file
Reimplemented from protocols::topology_broker::TopologyClaimer.
References bSuperimpose_, bUseXYZ_in_cstfile_, protocols::loops::Loops::clear(), cst_filename_, filename_, perturb_, root_, root_from_label_, protocols::topology_broker::TopologyClaimer::set_defaults(), and superimpose_regions_.
◆ superimpose()
| void protocols::topology_broker::CoordConstraintClaimer::superimpose | ( | core::pose::Pose const & | pose | ) | const |
superimpose xyz coords in constraints_ with pose
References constraints_, protocols::simple_filters::coords(), protocols::toolbox::fit_centered_coords(), protocols::loops::Loops::is_loop_residue(), protocols::topology_broker::TopologyClaimer::label(), protocols::toolbox::reset_x(), protocols::loops::Loops::size(), superimpose_regions_, tr(), and core::pose::Pose::xyz().
Referenced by add_constraints().
◆ type()
|
inlineoverridevirtual |
type() is specifying the output name of the TopologyClaimer
Implements protocols::topology_broker::TopologyClaimer.
References _static_type_name().
Referenced by init_after_reading(), and read_tag().
Member Data Documentation
◆ bCentroid_
|
private |
true if constraints are active in centroid mode
Referenced by add_constraints(), and read_tag().
◆ bFullatom_
|
private |
true if constraints are active in full-atom mode
Referenced by add_constraints(), and read_tag().
◆ bLocal_
|
private |
tmp for backwards compatibility
Referenced by generate_claims(), generate_constraints(), and read_tag().
◆ bRegenerateFromInputPose_
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private |
Referenced by new_decoy(), and read_tag().
◆ bSuperimpose_
|
private |
superimpose xyz coordinates with pose in add_constraints()
Referenced by add_constraints(), new_decoy(), read_tag(), and set_defaults().
◆ bUseXYZ_in_cstfile_
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private |
Referenced by add_constraints(), generate_claims(), new_decoy(), read_tag(), and set_defaults().
◆ constraints_
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mutableprivate |
Referenced by add_constraints(), generate_claims(), generate_constraints(), new_decoy(), read_constraints_from_file(), set_cst_root(), and superimpose().
◆ cst_filename_
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private |
Referenced by init_after_reading(), read_constraints_from_file(), read_tag(), and set_defaults().
◆ cst_func_
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private |
Referenced by generate_constraints(), init_after_reading(), and read_tag().
◆ cst_pose_
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private |
Referenced by add_constraints(), generate_claims(), init_after_reading(), new_decoy(), read_cst_pose(), and set_cst_root().
◆ filename_
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private |
Referenced by read_cst_pose(), read_tag(), and set_defaults().
◆ perturb_
|
private |
add 0..perturb_ random number to xyz-coords.
Referenced by generate_constraints(), read_tag(), and set_defaults().
◆ rigid_
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private |
Referenced by generate_constraints(), and read_tag().
◆ root_
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private |
Referenced by generate_claims(), generate_constraints(), read_tag(), set_cst_root(), and set_defaults().
◆ root_from_label_
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private |
Referenced by generate_claims(), read_tag(), and set_defaults().
◆ sequence_
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mutableprivate |
Referenced by add_constraints(), init_after_reading(), new_decoy(), and read_cst_pose().
◆ superimpose_regions_
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private |
superimpose on these residues
Referenced by read_tag(), set_defaults(), and superimpose().
The documentation for this class was generated from the following files:
- src/protocols/topology_broker/CoordConstraintClaimer.hh
- src/protocols/topology_broker/CoordConstraintClaimer.cc
