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Rosetta 3.5
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Rosetta 3.5
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#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... | |
| virtual | ~AnchoredDesignMover () |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| virtual bool | reinitialize_for_new_input () const |
| virtual bool | reinitialize_for_each_job () const |
| this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual protocols::moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). 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 | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| 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... | |
| void | set_current_tag (std::string const &new_tag) |
| 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 | 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... | |
| void | type (const std::string &type_in) |
| virtual void | parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| std::string | get_type () const |
| 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... | |
| 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Member Functions | |
| void | init_on_new_input (core::pose::Pose const &pose) |
| 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::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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... | |
Definition at line 35 of file AnchorMovers.hh.
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | protocols::anchored_design::AnchorMoversDataOP | interface_in) |
constructor with arguments
Definition at line 170 of file AnchorMovers.cc.
References protocols::moves::Mover::type().
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | ) |
ctor with no arguments
Definition at line 194 of file AnchorMovers.cc.
References protocols::moves::Mover::type().
Referenced by clone(), and fresh_instance().
| protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover | ( | AnchoredDesignMover const & | rhs) |
copy ctor
Definition at line 217 of file AnchorMovers.cc.
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virtual |
Definition at line 251 of file AnchorMovers.cc.
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virtual |
AnchoredDesignMover is mostly a container for other movers for the anchored design protocol.
Implements protocols::moves::Mover.
Definition at line 276 of file AnchorMovers.cc.
References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), calculate_rmsd(), core::pose::Pose::constraint_set(), protocols::jd2::JobDistributor::current_job(), protocols::nonlocal::current_job(), delete_interface_native_sidechains(), delete_interface_native_sidechains_, protocols::anchored_design::EMPTY_STRING(), filter(), forget_initial_loops(), protocols::jd2::JobDistributor::get_instance(), IAM_, init_for_input_yet_, init_on_new_input(), interface_, perturb_anchor(), core::import_pose::pose_from_pdb(), 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_.
| void protocols::anchored_design::AnchoredDesignMover::calculate_rmsd | ( | core::pose::Pose const & | pose, |
| core::pose::PoseCOP | start_pose | ||
| ) |
calculate RMSD if desired; protected internally
Definition at line 360 of file AnchorMovers.cc.
References core::scoring::CA_rmsd(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::jd2::JobDistributor::current_job(), core::sequence::end, protocols::jd2::JobDistributor::get_instance(), 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(), T_design(), and core::pose::Pose::total_residue().
Referenced by apply().
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virtual |
clone has to be overridden only if clone invocation is expected.
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.
Definition at line 628 of file AnchorMovers.cc.
References AnchoredDesignMover().
| 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.
Definition at line 530 of file AnchorMovers.cc.
References core::sequence::end, core::pack::task::EX_ONE_STDDEV, interface_, protocols::simple_moves::PackRotamersMover::task_factory(), and core::pose::Pose::total_residue().
Referenced by apply(), and set_delete_interface_native_sidechains().
| void protocols::anchored_design::AnchoredDesignMover::filter | ( | core::pose::Pose & | pose) |
runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed
Definition at line 637 of file AnchorMovers.cc.
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::scoring::omega, core::pose::Pose::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().
| 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.
Definition at line 772 of file AnchorMovers.cc.
References interface_, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().
Referenced by apply().
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virtual |
this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
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.
Definition at line 624 of file AnchorMovers.cc.
References AnchoredDesignMover().
| bool protocols::anchored_design::AnchoredDesignMover::get_autoinitialize | ( | ) | const |
whether to automatically initialize from the options system; defaults to true
Definition at line 818 of file AnchorMovers.cc.
References autoinitialize_.
Referenced by operator=().
| 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
Definition at line 802 of file AnchorMovers.cc.
References delete_interface_native_sidechains_.
Referenced by operator=().
| bool protocols::anchored_design::AnchoredDesignMover::get_filter_omega | ( | ) | const |
filter based on omega angles in the loops - filter out cis omegas
Definition at line 816 of file AnchorMovers.cc.
References use_filter_omega_.
Referenced by operator=().
| core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_SASA | ( | ) | const |
filter based on complex SASA
Definition at line 814 of file AnchorMovers.cc.
References filter_SASA_.
Referenced by operator=().
| core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_score | ( | ) | const |
filter based on total complex score
Definition at line 812 of file AnchorMovers.cc.
References filter_score_.
Referenced by operator=().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 620 of file AnchorMovers.cc.
| bool protocols::anchored_design::AnchoredDesignMover::get_randomize_input_sequence | ( | ) | const |
randomize_input_sequence to complement loop extension in forgetting the input
Definition at line 806 of file AnchorMovers.cc.
References randomize_input_sequence_.
Referenced by operator=().
| bool protocols::anchored_design::AnchoredDesignMover::get_refine_only | ( | ) | const |
skip the perturbation step - useful when you already have a good structure
Definition at line 810 of file AnchorMovers.cc.
References refine_only_.
Referenced by operator=().
| bool protocols::anchored_design::AnchoredDesignMover::get_rmsd | ( | ) | const |
run RMSD calculations
Definition at line 798 of file AnchorMovers.cc.
References rmsd_.
Referenced by operator=().
| std::string const & protocols::anchored_design::AnchoredDesignMover::get_RMSD_only_this | ( | ) | const |
run only RMSD calculations against this input, don't do actual AnchoredDesign
Definition at line 800 of file AnchorMovers.cc.
References RMSD_only_this_.
Referenced by operator=().
| bool protocols::anchored_design::AnchoredDesignMover::get_show_extended | ( | ) | const |
show_extended demonstrates that the code really forgets the input structure
Definition at line 804 of file AnchorMovers.cc.
References show_extended_.
Referenced by operator=().
| bool protocols::anchored_design::AnchoredDesignMover::get_vary_cutpoints | ( | ) | const |
pick a different cutpoint than the input; useful when you want to sample cutpoints
Definition at line 808 of file AnchorMovers.cc.
References vary_cutpoints_.
Referenced by operator=().
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private |
internals; must wait for a pose to initialize
Definition at line 253 of file AnchorMovers.cc.
References autoinitialize_, protocols::anchored_design::EMPTY_STRING(), init_for_input_yet_, interface_, core::import_pose::pose_from_pdb(), read_options(), RMSD_only_this_, and RMSD_only_this_pose_.
Referenced by apply().
| AnchoredDesignMover & protocols::anchored_design::AnchoredDesignMover::operator= | ( | AnchoredDesignMover const & | rhs) |
assignment operator
Definition at line 224 of file AnchorMovers.cc.
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_.
| 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.
Definition at line 581 of file AnchorMovers.cc.
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::pose::Pose::residue_type(), protocols::RG(), core::pose::Pose::set_jump(), T_design(), core::conformation::Conformation::upstream_jump_stub(), and core::pose::Pose::xyz().
Referenced by apply().
| 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).
Definition at line 443 of file AnchorMovers.cc.
References core::chemical::aa_his, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), interface_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), protocols::RG(), T_design(), and core::pose::Pose::total_residue().
Referenced by apply(), and set_randomize_input_sequence().
| void protocols::anchored_design::AnchoredDesignMover::read_options | ( | ) |
read in options from the options system
Definition at line 847 of file AnchorMovers.cc.
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_, show_extended_, use_filter_omega_, use_filter_SASA_, use_filter_score_, and vary_cutpoints_.
Referenced by init_on_new_input().
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virtual |
this function informs 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.
Definition at line 632 of file AnchorMovers.cc.
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virtual |
generally returns true; will return false for RMSD_only_this mode
Reimplemented from protocols::moves::Mover.
Definition at line 635 of file AnchorMovers.cc.
References protocols::anchored_design::EMPTY_STRING(), and RMSD_only_this_.
| void protocols::anchored_design::AnchoredDesignMover::set_autoinitialize | ( | bool const | autoinitialize) |
whether to automatically initialize from the options system; defaults to true
Definition at line 845 of file AnchorMovers.cc.
References autoinitialize_.
| 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
Definition at line 825 of file AnchorMovers.cc.
References delete_interface_native_sidechains(), and delete_interface_native_sidechains_.
| void protocols::anchored_design::AnchoredDesignMover::set_filter_omega | ( | bool const | filter_omega) |
filter based on omega angles in the loops - filter out cis omegas
Definition at line 843 of file AnchorMovers.cc.
References use_filter_omega_.
| void protocols::anchored_design::AnchoredDesignMover::set_filter_SASA | ( | core::Real const | filter_SASA) |
filter based on complex SASA
Definition at line 839 of file AnchorMovers.cc.
References filter_SASA_, and use_filter_SASA_.
| void protocols::anchored_design::AnchoredDesignMover::set_filter_score | ( | core::Real const | filter_score) |
filter based on total complex score
Definition at line 835 of file AnchorMovers.cc.
References filter_score_, and use_filter_score_.
| 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
Definition at line 689 of file AnchorMovers.cc.
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::kinematics::FoldTree::jump_edge(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), T_design(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().
Referenced by apply().
| 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
Definition at line 829 of file AnchorMovers.cc.
References randomize_input_sequence(), and randomize_input_sequence_.
| void protocols::anchored_design::AnchoredDesignMover::set_refine_only | ( | bool const | refine_only) |
skip the perturbation step - useful when you already have a good structure
Definition at line 833 of file AnchorMovers.cc.
References refine_only_.
| void protocols::anchored_design::AnchoredDesignMover::set_rmsd | ( | bool const | rmsd) |
| 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
Definition at line 823 of file AnchorMovers.cc.
References RMSD_only_this_.
| void protocols::anchored_design::AnchoredDesignMover::set_show_extended | ( | bool const | show_extended) |
show_extended demonstrates that the code really forsets the input structure
Definition at line 827 of file AnchorMovers.cc.
References show_extended_.
| 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
Definition at line 831 of file AnchorMovers.cc.
References vary_cutpoints_.
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whether to automatically initialize from the options system; defaults to true
Definition at line 174 of file AnchorMovers.hh.
Referenced by get_autoinitialize(), init_on_new_input(), operator=(), and set_autoinitialize().
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delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
Definition at line 152 of file AnchorMovers.hh.
Referenced by apply(), get_delete_interface_native_sidechains(), operator=(), read_options(), and set_delete_interface_native_sidechains().
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filter based on complex SASA
Definition at line 168 of file AnchorMovers.hh.
Referenced by filter(), get_filter_SASA(), operator=(), read_options(), and set_filter_SASA().
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filter based on total complex score
Definition at line 164 of file AnchorMovers.hh.
Referenced by filter(), get_filter_score(), operator=(), read_options(), and set_filter_score().
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Definition at line 143 of file AnchorMovers.hh.
Referenced by apply(), and operator=().
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used to determine the validity of the rest of the internals, especially the interface_ object
Definition at line 177 of file AnchorMovers.hh.
Referenced by apply(), init_on_new_input(), and operator=().
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Definition at line 138 of file AnchorMovers.hh.
Referenced by apply(), calculate_rmsd(), delete_interface_native_sidechains(), filter(), forget_initial_loops(), init_on_new_input(), operator=(), perturb_anchor(), randomize_input_sequence(), and set_fold_tree_and_cutpoints().
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randomize_input_sequence to complement loop extension in forgetting the input
Definition at line 156 of file AnchorMovers.hh.
Referenced by apply(), get_randomize_input_sequence(), operator=(), read_options(), and set_randomize_input_sequence().
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skip the perturbation step - useful when you already have a good structure
Definition at line 161 of file AnchorMovers.hh.
Referenced by apply(), get_refine_only(), operator=(), read_options(), and set_refine_only().
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run RMSD calculations
Definition at line 148 of file AnchorMovers.hh.
Referenced by apply(), calculate_rmsd(), get_rmsd(), operator=(), read_options(), and set_rmsd().
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run only RMSD calculations against this input, don't do actual AnchoredDesign
Definition at line 150 of file AnchorMovers.hh.
Referenced by apply(), get_RMSD_only_this(), init_on_new_input(), operator=(), read_options(), reinitialize_for_new_input(), and set_RMSD_only_this().
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used for RMSD comparisons with RMSD_only_this mode
Definition at line 141 of file AnchorMovers.hh.
Referenced by apply(), init_on_new_input(), and operator=().
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show_extended demonstrates that the code really forgets the input structure
Definition at line 154 of file AnchorMovers.hh.
Referenced by apply(), get_show_extended(), operator=(), read_options(), and set_show_extended().
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filter based on omega angles in the loops - filter out cis omegas
Definition at line 172 of file AnchorMovers.hh.
Referenced by filter(), get_filter_omega(), operator=(), read_options(), and set_filter_omega().
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filter based on complex SASA
Definition at line 170 of file AnchorMovers.hh.
Referenced by filter(), operator=(), read_options(), and set_filter_SASA().
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filter based on total complex score
Definition at line 166 of file AnchorMovers.hh.
Referenced by filter(), operator=(), read_options(), and set_filter_score().
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pick a different cutpoint than the input; useful when you want to sample cutpoints
Definition at line 159 of file AnchorMovers.hh.
Referenced by apply(), get_vary_cutpoints(), operator=(), read_options(), and set_vary_cutpoints().
1.8.4