#include <AnchorMovers.hh>
Public Member Functions | |
| AnchoredDesignMover (protocols::anchored_design::AnchorMoversDataOP interface_in) | |
| constructor with arguments More... | |
| AnchoredDesignMover () | |
| ctor with no arguments More... | |
| AnchoredDesignMover (AnchoredDesignMover const &rhs) | |
| copy ctor More... | |
| AnchoredDesignMover & | operator= (AnchoredDesignMover const &rhs) |
| assignment operator More... | |
| ~AnchoredDesignMover () override | |
| void | apply (core::pose::Pose &pose) override |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| bool | reinitialize_for_new_input () const override |
| bool | reinitialize_for_each_job () const override |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | set_fold_tree_and_cutpoints (core::pose::Pose &pose) |
| creates the anchored design fold tree and applies it to the pose More... | |
| void | filter (core::pose::Pose &pose) |
| runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed More... | |
| void | forget_initial_loops (core::pose::Pose &pose) |
| implements the "extended" field of the loop file specification - sets extended phi/psi as needed More... | |
| void | calculate_rmsd (core::pose::Pose const &pose, core::pose::PoseCOP start_pose) |
| calculate RMSD if desired; protected internally More... | |
| void | randomize_input_sequence (core::pose::Pose &pose) const |
| randomize the input loop sequence. Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode. Acts only on designable positions. More... | |
| void | delete_interface_native_sidechains (core::pose::Pose &pose) const |
| This function repacks the interface with use_input_sc forcibly off for benchmarking purposes. More... | |
| void | perturb_anchor (core::pose::Pose &pose) const |
| handles perturbing the initial anchor placement More... | |
| bool | get_rmsd () const |
| run RMSD calculations More... | |
| std::string const & | get_RMSD_only_this () const |
| run only RMSD calculations against this input, don't do actual AnchoredDesign More... | |
| bool | get_delete_interface_native_sidechains () const |
| delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More... | |
| bool | get_show_extended () const |
| show_extended demonstrates that the code really forgets the input structure More... | |
| bool | get_randomize_input_sequence () const |
| randomize_input_sequence to complement loop extension in forgetting the input More... | |
| bool | get_vary_cutpoints () const |
| pick a different cutpoint than the input; useful when you want to sample cutpoints More... | |
| bool | get_refine_only () const |
| skip the perturbation step - useful when you already have a good structure More... | |
| core::Real | get_filter_score () const |
| filter based on total complex score More... | |
| core::Real | get_filter_SASA () const |
| filter based on complex SASA More... | |
| bool | get_filter_omega () const |
| filter based on omega angles in the loops - filter out cis omegas More... | |
| bool | get_autoinitialize () const |
| whether to automatically initialize from the options system; defaults to true More... | |
| void | set_rmsd (bool const rmsd) |
| run RMSD calculations More... | |
| void | set_RMSD_only_this (std::string const &RMSD_only_this) |
| run only RMSD calculations against this input, don't do actual AnchoredDesign More... | |
| void | set_delete_interface_native_sidechains (bool const delete_interface_native_sidechains) |
| delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More... | |
| void | set_show_extended (bool const show_extended) |
| show_extended demonstrates that the code really forsets the input structure More... | |
| void | set_randomize_input_sequence (bool const randomize_input_sequence) |
| randomize_input_sequence to complement loop extension in forgetting the input More... | |
| void | set_vary_cutpoints (bool const vary_cutpoints) |
| pick a different cutpoint than the input; useful when you want to sample cutpoints More... | |
| void | set_refine_only (bool const refine_only) |
| skip the perturbation step - useful when you already have a good structure More... | |
| void | set_filter_score (core::Real const filter_score) |
| filter based on total complex score More... | |
| void | set_filter_SASA (core::Real const filter_SASA) |
| filter based on complex SASA More... | |
| void | set_filter_omega (bool const filter_omega) |
| filter based on omega angles in the loops - filter out cis omegas More... | |
| void | set_autoinitialize (bool const autoinitialize) |
| whether to automatically initialize from the options system; defaults to true More... | |
| void | read_options () |
| read in options from the options system More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Private Member Functions | |
| void | init_on_new_input (core::pose::Pose const &pose) |
| @initializes internals; must wait for a pose to initialize More... | |
Private Attributes | |
| protocols::anchored_design::AnchorMoversDataOP | interface_ |
| core::pose::PoseCOP | RMSD_only_this_pose_ |
| protocols::analysis::InterfaceAnalyzerMoverOP | IAM_ |
| bool | rmsd_ |
| run RMSD calculations More... | |
| std::string | RMSD_only_this_ |
| run only RMSD calculations against this input, don't do actual AnchoredDesign More... | |
| bool | delete_interface_native_sidechains_ |
| delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More... | |
| bool | show_extended_ |
| show_extended demonstrates that the code really forgets the input structure More... | |
| bool | randomize_input_sequence_ |
| randomize_input_sequence to complement loop extension in forgetting the input More... | |
| bool | vary_cutpoints_ |
| pick a different cutpoint than the input; useful when you want to sample cutpoints More... | |
| bool | refine_only_ |
| skip the perturbation step - useful when you already have a good structure More... | |
| core::Real | filter_score_ |
| filter based on total complex score More... | |
| bool | use_filter_score_ |
| filter based on total complex score More... | |
| core::Real | filter_SASA_ |
| filter based on complex SASA More... | |
| bool | use_filter_SASA_ |
| filter based on complex SASA More... | |
| bool | use_filter_omega_ |
| filter based on omega angles in the loops - filter out cis omegas More... | |
| bool | autoinitialize_ |
| whether to automatically initialize from the options system; defaults to true More... | |
| bool | init_for_input_yet_ |
| used to determine the validity of the rest of the internals, especially the interface_ object More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Constructor & Destructor Documentation
◆ AnchoredDesignMover() [1/3]
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | protocols::anchored_design::AnchorMoversDataOP | interface_in | ) |
constructor with arguments
References protocols::moves::Mover::type().
◆ AnchoredDesignMover() [2/3]
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | ) |
ctor with no arguments
References protocols::moves::Mover::type().
◆ AnchoredDesignMover() [3/3]
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | AnchoredDesignMover const & | rhs | ) |
copy ctor
◆ ~AnchoredDesignMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
AnchoredDesignMover is mostly a container for other movers for the anchored design protocol.
Implements protocols::moves::Mover.
References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::jd2::add_string_real_pair_to_current_job(), protocols::jd2::add_string_to_current_job(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), calculate_rmsd(), core::pose::Pose::constraint_set(), delete_interface_native_sidechains(), delete_interface_native_sidechains_, protocols::anchored_design::EMPTY_STRING(), filter(), forget_initial_loops(), IAM_, init_for_input_yet_, init_on_new_input(), interface_, protocols::jd2::output_intermediate_pose(), core::import_pose::PDB_file, perturb_anchor(), core::import_pose::pose_from_file(), randomize_input_sequence(), randomize_input_sequence_, refine_only_, core::pose::Pose::remove_constraints(), rmsd_, RMSD_only_this_, RMSD_only_this_pose_, core::pose::Pose::sequence(), set_fold_tree_and_cutpoints(), show_extended_, T_design(), and vary_cutpoints_.
◆ calculate_rmsd()
| void protocols::anchored_design::AnchoredDesignMover::calculate_rmsd | ( | core::pose::Pose const & | pose, |
| core::pose::PoseCOP | start_pose | ||
| ) |
calculate RMSD if desired; protected internally
References protocols::jd2::add_string_real_pair_to_current_job(), core::scoring::CA_rmsd(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, interface_, core::scoring::is_protein_backbone(), core::scoring::is_protein_CA(), protocols::loops::loop_rmsd(), rmsd_, core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super_subset(), core::pose::Pose::size(), and T_design().
Referenced by apply().
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
◆ delete_interface_native_sidechains()
| void protocols::anchored_design::AnchoredDesignMover::delete_interface_native_sidechains | ( | core::pose::Pose & | pose | ) | const |
This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.
For benchmarking, it is a minor sin to allow native sidechains to leak through from the starting structure. AnchoredDesign runs best with use_input_sc because it does sidechain minimization, not because it needs starting sidechains. This function deletes the native sidechains by repacking the interface with use_input_sc forcibly off. DO NOT USE THIS FUNCTION for proper designs - it is meant for a specific benchmarking purpose.
References core::sequence::end, core::pack::task::EX_ONE_STDDEV, interface_, and core::pose::Pose::size().
Referenced by apply(), and set_delete_interface_native_sidechains().
◆ filter()
| void protocols::anchored_design::AnchoredDesignMover::filter | ( | core::pose::Pose & | pose | ) |
runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed
References protocols::moves::FAIL_RETRY, filter_SASA_, filter_score_, interface_, core::conformation::Residue::is_upper_terminus(), core::pose::Pose::metric(), protocols::moves::MS_SUCCESS, core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::residue(), protocols::moves::Mover::set_last_move_status(), T_design(), use_filter_omega_, use_filter_SASA_, and use_filter_score_.
Referenced by apply().
◆ forget_initial_loops()
| void protocols::anchored_design::AnchoredDesignMover::forget_initial_loops | ( | core::pose::Pose & | pose | ) |
implements the "extended" field of the loop file specification - sets extended phi/psi as needed
implements the is_extended boolean for the Loop class. If the boolean is on, this function resets phi/psi for those regions to be extended (-150phi, 150psi). This function does not affect omega, or residues outside of defined loops, or the anchor.
References interface_, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().
Referenced by apply().
◆ fresh_instance()
|
overridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
◆ get_autoinitialize()
| bool protocols::anchored_design::AnchoredDesignMover::get_autoinitialize | ( | ) | const |
whether to automatically initialize from the options system; defaults to true
References autoinitialize_.
Referenced by operator=().
◆ get_delete_interface_native_sidechains()
| bool protocols::anchored_design::AnchoredDesignMover::get_delete_interface_native_sidechains | ( | ) | const |
delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
References delete_interface_native_sidechains_.
Referenced by operator=().
◆ get_filter_omega()
| bool protocols::anchored_design::AnchoredDesignMover::get_filter_omega | ( | ) | const |
filter based on omega angles in the loops - filter out cis omegas
References use_filter_omega_.
Referenced by operator=().
◆ get_filter_SASA()
| core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_SASA | ( | ) | const |
◆ get_filter_score()
| core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_score | ( | ) | const |
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_randomize_input_sequence()
| bool protocols::anchored_design::AnchoredDesignMover::get_randomize_input_sequence | ( | ) | const |
randomize_input_sequence to complement loop extension in forgetting the input
References randomize_input_sequence_.
Referenced by operator=().
◆ get_refine_only()
| bool protocols::anchored_design::AnchoredDesignMover::get_refine_only | ( | ) | const |
skip the perturbation step - useful when you already have a good structure
References refine_only_.
Referenced by operator=().
◆ get_rmsd()
| bool protocols::anchored_design::AnchoredDesignMover::get_rmsd | ( | ) | const |
◆ get_RMSD_only_this()
| std::string const & protocols::anchored_design::AnchoredDesignMover::get_RMSD_only_this | ( | ) | const |
run only RMSD calculations against this input, don't do actual AnchoredDesign
References RMSD_only_this_.
Referenced by operator=().
◆ get_show_extended()
| bool protocols::anchored_design::AnchoredDesignMover::get_show_extended | ( | ) | const |
show_extended demonstrates that the code really forgets the input structure
References show_extended_.
Referenced by operator=().
◆ get_vary_cutpoints()
| bool protocols::anchored_design::AnchoredDesignMover::get_vary_cutpoints | ( | ) | const |
pick a different cutpoint than the input; useful when you want to sample cutpoints
References vary_cutpoints_.
Referenced by operator=().
◆ init_on_new_input()
|
private |
@initializes internals; must wait for a pose to initialize
References autoinitialize_, protocols::anchored_design::EMPTY_STRING(), init_for_input_yet_, interface_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), read_options(), RMSD_only_this_, and RMSD_only_this_pose_.
Referenced by apply().
◆ operator=()
| AnchoredDesignMover & protocols::anchored_design::AnchoredDesignMover::operator= | ( | AnchoredDesignMover const & | rhs | ) |
assignment operator
References autoinitialize_, delete_interface_native_sidechains_, filter_SASA_, filter_score_, get_autoinitialize(), get_delete_interface_native_sidechains(), get_filter_omega(), get_filter_SASA(), get_filter_score(), get_randomize_input_sequence(), get_refine_only(), get_rmsd(), get_RMSD_only_this(), get_show_extended(), get_vary_cutpoints(), IAM_, init_for_input_yet_, interface_, randomize_input_sequence_, refine_only_, rmsd_, RMSD_only_this_, RMSD_only_this_pose_, show_extended_, use_filter_omega_, use_filter_SASA_, use_filter_score_, and vary_cutpoints_.
◆ perturb_anchor()
| void protocols::anchored_design::AnchoredDesignMover::perturb_anchor | ( | core::pose::Pose & | pose | ) | const |
handles perturbing the initial anchor placement
when using anchor_noise_constraints_mode, this function perturbs the initial anchor a bit. Requested test by a reviewer.
References protocols::anchored_design::ANCHOR_TARGET(), core::chemical::ResidueType::atom_index(), protocols::frag_picker::CA, core::pose::Pose::conformation(), core::conformation::Conformation::downstream_jump_stub(), interface_, core::kinematics::Stub::M, core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::set_jump(), T_design(), core::conformation::Conformation::upstream_jump_stub(), core::kinematics::Stub::v, and core::pose::Pose::xyz().
Referenced by apply().
◆ randomize_input_sequence()
| void protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence | ( | core::pose::Pose & | pose | ) | const |
randomize the input loop sequence. Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode. Acts only on designable positions.
This is crazy. Sometimes loop redesign is overly biased by the starting loop sequence, because the centroid phase won't change the sequence, and the rama term may remember the conformation to well due to sequence preferences. This restricts sampling. So, this function creates a random sequence in the designable positions, based on what the design PackerTask thinks they can become. This code special cases histidine (to avoid double-allowing histidine, based on its two protonations).
References core::chemical::aa_his, protocols::mean_field::add(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), interface_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::size(), T_design(), and protocols::moves::Mover::type().
Referenced by apply(), and set_randomize_input_sequence().
◆ read_options()
| void protocols::anchored_design::AnchoredDesignMover::read_options | ( | ) |
read in options from the options system
References delete_interface_native_sidechains_, protocols::anchored_design::EMPTY_STRING(), filter_SASA_, filter_score_, core::scoring::omega, randomize_input_sequence_, refine_only_, rmsd_, RMSD_only_this_, protocols::hybridization::score, show_extended_, use_filter_omega_, use_filter_SASA_, use_filter_score_, and vary_cutpoints_.
Referenced by init_on_new_input().
◆ reinitialize_for_each_job()
|
overridevirtual |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.
Movers default to not regenerating
Reimplemented from protocols::moves::Mover.
◆ reinitialize_for_new_input()
|
overridevirtual |
generally returns true; will return false for RMSD_only_this mode
Reimplemented from protocols::moves::Mover.
References protocols::anchored_design::EMPTY_STRING(), and RMSD_only_this_.
◆ set_autoinitialize()
| void protocols::anchored_design::AnchoredDesignMover::set_autoinitialize | ( | bool const | autoinitialize | ) |
whether to automatically initialize from the options system; defaults to true
References autoinitialize_.
◆ set_delete_interface_native_sidechains()
| void protocols::anchored_design::AnchoredDesignMover::set_delete_interface_native_sidechains | ( | bool const | delete_interface_native_sidechains | ) |
delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
References delete_interface_native_sidechains(), and delete_interface_native_sidechains_.
◆ set_filter_omega()
| void protocols::anchored_design::AnchoredDesignMover::set_filter_omega | ( | bool const | filter_omega | ) |
filter based on omega angles in the loops - filter out cis omegas
References use_filter_omega_.
◆ set_filter_SASA()
| void protocols::anchored_design::AnchoredDesignMover::set_filter_SASA | ( | core::Real const | filter_SASA | ) |
filter based on complex SASA
References filter_SASA_, and use_filter_SASA_.
◆ set_filter_score()
| void protocols::anchored_design::AnchoredDesignMover::set_filter_score | ( | core::Real const | filter_score | ) |
filter based on total complex score
References filter_score_, and use_filter_score_.
◆ set_fold_tree_and_cutpoints()
| void protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints | ( | core::pose::Pose & | pose | ) |
creates the anchored design fold tree and applies it to the pose
uses fold_tree::tree_from_jumps_and_cuts to make the necessary fold tree and apply it to the pose
References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), protocols::anchored_design::ANCHOR_TARGET(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_edge(), protocols::anchored_design::dump_cutpoint_info(), core::pose::Pose::fold_tree(), interface_, core::conformation::Residue::is_terminus(), core::kinematics::FoldTree::jump_edge(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::size(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), T_design(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().
Referenced by apply().
◆ set_randomize_input_sequence()
| void protocols::anchored_design::AnchoredDesignMover::set_randomize_input_sequence | ( | bool const | randomize_input_sequence | ) |
randomize_input_sequence to complement loop extension in forgetting the input
References randomize_input_sequence(), and randomize_input_sequence_.
◆ set_refine_only()
| void protocols::anchored_design::AnchoredDesignMover::set_refine_only | ( | bool const | refine_only | ) |
skip the perturbation step - useful when you already have a good structure
References refine_only_.
◆ set_rmsd()
| void protocols::anchored_design::AnchoredDesignMover::set_rmsd | ( | bool const | rmsd | ) |
run RMSD calculations
References rmsd_.
◆ set_RMSD_only_this()
| void protocols::anchored_design::AnchoredDesignMover::set_RMSD_only_this | ( | std::string const & | RMSD_only_this | ) |
run only RMSD calculations against this input, don't do actual AnchoredDesign
References RMSD_only_this_.
◆ set_show_extended()
| void protocols::anchored_design::AnchoredDesignMover::set_show_extended | ( | bool const | show_extended | ) |
show_extended demonstrates that the code really forsets the input structure
References show_extended_.
◆ set_vary_cutpoints()
| void protocols::anchored_design::AnchoredDesignMover::set_vary_cutpoints | ( | bool const | vary_cutpoints | ) |
pick a different cutpoint than the input; useful when you want to sample cutpoints
pick a different cutpoint than the input { _ = ;} useful when you want to sample cutpoints
References vary_cutpoints_.
Member Data Documentation
◆ autoinitialize_
|
private |
whether to automatically initialize from the options system; defaults to true
Referenced by get_autoinitialize(), init_on_new_input(), operator=(), and set_autoinitialize().
◆ delete_interface_native_sidechains_
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private |
delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
Referenced by apply(), get_delete_interface_native_sidechains(), operator=(), read_options(), and set_delete_interface_native_sidechains().
◆ filter_SASA_
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private |
filter based on complex SASA
Referenced by filter(), get_filter_SASA(), operator=(), read_options(), and set_filter_SASA().
◆ filter_score_
|
private |
filter based on total complex score
Referenced by filter(), get_filter_score(), operator=(), read_options(), and set_filter_score().
◆ IAM_
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private |
Referenced by apply(), and operator=().
◆ init_for_input_yet_
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private |
used to determine the validity of the rest of the internals, especially the interface_ object
Referenced by apply(), init_on_new_input(), and operator=().
◆ interface_
|
private |
◆ randomize_input_sequence_
|
private |
randomize_input_sequence to complement loop extension in forgetting the input
Referenced by apply(), get_randomize_input_sequence(), operator=(), read_options(), and set_randomize_input_sequence().
◆ refine_only_
|
private |
skip the perturbation step - useful when you already have a good structure
Referenced by apply(), get_refine_only(), operator=(), read_options(), and set_refine_only().
◆ rmsd_
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private |
run RMSD calculations
Referenced by apply(), calculate_rmsd(), get_rmsd(), operator=(), read_options(), and set_rmsd().
◆ RMSD_only_this_
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private |
run only RMSD calculations against this input, don't do actual AnchoredDesign
Referenced by apply(), get_RMSD_only_this(), init_on_new_input(), operator=(), read_options(), reinitialize_for_new_input(), and set_RMSD_only_this().
◆ RMSD_only_this_pose_
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private |
used for RMSD comparisons with RMSD_only_this mode
Referenced by apply(), init_on_new_input(), and operator=().
◆ show_extended_
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private |
show_extended demonstrates that the code really forgets the input structure
Referenced by apply(), get_show_extended(), operator=(), read_options(), and set_show_extended().
◆ use_filter_omega_
|
private |
filter based on omega angles in the loops - filter out cis omegas
Referenced by filter(), get_filter_omega(), operator=(), read_options(), and set_filter_omega().
◆ use_filter_SASA_
|
private |
filter based on complex SASA
Referenced by filter(), operator=(), read_options(), and set_filter_SASA().
◆ use_filter_score_
|
private |
filter based on total complex score
Referenced by filter(), operator=(), read_options(), and set_filter_score().
◆ vary_cutpoints_
|
private |
pick a different cutpoint than the input; useful when you want to sample cutpoints
Referenced by apply(), get_vary_cutpoints(), operator=(), read_options(), and set_vary_cutpoints().
The documentation for this class was generated from the following files:
- src/protocols/anchored_design/AnchorMovers.hh
- src/protocols/anchored_design/AnchorMovers.cc
