#include <PhosphateMover.hh>
Public Member Functions | |
| PhosphateMover (core::Size const sample_res, PhosphateTerminus which_terminus_, core::scoring::ScoreFunctionCOP scorefxn) | |
| PhosphateMover (PhosphateMove const &phosphate_move, core::scoring::ScoreFunctionCOP scorefxn) | |
| ~PhosphateMover () override | |
| void | apply (core::pose::Pose &pose_to_visualize) override |
| Main Method. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | screen_phosphate (core::pose::Pose &pose) |
| bool | instantiated_phosphate () const |
| void | set_force_phosphate_instantiation (bool const &setting) |
| bool | force_phosphate_instantiation () const |
 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... | |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. 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 | initialize_variables () |
| void | setup_variants_and_free_pose_for_terminal_phosphate (core::pose::Pose &pose) |
| void | setup_variants_and_free_pose_for_five_prime_phosphate (core::pose::Pose &pose) |
| void | setup_variants_and_free_pose_for_three_prime_phosphate (core::pose::Pose &pose) |
| void | screen_five_prime_phosphate (core::pose::Pose &pose) |
| void | screen_three_prime_phosphate (core::pose::Pose &pose) |
| void | setup_atom_and_neighbor_list (core::pose::Pose &pose) |
| bool | check_phosphate_contacts_donor (core::pose::Pose &pose) const |
| bool | pass_clash_check (std::string const &atom_name, core::Size const n, core::pose::Pose &pose) |
| void | apply_Aform_torsions_to_five_prime_phosphate (core::pose::Pose &pose, core::Size const sample_res) const |
| void | apply_Aform_torsions_to_three_prime_phosphate (core::pose::Pose &pose, core::Size const sample_res) const |
Private Attributes | |
| PhosphateMove const | phosphate_move_ |
| core::scoring::ScoreFunctionCOP | scorefxn_ |
| bool | do_screening_ |
| bool | screen_for_donor_contact_ |
| bool | instantiated_phosphate_ |
| bool | force_phosphate_instantiation_ |
| core::pose::PoseOP | pose_free_ |
| utility::vector1< core::Vector > | donor_atom_xyz_list_ |
| utility::vector1< core::Vector > | donor_base_atom_xyz_list_ |
| utility::vector1< core::Size > | neighbor_copy_dofs_ |
| core::Size | op1_atom_idx_ |
| core::Size | op2_atom_idx_ |
| core::Size | number_score_calls_ |
| core::chemical::rna::RNA_FittedTorsionInfo const | torsion_info_ |
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
◆ PhosphateMover() [1/2]
| protocols::stepwise::modeler::rna::phosphate::PhosphateMover::PhosphateMover | ( | core::Size const | sample_res, |
| PhosphateTerminus | which_terminus_, | ||
| core::scoring::ScoreFunctionCOP | scorefxn | ||
| ) |
References initialize_variables().
◆ PhosphateMover() [2/2]
| protocols::stepwise::modeler::rna::phosphate::PhosphateMover::PhosphateMover | ( | PhosphateMove const & | phosphate_move, |
| core::scoring::ScoreFunctionCOP | scorefxn | ||
| ) |
References initialize_variables().
◆ ~PhosphateMover()
|
overridedefault |
Member Function Documentation
◆ apply()
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References do_screening_, screen_phosphate(), and setup_variants_and_free_pose_for_terminal_phosphate().
Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().
◆ apply_Aform_torsions_to_five_prime_phosphate()
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private |
References core::chemical::rna::ALPHA, core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform(), core::id::BB, core::chemical::rna::BETA, core::chemical::rna::RNA_FittedTorsionInfo::beta_aform(), core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::rna::GAMMA, core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), core::pose::Pose::set_torsion(), and torsion_info_.
Referenced by setup_variants_and_free_pose_for_five_prime_phosphate().
◆ apply_Aform_torsions_to_three_prime_phosphate()
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private |
References core::id::BB, core::chemical::rna::EPSILON, core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), core::pose::Pose::set_torsion(), core::chemical::THREE_PRIME_PHOSPHATE, torsion_info_, core::chemical::rna::ZETA, and core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform().
Referenced by setup_variants_and_free_pose_for_three_prime_phosphate().
◆ check_phosphate_contacts_donor()
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private |
References core::pose::rna::check_phosphate_contacts_donor(), donor_atom_xyz_list_, donor_base_atom_xyz_list_, op1_atom_idx_, op2_atom_idx_, phosphate_move_, core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), and core::conformation::Residue::xyz().
Referenced by screen_five_prime_phosphate(), and screen_three_prime_phosphate().
◆ force_phosphate_instantiation()
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inline |
References force_phosphate_instantiation_.
◆ get_name()
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ initialize_variables()
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private |
References do_screening_, force_phosphate_instantiation_, instantiated_phosphate_, number_score_calls_, and screen_for_donor_contact_.
Referenced by PhosphateMover().
◆ instantiated_phosphate()
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inline |
References instantiated_phosphate_.
Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().
◆ pass_clash_check()
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private |
References core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_type(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), neighbor_copy_dofs_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().
Referenced by screen_five_prime_phosphate(), and screen_three_prime_phosphate().
◆ screen_five_prime_phosphate()
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private |
References core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, check_phosphate_contacts_donor(), force_phosphate_instantiation_, core::chemical::rna::GAMMA, core::chemical::rna::get_full_torsions(), instantiated_phosphate_, number_score_calls_, pass_clash_check(), phosphate_move_, pose_free_, protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), protocols::hybridization::score, screen_for_donor_contact_, and core::pose::Pose::set_torsion().
Referenced by screen_phosphate().
◆ screen_phosphate()
| void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_phosphate | ( | core::pose::Pose & | pose | ) |
References protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, instantiated_phosphate_, number_score_calls_, phosphate_move_, screen_five_prime_phosphate(), screen_three_prime_phosphate(), setup_atom_and_neighbor_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.
Referenced by apply().
◆ screen_three_prime_phosphate()
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private |
References core::id::BB, check_phosphate_contacts_donor(), core::pose::Pose::delta(), core::chemical::rna::EPSILON, force_phosphate_instantiation_, core::chemical::rna::get_epsilon_torsions(), core::chemical::rna::get_full_torsions(), instantiated_phosphate_, number_score_calls_, pass_clash_check(), phosphate_move_, pose_free_, protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), protocols::hybridization::score, screen_for_donor_contact_, core::pose::Pose::set_torsion(), and core::chemical::rna::ZETA.
Referenced by screen_phosphate().
◆ set_force_phosphate_instantiation()
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inline |
◆ setup_atom_and_neighbor_list()
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private |
References core::conformation::Residue::atom_index(), donor_atom_xyz_list_, donor_base_atom_xyz_list_, core::pose::rna::FIVE_PRIME, protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, core::pose::rna::get_phosphate_atom_and_neighbor_list(), neighbor_copy_dofs_, op1_atom_idx_, op2_atom_idx_, phosphate_move_, core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and core::pose::rna::THREE_PRIME.
Referenced by screen_phosphate().
◆ setup_variants_and_free_pose_for_five_prime_phosphate()
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private |
References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), apply_Aform_torsions_to_five_prime_phosphate(), core::pose::Pose::clone(), core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::LOWER_TERMINUS_VARIANT, phosphate_move_, pose_free_, protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.
Referenced by setup_variants_and_free_pose_for_terminal_phosphate().
◆ setup_variants_and_free_pose_for_terminal_phosphate()
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private |
References protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, phosphate_move_, setup_variants_and_free_pose_for_five_prime_phosphate(), setup_variants_and_free_pose_for_three_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.
Referenced by apply().
◆ setup_variants_and_free_pose_for_three_prime_phosphate()
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private |
References core::pose::add_variant_type_to_pose_residue(), apply_Aform_torsions_to_three_prime_phosphate(), core::pose::Pose::clone(), core::conformation::Residue::has_variant_type(), phosphate_move_, pose_free_, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::VIRTUAL_RIBOSE.
Referenced by setup_variants_and_free_pose_for_terminal_phosphate().
Member Data Documentation
◆ do_screening_
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private |
Referenced by apply(), and initialize_variables().
◆ donor_atom_xyz_list_
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private |
Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().
◆ donor_base_atom_xyz_list_
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private |
Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().
◆ force_phosphate_instantiation_
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private |
◆ instantiated_phosphate_
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private |
◆ neighbor_copy_dofs_
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private |
Referenced by pass_clash_check(), and setup_atom_and_neighbor_list().
◆ number_score_calls_
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private |
Referenced by initialize_variables(), screen_five_prime_phosphate(), screen_phosphate(), and screen_three_prime_phosphate().
◆ op1_atom_idx_
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private |
Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().
◆ op2_atom_idx_
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private |
Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().
◆ phosphate_move_
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private |
Referenced by check_phosphate_contacts_donor(), screen_five_prime_phosphate(), screen_phosphate(), screen_three_prime_phosphate(), setup_atom_and_neighbor_list(), setup_variants_and_free_pose_for_five_prime_phosphate(), setup_variants_and_free_pose_for_terminal_phosphate(), and setup_variants_and_free_pose_for_three_prime_phosphate().
◆ pose_free_
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private |
◆ scorefxn_
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private |
◆ screen_for_donor_contact_
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private |
Referenced by initialize_variables(), screen_five_prime_phosphate(), and screen_three_prime_phosphate().
◆ torsion_info_
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private |
The documentation for this class was generated from the following files:
- src/protocols/stepwise/modeler/rna/phosphate/PhosphateMover.hh
- src/protocols/stepwise/modeler/rna/phosphate/PhosphateMover.cc
